* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/GPArotation.Rcheck’ * using R Under development (unstable) (2026-07-18 r90269) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-07-18 12:31:32 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘GPArotation/DESCRIPTION’ ... OK * this is package ‘GPArotation’ version ‘2026.6-1’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GPArotation’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found calls to structure() using deprecated special names: GPArotation/tests/Revelle.R (.Dim: 1, .Dimnames: 1) '.Dim' should be changed to 'dim'. '.Dimnames' should be changed to 'dimnames'. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [20s/21s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Harman.R’ [62s/65s] Running ‘Jennrich2002.R’ Running ‘KaiserNormalization.R’ [63s/65s] Running ‘MASSoblimin.R’ [77s/80s] Running ‘Revelle.R’ Running ‘Thurstone.R’ [67s/69s] Running ‘WansbeekMeijer.R’ [64s/65s] Running ‘algorithmTests.R’ Running ‘errormessages.R’ [70s/72s] Running ‘legacyVsBB.R’ Running ‘legacyVsNew.R’ Running ‘lp.R’ [79s/81s] Running ‘normalizationTests.R’ Running ‘print-GPArotation.R’ [65s/67s] Running ‘rotations.R’ [92s/95s] Running ‘rotationsRS.R’ [94s/97s] Running ‘rotbbcayley.R’ Running ‘tableTests.r’ Running ‘target_vs_bb_clash.R’ Running ‘varimaxVarimax.R’ [63s/65s] Running ‘vgQOLD.R’ Running ‘vgQtestOldVsNew.R’ [14m/14m] ERROR Running the tests in ‘tests/rotations.R’ failed. Complete output: > # Tests here only compare against values computed previously with this code, > # to ensure there was no accidental change. It would be better to have > # comparisons with known correct values. > > # Test for oblimax is commented out as it appears to be unstable. > > > Sys.getenv("R_LIBS") [1] "/data/localhost/ripley/R/packages/tests-MKL/GPArotation.Rcheck:/data/localhost/ripley/R/test-MKL:/data/localhost/ripley/R/test-dev:/data/localhost/ripley/R/test-BioCdata" > library() Packages in library '/data/localhost/ripley/R/packages/tests-MKL/GPArotation.Rcheck': GPArotation Gradient Projection Factor Rotation Packages in library '/data/localhost/ripley/R/test-MKL': ABCoptim Implementation of Artificial Bee Colony (ABC) Optimization ABM Agent Based Model Simulation Framework ACDm Tools for Autoregressive Conditional Duration Models ACEt Estimating Dynamic Heritability and Twin Model Comparison ACTCD Asymptotic Classification Theory for Cognitive Diagnosis ADMM Algorithms using Alternating Direction Method of Multipliers ADSIHT Adaptive Double Sparse Iterative Hard Thresholding AGCA4extremes Anchored Geodesic Component Analysis for Extremes ALDEx3 Linear Models for Sequence Count Data ALFAM2 Dynamic Model of Ammonia Emission from Field-Applied Manure ALUES Agricultural Land Use Evaluation System ALassoSurvIC Adaptive Lasso for the Cox Regression with Interval Censored and Possibly Left Truncated Data AMISforInfectiousDiseases Implement the AMIS Algorithm for Infectious Disease Models ANN2 Artificial Neural Networks for Anomaly Detection APIS Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents APML0 Augmented and Penalized Minimization Method L0 APRScenario Structural Scenario Analysis for Bayesian Structural Vector Autoregression Models APackOfTheClones Visualization of Clonal Expansion for Single Cell Immune Profiles ARCensReg Fitting Univariate Censored Linear Regression Model with Autoregressive Errors ARCokrig Autoregressive Cokriging Models for Multifidelity Codes ASSA Applied Singular Spectrum Analysis (ASSA) ASV Stochastic Volatility Models with or without Leverage ATAforecasting Automatic Time Series Analysis and Forecasting using the Ata Method ATNr Run Allometric Trophic Networks Models AV1R 'AV1' Video Encoding for Biological Microscopy Data AcceptReject Acceptance-Rejection Method for Generating Pseudo-Random Observations ActiveLearning4SPM Active Learning for Process Monitoring AdMit Adaptive Mixture of Student-t Distributions AdaptGauss Gaussian Mixture Models (GMM) AddiVortes (Bayesian) Additive Voronoi Tessellations AdmixPoly Global and Local Admixture Inference in Polyploids AhoCorasickTrie Fast Searching for Multiple Keywords in Multiple Texts AlgDesign Algorithmic Experimental Design AllelicSeries Allelic Series Test AlphaPart Partition/Decomposition of Breeding Values by Paths of Information AlphaSimR Breeding Program Simulations Amelia A Program for Missing Data AnalyzeFMRI Functions for Analysis of fMRI Datasets Stored in the ANALYZE or 'NIFTI' Format AnimalSequences Analyse Animal Sequential Behaviour and Communication Anthropometry Statistical Methods for Anthropometric Data Apoderoides Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree AsianOption Asian Option Pricing under Price Impact AteMeVs Average Treatment Effects with Measurement Error and Variable Selection for Confounders BAMBI Bivariate Angular Mixture Models BAMMtools Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees BAREB A Bayesian Repulsive Biclustering Model for Periodontal Data BART Bayesian Additive Regression Trees BAS Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling BBmisc Miscellaneous Helper Functions for B. Bischl BCBCSF Bias-Corrected Bayesian Classification with Selected Features BCClong Bayesian Consensus Clustering for Multiple Longitudinal Features BCEE The Bayesian Causal Effect Estimation Algorithm BCFM Bayesian Clustering Factor Models BDgraph Bayesian Structure Learning in Graphical Models using Birth-Death MCMC BED Biological Entity Dictionary (BED) BEDMatrix Extract Genotypes from a PLINK .bed File BEKKs Multivariate Conditional Volatility Modelling and Forecasting BET Binary Expansion Testing BFpack Flexible Bayes Factor Testing of Scientific Expectations BGData A Suite of Packages for Analysis of Big Genomic Data BGGM Bayesian Gaussian Graphical Models BGLR Bayesian Generalized Linear Regression BGVAR Bayesian Global Vector Autoregressions BHMSMAfMRI Bayesian Hierarchical Multi-Subject Multiscale Analysis of Functional MRI (fMRI) Data BHSBVAR Structural Bayesian Vector Autoregression Models BIDistances Bioinformatic Distances BIFIEsurvey Tools for Survey Statistics in Educational Assessment BKP Beta Kernel Process Modeling BKPC Bayesian Kernel Projection Classifier BLMEngineInR Biotic Ligand Model Engine BLPestimatoR Performs a BLP Demand Estimation BLR Bayesian Linear Regression BLSM Bayesian Latent Space Model BMA Bayesian Model Averaging BMAmevt Multivariate Extremes: Bayesian Estimation of the Spectral Measure BMIselect Bayesian MI-LASSO for Variable Selection on Multiply-Imputed Datasets BMisc Miscellaneous Functions for Panel Data, Quantiles, and Printing Results BNPmix Bayesian Nonparametric Mixture Models BNSP Bayesian Non- And Semi-Parametric Model Fitting BORG Bounded Outcome Risk Guard for Model Evaluation BORT Beyond Pareto: Bi-Objective and Multi-Objective Regression Trees’ BPrinStratTTE Causal Effects in Principal Strata Defined by Antidrug Antibodies BRISC Fast Inference for Large Spatial Datasets using BRISC BRL Beta Record Linkage BRRAT Bayesian Regression Robustness Assessment Test BSCB Bayesian Simultaneous Credible Bands for Polynomial Regression BSL Bayesian Synthetic Likelihood BSPBSS Bayesian Spatial Blind Source Separation BSSasymp Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates BSSprep Whitening Data as Preparation for Blind Source Separation BSTFA Bayesian Spatio-Temporal Factor Analysis Model BTLLasso Modelling Heterogeneity in Paired Comparison Data BTM Biterm Topic Models for Short Text BTSR Bounded Time Series Regression BTtest Estimate the Number of Factors in Large Nonstationary Datasets BWStest Baumgartner Weiss Schindler Test of Equal Distributions BalancedSampling Balanced and Spatially Balanced Sampling Ball Statistical Inference and Sure Independence Screening via Ball Statistics Barnard Barnard's Unconditional Test Bayenet Robust Bayesian Elastic Net BayesChange Bayesian Methods for Change Point Analysis BayesDecon Density Deconvolution Using Bayesian Semiparametric Methods BayesESS Determining Effective Sample Size BayesFM Bayesian Inference for Factor Modeling BayesFactor Computation of Bayes Factors for Common Designs BayesGP Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models BayesGPfit Fast Bayesian Gaussian Process Regression Fitting BayesGmed Bayesian Causal Mediation Analysis using 'Stan' BayesGrowth Estimate Fish Growth Using MCMC Analysis BayesLN Bayesian Inference for Log-Normal Data BayesLogit PolyaGamma Sampling BayesMFSurv Bayesian Misclassified-Failure Survival Model BayesMallows Bayesian Preference Learning with the Mallows Rank Model BayesMallowsSMC2 Nested Sequential Monte Carlo for the Bayesian Mallows Model BayesPET Bayesian Prediction of Event Times for Blinded Randomized Controlled Trials BayesPIM Bayesian Prevalence-Incidence Mixture Model BayesPPD Bayesian Power Prior Design BayesPPDSurv Bayesian Power Prior Design for Survival Data BayesPower Sample Size and Power Calculation for Bayesian Testing with Bayes Factor BayesProject Fast Projection Direction for Multivariate Changepoint Detection BayesRegDTR Bayesian Regression for Dynamic Treatment Regimes BayesSUR Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings BayesSurvive Bayesian Survival Models for High-Dimensional Data BayesTSM Bayesian Progressive Three State Model with Censoring Due to Intervention BayesTree Bayesian Additive Regression Trees BayesVarSel Bayes Factors, Model Choice and Variable Selection in Linear Models BayesXsrc Distribution of the 'BayesX' C++ Sources BayesfMRI Spatial Bayesian Methods for Task Functional MRI Studies BayesianLasso Bayesian Lasso Regression and Tools for the Lasso Distribution BayesianPlatformDesignTimeTrend Simulate and Analyse Bayesian Platform Trial with Time Trend BayesianTools General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics Bayesrel Bayesian Reliability Estimation Bchron Age-Depth Radiocarbon Modelling BeSS Best Subset Selection in Linear, Logistic and CoxPH Models BeadDataPackR Compression of Illumina BeadArray data Benchmarking Benchmark and Frontier Analysis Using DEA and SFA BenfordTests Statistical Tests for Evaluating Conformity to Benford's Law Bernadette Bayesian Inference and Model Selection for Stochastic Epidemics Bessel Computations and Approximations for Bessel Functions Bestie Bayesian Estimation of Intervention Effects BeviMed Bayesian Evaluation of Variant Involvement in Mendelian Disease BiDAG Bayesian Inference for Directed Acyclic Graphs BiTrinA Binarization and Trinarization of One-Dimensional Data BiasedUrn Biased Urn Model Distributions BicARE Biclustering Analysis and Results Exploration BigDataStatMeth Scalable Statistical Computing with HDF5-Backed Matrices BigVAR Dimension Reduction Methods for Multivariate Time Series BinSegBstrap Piecewise Smooth Regression by Bootstrapped Binary Segmentation Binarize Binarization of One-Dimensional Data BinaryDosage Creates, Merges, and Reads Binary Dosage Files BinaryReplicates Dealing with Binary Replicates BioCro Modular Crop Growth Simulations Biobase Biobase: Base functions for Bioconductor BiocNeighbors Nearest Neighbor Detection for Bioconductor Packages BiocParallel Bioconductor facilities for parallel evaluation BiocSingular Singular Value Decomposition for Bioconductor Packages Bioi Biological Image Analysis BipartiteModularityMaximization Partition Bipartite Network into Non-Overlapping Biclusters by Optimizing Bipartite Modularity BivLaplaceRL Bivariate Laplace Transforms, Stochastic Orders, and Entropy Measures in Reliability BivRec Bivariate Alternating Recurrent Event Data Analysis Blend Robust Bayesian Longitudinal Regularized Semiparametric Mixed Models BoltzMM Boltzmann Machines with MM Algorithms BondValuation Fixed Coupon Bond Valuation Allowing for Odd Coupon Periods and Various Day Count Conventions BoolNet Construction, Simulation and Analysis of Boolean Networks Boom Bayesian Object Oriented Modeling BoomSpikeSlab MCMC for Spike and Slab Regression BoostMLR Boosting for Multivariate Longitudinal Responses BosonSampling Classical Boson Sampling BoundIRT Fit Bounded Continuous Item Response Theory Models to Data BoutrosLab.plotting.general Functions to Create Publication-Quality Plots BranchGLM Efficient Best Subset Selection for GLMs via Branch and Bound Algorithms Branching Simulation and Estimation for Branching Processes BsMD Bayes Screening and Model Discrimination Buddle A Deep Learning for Statistical Classification and Regression Analysis with Random Effects BuyseTest Generalized Pairwise Comparisons BwQuant Bandwidth Selectors for Local Linear Quantile Regression C50 C5.0 Decision Trees and Rule-Based Models CAESAR.Suite CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation CARBayes Spatial Generalised Linear Mixed Models for Areal Unit Data CARBayesST Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data CARME CAR-MM Modelling in Stan CARMS Continuous Time Markov Rate Modeling for Reliability Analysis CARRoT Predicting Categorical and Continuous Outcomes Using One in Ten Rule CB2 CRISPR Pooled Screen Analysis using Beta-Binomial Test CBnetworkMA Contrast-Based Bayesian Network Meta Analysis CCMMR Minimization of the Convex Clustering Loss Function CCMnet Congruence Class Models for Networks CDM Cognitive Diagnosis Modeling CDatanet Econometrics of Network Data CEC Cross-Entropy Clustering CEGO Combinatorial Efficient Global Optimization CERFIT Causal Effect Random Forest of Interaction Trees CFC Cause-Specific Framework for Competing-Risk Analysis CGGP Composite Grid Gaussian Processes CGManalyzer Continuous Glucose Monitoring Data Analyzer CHMM Coupled Hidden Markov Models CHNOSZ Thermodynamic Calculations and Diagrams for Geochemistry CIMEHR Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data CKLRT Composite Kernel Machine Regression Based on Likelihood Ratio Test CLVTools Tools for Customer Lifetime Value Estimation CMAPSS Commercial Modular Aero-Propulsion System Simulation Data Set CMF Collective Matrix Factorization CMGFM Covariate-Augumented Generalized Factor Model COAP High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model COMIX Coarsened Mixtures of Hierarchical Skew Kernels COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression COveR Clustering with Overlaps CPE Concordance Probability Estimates in Survival Analysis CPGLIB Competing Proximal Gradients Library CPoptim Convex Partition Optimisation CRTConjoint Conditional Randomization Testing (CRT) Approach for Conjoint Analysis CSTE Covariate Specific Treatment Effect (CSTE) Curve CSTools Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales CSeQTL Cell Type-Specific Expression Quantitative Trait Loci Mapping CUSUMdesign Compute Decision Interval and Average Run Length for CUSUM Charts CVXR Disciplined Convex Optimization CWT Continuous Wavelet Transformation for Spectroscopy Cairo R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output CalSim The Calibration Simplex CamelUp 'CamelUp' Board Game as a Teaching Aid for Introductory Statistics Carlson Carlson Elliptic Integrals and Incomplete Elliptic Integrals CaseBasedReasoning Case Based Reasoning CaseCohortCoxSurvival Case-Cohort Cox Survival Inference CatReg Solution Paths for Linear and Logistic Regression Models with Categorical Predictors, with SCOPE Penalty CausalGPS Matching on Generalized Propensity Scores with Continuous Exposures CausalQueries Make, Update, and Query Binary Causal Models CautiousLearning Control Charts with Guaranteed In-Control Performance and Cautious Parameters Learning CellNOptR Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data ChangePointTaylor Identify Changes in Mean ChannelAttribution Markov Model for Online Multi-Channel Attribution Chaos01 0-1 Test for Chaos CholWishart Cholesky Decomposition of the Wishart Distribution CircularDDM Circular Drift-Diffusion Model CircularSilhouette Fast Silhouette on Circular or Linear Data Clusters Ckmeans.1d.dp Optimal, Fast, and Reproducible Univariate Clustering Cleanet Automated Doublet Detection and Classification for Cytometry Data ClickClust Model-Based Clustering of Categorical Sequences ClimProjDiags Set of Tools to Compute Various Climate Indices ClinicalTrialSummary Summary Measures for Clinical Trials with Survival Outcomes ClusPred Simultaneous Semi-Parametric Estimation of Clustering and Regression ClusROC ROC Analysis in Three-Class Classification Problems for Clustered Data ClustAssess Tools for Assessing Clustering ClustVarLV Clustering of Variables Around Latent Variables ClusterR Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering ClusterStability Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions CoMiRe Convex Mixture Regression CoSMoS Complete Stochastic Modelling Solution CohortMethod Comparative Cohort Method with Large Scale Propensity and Outcome Models Colossus "Risk Model Regression and Analysis with Complex Non-Linear Models" CompModels Pseudo Computer Models for Optimization CompQuadForm Distribution Function of Quadratic Forms in Normal Variables CompositionalRF Multivariate Random Forest with Compositional Responses ConjointChecks Implementation of a Method to Check the Cancellation Axioms of Additive Conjoint Measurement ConsRank Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach ConsReg Fits Regression & ARMA Models Subject to Constraints to the Coefficient ContaminatedMixt Clustering and Classification with the Contaminated Normal CopulaGAMM Copula-Based Mixed Regression Models CopulaInference Estimation and Goodness-of-Fit of Copula-Based Models with Arbitrary Distributions CopulaSCR Analysis of Semi-Competing Risks Data Using Copula-Based Models CorMID Correct Mass Isotopologue Distribution Vectors CorrBin Nonparametrics with Clustered Binary and Multinomial Data Countr Flexible Univariate Count Models Based on Renewal Processes CovTools Statistical Tools for Covariance Analysis CoxBoost Cox Models by Likelihood Based Boosting for a Single Survival Endpoint or Competing Risks CoxPlus Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects Coxmos Cox MultiBlock Survival CptNonPar Nonparametric Change Point Detection for Multivariate Time Series Crossover Analysis and Search of Crossover Designs Cubist Rule- And Instance-Based Regression Modeling Cyclops Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis CytoSimplex Simplex Visualization of Cell Fate Similarity in Single-Cell Data DAISIE Dynamical Assembly of Islands by Speciation, Immigration and Extinction DALY The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R DAST Spatio-Temporal Disaggregation for Maps with Changing Areal Boundaries DCCA Detrended Fluctuation and Detrended Cross-Correlation Analysis DCEM Clustering Big Data using Expectation Maximization Star (EM*) Algorithm DCLEAR Distance Based Cell Lineage Reconstruction DCluster Functions for the Detection of Spatial Clusters of Diseases DDD Diversity-Dependent Diversification DDHFm Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays) DDRTree Learning Principal Graphs with DDRTree DECIPHER Tools for curating, analyzing, and manipulating biological sequences DER Income Polarization Index DESeq2 Differential gene expression analysis based on the negative binomial distribution DEoptim Global Optimization by Differential Evolution DEploid Deconvolute Mixed Genomes with Unknown Proportions DEploid.utils 'DEploid' Data Analysis and Results Interpretation DGP4LCF Dependent Gaussian Processes for Longitudinal Correlated Factors DIDmultiplegtDYN Estimation in Staggered First Switch Designs, where Groups Experience their First Treatment Change at Different Points in Time DIFM Dynamic ICAR Spatiotemporal Factor Models DIME Differential Identification using Mixture Ensemble DIRECT Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior DLMtool Data-Limited Methods Toolkit DMCfun Diffusion Model of Conflict (DMC) in Reaction Time Tasks DMMF Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model DNAcopy DNA Copy Number Data Analysis DNAmotif DNA Sequence Motifs DNAtools Tools for Analysing Forensic Genetic DNA Data DOVE Durability of Vaccine Efficacy DPP Inference of Parameters of Normal Distributions from a Mixture of Normals DPQ Density, Probability, Quantile ('DPQ') Computations DPTM Dynamic Panel Multiple Threshold Model with Fixed Effects DR.SC Joint Dimension Reduction and Spatial Clustering DRDID Doubly Robust Difference-in-Differences Estimators DRIP Discontinuous Regression and Image Processing DRPT Density Ratio Permutation Test DRsurvCRT Doubly-Robust Estimation for Survival Outcomes in Cluster-Randomized Trials DSGEr Transcriptional Disruption Score for Gene Sets DSL Distributed Storage and List DSWE Data Science for Wind Energy DTDA.cif Doubly Truncated Data Analysis, Cumulative Incidence Functions DTRKernSmooth Estimate and Make Inference About Optimal Treatment Regimes via Smoothed Methods DataGraph Export Data from 'R' to 'DataGraph' DataVisualizations Visualizations of High-Dimensional Data DataViz Data Visualisation Using an HTML Page and 'D3.js' DatabionicSwarm Swarm Intelligence for Self-Organized Clustering Dcurvature Discrete Curvature with 'shiny' Explorer DeCAFS Detecting Changes in Autocorrelated and Fluctuating Signals Delaporte Statistical Functions for the Delaporte Distribution DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets DelayedEffect.Design Sample Size and Power Calculations using the APPLE, SEPPLE, APPLE+ and SEPPLE+ Methods DendSer Dendrogram Seriation: Ordering for Visualisation DepthProc Statistical Depth Functions for Multivariate Analysis DescTools Tools for Descriptive Statistics DetMCD Implementation of the DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter) DiceDesign Designs of Computer Experiments DiceKriging Kriging Methods for Computer Experiments DiceOptim Kriging-Based Optimization for Computer Experiments Dimodal Spacing Tests for Multi-Modality DirStats Nonparametric Methods for Directional Data Dire Linear Regressions with a Latent Outcome Variable DirichletMultinomial Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data DirichletRF "Dirichlet Random Forest" DirichletReg Dirichlet Regression DiscreteDLM Bayesian Distributed Lag Model Fitting for Binary and Count Response Data DiscreteDists Discrete Statistical Distributions DiscreteFDR FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteFWER FWER-Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteTests Vectorised Computation of P-Values and Their Supports for Several Discrete Statistical Tests DistributionUtils Distribution Utilities DoseFinding Planning and Analyzing Dose Finding Experiments DrImpute Imputing Dropout Events in Single-Cell RNA-Sequencing Data DropletUtils Utilities for Handling Single-Cell Droplet Data DstarM Analyze Two Choice Reaction Time Data with the D*M Method DySS Dynamic Screening Systems DyadRatios Dyad Ratios Algorithm for Latent Variable Estimation DyadiCarma Dyadic Matrices and their Algebra using 'Rcpp' and 'RcppArmadillo' DysPIA Dysregulated Pathway Identification Analysis EBEN Empirical Bayesian Elastic Net EBImage Image processing and analysis toolbox for R EBMAforecast Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs Sampling or EM-Algorithms EBarrays Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification ECGofTestDx A Goodness-of-Fit Test for Elliptical Distributions with Diagnostic Capabilities ECOSolveR Embedded Conic Solver in R EDOtrans Euclidean Distance-Optimized Data Transformation EFAfactors Determining the Number of Factors in Exploratory Factor Analysis EFAtools Fast and Flexible Implementations of Exploratory Factor Analysis Tools EGAnet Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics EGM Intracardiac Electrograms EHRmuse Multi-Cohort Selection Bias Correction using IPW and AIPW Methods EL Two-Sample Empirical Likelihood ELAplus Energy Landscape Analysis for Ecological Communities ELYP Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model EMC2 Bayesian Hierarchical Analysis of Cognitive Models of Choice EMCluster EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution EMD Empirical Mode Decomposition and Hilbert Spectral Analysis EMMIXgene A Mixture Model-Based Approach to the Clustering of Microarray Expression Data EMMIXmfa Mixture Models with Component-Wise Factor Analyzers EMbC Expectation-Maximization Binary Clustering EMgaussian Expectation-Maximization Algorithm for Multivariate Normal (Gaussian) with Missing Data EPX Ensemble of Phalanxes ETAS Modeling Earthquake Data Using 'ETAS' Model EWGoF Goodness-of-Fit Tests for the Exponential and Two-Parameter Weibull Distributions Eagle Multiple Locus Association Mapping on a Genome-Wide Scale Ease Simulating Explicit Population Genetics Models EasyABC Efficient Approximate Bayesian Computation Sampling Schemes EcoEnsemble A General Framework for Combining Ecosystem Models EcoNetGen Simulate and Sample from Ecological Interaction Networks EloChoice Preference Rating for Visual Stimuli Based on Elo Ratings EloRating Animal Dominance Hierarchies by Elo Rating EmbedSOM Fast Embedding Guided by Self-Organizing Map EmiR Evolutionary Minimizer for R EmpiricalCalibration Routines for Performing Empirical Calibration of Observational Study Estimates EnrichIntersect Enrichment Analysis and Intersecting Sankey Diagram EntropyEstimation Estimation of Entropy and Related Quantities EnvCpt Detection of Structural Changes in Climate and Environment Time Series Epi Statistical Analysis in Epidemiology EpiContactTrace Epidemiological Tool for Contact Tracing EpiILM Spatial and Network Based Individual Level Models for Epidemics EpiInvert Variational Techniques in Epidemiology EpiLPS A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters EpiModel Mathematical Modeling of Infectious Disease Dynamics EpiPvr Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays Equalden.HD Testing the Equality of a High Dimensional Set of Densities EquiTrends Equivalence Testing for Pre-Trends in Difference-in-Differences Designs EthSEQ Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data Euclimatch Euclidean Climatch Algorithm ExactMultinom Multinomial Goodness-of-Fit Tests ExactVaRTest Exact Finite-Sample Value-at-Risk Back-Testing ExhaustiveSearch A Fast and Scalable Exhaustive Feature Selection Framework ExtremalDep Extremal Dependence Models ExtremeRisks Extreme Risk Measures FAS Factor-Augmented Sparse Regression Tuning-Free Testing FAmle Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions FBFsearch Algorithm for Searching the Space of Gaussian Directed Acyclic Graph Models Through Moment Fractional Bayes Factors FBMS Flexible Bayesian Model Selection and Model Averaging FD Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology FDOTT Optimal Transport Based Testing in Factorial Design FDX False Discovery Exceedance Controlling Multiple Testing Procedures FENmlm Fixed Effects Nonlinear Maximum Likelihood Models FGLMtrunc Truncated Functional Generalized Linear Models FHDI Fractional Hot Deck and Fully Efficient Fractional Imputation FIESTAutils Utility Functions for Forest Inventory Estimation and Analysis FIRM Flexible Integration of Single-Cell RNA-Seq Data FKF Fast Kalman Filter FKSUM Fast Kernel Sums FLOPART Functional Labeled Optimal Partitioning FLORAL Fit Log-Ratio Lasso Regression for Compositional Data FLSSS Mining Rigs for Problems in the Subset Sum Family FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis FMStable Finite Moment Stable Distributions FNN Fast Nearest Neighbor Search Algorithms and Applications FRESA.CAD Feature Selection Algorithms for Computer Aided Diagnosis FRK Fixed Rank Kriging FSSF Generate Fully-Sequential Space-Filling Designs Inside a Unit Hypercube FSelectorRcpp 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support FVDDPpkg Implement Fleming-Viot-Dependent Dirichlet Processes FactoClass Combination of Factorial Methods and Cluster Analysis FactoMineR Multivariate Exploratory Data Analysis and Data Mining FactorCopula Factor, Bi-Factor, Second-Order and Factor Tree Copula Models FactorCopulaModel Factor Copula Models FactorHet Estimate Heterogeneous Effects in Factorial Experiments Using Grouping and Sparsity Familias Probabilities for Pedigrees Given DNA Data FastBandChol Fast Estimation of a Covariance Matrix by Banding the Cholesky Factor FastGP Efficiently Using Gaussian Processes with Rcpp and RcppEigen FastGaSP Fast and Exact Computation of Gaussian Stochastic Process FastHamming Fast Computation of Pairwise Hamming Distances FastJM Semi-Parametric Joint Modeling of Longitudinal and Survival Data FastKRR Kernel Ridge Regression using 'RcppArmadillo' FastPCS FastPCS Robust Fit of Multivariate Location and Scatter FastRCS Fits the FastRCS Robust Multivariable Linear Regression Model FastRWeb Fast Interactive Framework for Web Scripting Using R FastSurvival Fast Kaplan-Meier, Log-Rank, and Hazard Ratio Estimation for Survival Analysis FastUtils Fast, Readable Utility Functions FaultTree Fault Trees for Risk and Reliability Analysis FiRE Finder of Rare Entities (FiRE) FinNet Quickly Build and Manipulate Financial Networks FisPro Fuzzy Inference System Design and Optimization FlexRL A Flexible Model for Record Linkage FlexVarJM Estimate Joint Models with Subject-Specific Variance FlyingR Simulation of Bird Flight Range FunChisq Model-Free Functional Chi-Squared and Exact Tests FuncDiv Compute Contributional Diversity Metrics FuzzySimRes Simulation and Resampling Methods for Epistemic Fuzzy Data GA Genetic Algorithms GADAG A Genetic Algorithm for Learning Directed Acyclic Graphs GAGAs Global Adaptive Generative Adjustment Algorithm for Generalized Linear Models GAPR Generalized Association Plots GBJ Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies GBOP2 Generalized Bayesian Optimal Phase II Design (G-BOP2) GCPBayes Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure GCPM Generalized Credit Portfolio Model GCSM Implements Generic Composite Similarity Measure GDINA The Generalized DINA Model Framework GDSARM Gauss - Dantzig Selector: Aggregation over Random Models GEEaSPU Adaptive Association Tests for Multiple Phenotypes using Generalized Estimating Equations (GEE) GEMSS Generalization Error Minimization in SubSampling for Gaussian Processes GENEAclassify Segmentation and Classification of Accelerometer Data GENEAread Package for Reading Binary Files GENIE3 GEne Network Inference with Ensemble of trees GENLIB Genealogical Data Analysis GEOmap Topographic and Geologic Mapping GESE Gene-Based Segregation Test GFDmcv General Hypothesis Testing Problems for Multivariate Coefficients of Variation GFM Generalized Factor Model GGClassification Gabriel Graph Based Large-Margin Classifiers GGIRread Wearable Accelerometer Data File Readers GGMncv Gaussian Graphical Models with Nonconvex Regularization GIGrvg Random Variate Generator for the GIG Distribution GLAD Gain and Loss Analysis of DNA GLCMTextures GLCM Textures of Raster Layers GLDEX Fitting Single and Mixture of Generalised Lambda Distributions GLMcat Generalized Linear Models for Categorical Responses GMCM Fast Estimation of Gaussian Mixture Copula Models GMMAT Generalized Linear Mixed Model Association Tests GMSE Generalised Management Strategy Evaluation Simulator GNE Computation of Generalized Nash Equilibria GOFclustering Goodness-of-Fit Testing for Model-Based Clustering GOSemSim GO-terms Semantic Similarity Measures GPBayes Tools for Gaussian Process Modeling in Uncertainty Quantification GPCMlasso Differential Item Functioning in Generalized Partial Credit Models GPFDA Gaussian Process for Functional Data Analysis GPGame Solving Complex Game Problems using Gaussian Processes GPTCM Generalized Promotion Time Cure Model with Bayesian Shrinkage Priors GPareto Gaussian Processes for Pareto Front Estimation and Optimization GPpenalty Penalized Likelihood in Gaussian Processes GPvam Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling GPvecchia Scalable Gaussian-Process Approximations GRAB Genome-Wide Robust Analysis for Biobank Data (GRAB) GSE Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data GSVA Gene Set Variation Analysis for Microarray and RNA-Seq Data GTEs Group Technical Effects GUD Bayesian Modal Regression Based on the GUD Family GUILDS Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure GUTS Fast Calculation of the Likelihood of a Stochastic Survival Model GUniFrac Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis GWASExactHW Exact Hardy-Weinburg Testing for Genome Wide Association Studies GWASinlps Non-Local Prior Based Iterative Variable Selection Tool for Genome-Wide Association Studies GWEX Multi-Site Stochastic Models for Daily Precipitation and Temperature GWmodel Geographically-Weighted Models GWnorm G-Wishart Normalising Constants for Gaussian Graphical Models GaSP Train and Apply a Gaussian Stochastic Process Model GauPro Gaussian Process Fitting GaussianHMM1d Inference, Goodness-of-Fit and Forecast for Univariate Gaussian Hidden Markov Models GeDS Geometrically Designed Spline Regression GenEst Generalized Mortality Estimator GenSA R Functions for Generalized Simulated Annealing GeneralizedUmatrix Credible Visualization for Two-Dimensional Projections of Data GeneralizedUmatrixGPU Credible Visualization for Two-Dimensional Projections of Data GeneralizedWendland Fully Parameterized Generalized Wendland Covariance Function GenomeAdmixR Simulate Admixture of Genomes GenomicRanges Representation and manipulation of genomic intervals GeoAdjust Accounting for Random Displacements of True GPS Coordinates of Data GeoFIS Spatial Data Processing for Decision Making GeoModels Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis GiRaF Gibbs Random Fields Analysis Gifi Multivariate Analysis with Optimal Scaling GillespieSSA2 Gillespie's Stochastic Simulation Algorithm for Impatient People GiniDistance A New Gini Correlation Between Quantitative and Qualitative Variables Glarmadillo Solve the Graphical Lasso Problem with 'Armadillo' GlobalAncova Global test for groups of variables via model comparisons Gmedian Geometric Median, k-Medians Clustering and Robust Median PCA Gmisc Descriptive Statistics, Transition Plots, and More GowerSom Self-Organizing Maps for Mixed-Attribute Data Using Gower Distance GpGp Fast Gaussian Process Computation Using Vecchia's Approximation GreedyEPL Greedy Expected Posterior Loss GreedyExperimentalDesign Greedy Experimental Design Construction GridOnClusters Multivariate Joint Grid Discretization HACSim Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment HBV.IANIGLA Modular Hydrological Model HDANOVA High-Dimensional Analysis of Variance HDCD High-Dimensional Changepoint Detection HDCurves Hierarchical Derivative Curve Estimation HDGLM Tests for High Dimensional Generalized Linear Models HDLSSkST Distribution-Free Exact High Dimensional Low Sample Size k-Sample Tests HDMAADMM ADMM for High-Dimensional Mediation Models HDNRA High-Dimensional Location Testing with Normal-Reference Approaches HDOMDesign High-Dimensional Orthogonal Maximin Distance Designs HDSpatialScan Multivariate and Functional Spatial Scan Statistics HDTSA High Dimensional Time Series Analysis Tools HDclust Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks HDcpDetect Detect Change Points in Means of High Dimensional Data HDtweedie The Lasso for Tweedie's Compound Poisson Model Using an IRLS-BMD Algorithm HHBayes Bayesian Household Transmission Modeling with 'Stan' HLMdiag Diagnostic Tools for Hierarchical (Multilevel) Linear Models HLSM Hierarchical Latent Space Network Model HMMHSMM Inference and Estimation of Hidden Markov Models and Hidden Semi-Markov Models HMMextra0s Hidden Markov Models with Extra Zeros HRTnomaly Historical, Relational, and Tail Anomaly-Detection Algorithms HSAR Hierarchical Spatial Autoregressive Model HTLR Bayesian Logistic Regression with Heavy-Tailed Priors HTT Hypothesis Testing Tree HUM Compute HUM Value and Visualize ROC Curves HZIP Likelihood-Based Inference for Joint Modeling of Correlated Count and Binary Outcomes with Extra Variability and Zeros Haplin Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes HardyWeinberg Statistical Tests and Graphics for Hardy-Weinberg Equilibrium HausdorffGoF One- And Two-Sample Hausdorff Goodness-of-Fit Test HellCor The Hellinger Correlation HiCDOC A/B compartment detection and differential analysis HiClimR Hierarchical Climate Regionalization HiDimDA High Dimensional Discriminant Analysis HiGarrote Nonnegative Garrote Method Incorporating Hierarchical Relationships HiResTEC Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data HiddenMarkov Hidden Markov Models HistDAWass Histogram-Valued Data Analysis Hmisc Harrell Miscellaneous IAPWS95 Thermophysical Properties of Water and Steam IBGS Iterated Block Gibbs Sampler for Ultrahigh-Dimensional Variable Selection and Model Averaging IBMPopSim Individual Based Model Population Simulation IBclust Information Bottleneck Methods for Clustering Mixed-Type Data ICAOD Optimal Designs for Nonlinear Models via ICA ICEbox Individual Conditional Expectation Plot Toolbox ICSClust Tandem Clustering with Invariant Coordinate Selection ICSKAT Interval-Censored Sequence Kernel Association Test ICSNP Tools for Multivariate Nonparametrics ICcalib Cox Model with Interval-Censored Starting Time of a Covariate ICtest Estimating and Testing the Number of Interesting Components in Linear Dimension Reduction ICvectorfields Vector Fields from Spatial Time Series of Population Abundance IDPmisc 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)' IDSpatialStats Estimate Global Clustering in Infectious Disease IFC Tools for Imaging Flow Cytometry IHSEP Inhomogeneous Self-Exciting Process IMR Incomplete Matrix Regression INLAspacetime Spatial and Spatio-Temporal Models using 'INLA' INLAtools Functionalities for the 'INLA' Package INLAvaan Approximate Bayesian Latent Variable Analysis IRISSeismic Classes and Methods for Seismic Data Analysis IRTM Theory-Driven Item Response Theory (IRT) Models IRanges Foundation of integer range manipulation in Bioconductor IRon Solving Imbalanced Regression Tasks ISO6976.2016 Calorific Values and Properties of Natural Gas per ISO 6976:2016 Immigrate Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection Immutables Fast and Functional Data Structures ImpactEffectsize Calculation and Visualization of the Impact Effect Size Measure IncDTW Incremental Calculation of Dynamic Time Warping IndGenErrors Tests of Independence Between Innovations of Generalized Error Models IndependenceTests Non-Parametric Tests of Independence Between Random Vectors InteractionSet Base Classes for Storing Genomic Interaction Data IntervalSurgeon Operating on Integer-Bounded Intervals IrishDirectorates A Dynamic Bipartite Latent Space Model to Analyse Irish Companies' Boards from 2003 to 2013 IsingSampler Sampling Methods and Distribution Functions for the Ising Model Iso Functions to Perform Isotonic Regression IsoSpecR The IsoSpec Algorithm JADE Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria JANE Just Another Latent Space Network Clustering Algorithm JFM Rock Mass Structural Analysis from 3D Mesh of Point Cloud JLPM Joint Latent Process Models JMH Joint Model of Heterogeneous Repeated Measures and Survival Data JMI Jackknife Mutual Information JMbayes Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach JMbayes2 Extended Joint Models for Longitudinal and Time-to-Event Data JSM Semiparametric Joint Modeling of Survival and Longitudinal Data JUMP Replicability Analysis of High-Throughput Experiments JavaGD Java Graphics Device JuliaCall Seamless Integration Between R and 'Julia' KDEmcmc Kernel Density Estimation with a Markov Chain Monte Carlo Sample KFAS Kalman Filter and Smoother for Exponential Family State Space Models KODAMA Knowledge Discovery by Accuracy Maximization KONPsurv KONP Tests: Powerful K-Sample Tests for Right-Censored Data KSgeneral Computing P-Values of the One-Sample K-S Test and the Two-Sample K-S and Kuiper Tests for (Dis)Continuous Null Distribution KWCChangepoint Robust Changepoint Detection for Functional and Multivariate Data Kendall Kendall Rank Correlation and Mann-Kendall Trend Test KernSmoothIRT Nonparametric Item Response Theory KernelKnn Kernel k Nearest Neighbors Kira Machine Learning L0Learn Fast Algorithms for Best Subset Selection L0ggm Smooth L0 Penalty Approximations for Gaussian Graphical Models L1centrality Graph/Network Analysis Based on L1 Centrality L1pack Routines for L1 Estimation LA Lioness Algorithm (LA) LAM Some Latent Variable Models LARisk Estimation of Lifetime Attributable Risk of Cancer from Radiation Exposure LBSPR Length-Based Spawning Potential Ratio LCMCR Bayesian Non-Parametric Latent-Class Capture-Recapture LCPA A General Framework for Latent Classify and Profile Analysis LDAandLDAS Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS) LEA LEA: an R package for Landscape and Ecological Association Studies LGCU Implementation of Learning Gamma CUSUM (Cumulative Sum) Control Charts LMMsolver Linear Mixed Models with Sparse Matrix Methods and Smoothing LMN Inference for Linear Models with Nuisance Parameters LMest Generalized Latent Markov Models LOCOM2 A Logistic Regression Model for Testing Microbial Differential Abundance LOMAR Localization Microscopy Data Analysis LOPART Labeled Optimal Partitioning LPStimeSeries Learned Pattern Similarity and Representation for Time Series LPWC Lag Penalized Weighted Correlation for Time Series Clustering LRQVB Low Rank Correction Quantile Variational Bayesian Algorithm for Multi-Source Heterogeneous Models LS2W Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme LSMjml Fitting Latent Space Item Response Models using Joint Maximum Likelihood Estimation LSTMfactors Determining the Number of Factors in Exploratory Factor Analysis by LSTM LTFGRS Implementation of Several Phenotype-Based Family Genetic Risk Scores LTFHPlus Implementation of LT-FH++ LWFBrook90R Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90 LaF Fast Access to Large ASCII Files LakeMetabolizer Tools for the Analysis of Ecosystem Metabolism LambertW Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data Langevin Langevin Analysis in One and Two Dimensions LangevinFlow Langevin Diffusion Samplers with a C++ Backend LassoBacktracking Modelling Interactions in High-Dimensional Data with Backtracking LassoHiDFastGibbs Fast High-Dimensional Gibbs Samplers for Bayesian Lasso Regression LassoNet 3CoSE Algorithm LatticeDesign Lattice-Based Space-Filling Designs LatticeKrig Multi-Resolution Kriging Based on Markov Random Fields LeMaRns Length-Based Multispecies Analysis by Numerical Simulation LearnNonparam 'R6'-Based Flexible Framework for Permutation Tests LearningRlab Statistical Learning Functions LiblineaR Linear Predictive Models Based on the LIBLINEAR C/C++ Library Libra Linearized Bregman Algorithms for Generalized Linear Models LikertMakeR Synthesise and Correlate Likert Scale and Rating-Scale Data Based on Summary Statistics LipidMS Lipid Annotation for LC-MS/MS DDA or DIA Data Lmoments L-Moments and Quantile Mixtures LocalControl Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence LocalCop Local Likelihood Inference for Conditional Copula Models LogConcDEAD Log-Concave Density Estimation in Arbitrary Dimensions LogicReg Logic Regression LorenzRegression Lorenz and Penalized Lorenz Regressions LowRankQP Low Rank Quadratic Programming Luminescence Comprehensive Luminescence Dating Data Analysis MADMMplasso Multi Variate Multi Response ADMM with Interaction Effects MAGEE Mixed Model Association Test for GEne-Environment Interaction MAINT.Data Model and Analyse Interval Data MALDIquant Quantitative Analysis of Mass Spectrometry Data MAMS Designing Multi-Arm Multi-Stage Studies MAT Multidimensional Adaptive Testing MATES Multi-View Aggregated Two Sample Tests MAVE Methods for Dimension Reduction MAZE Mediation Analysis for Zero-Inflated Mediators MBA Multilevel B-Spline Approximation MBBEFDLite Statistical Functions for the Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of Distributions MBRM Mixed Regression Models with Generalized Log-Gamma Random Effects MCARtest Optimal Nonparametric Testing of Missing Completely at Random MCMCglmm MCMC Generalised Linear Mixed Models MCMChybridGP Hybrid Markov Chain Monte Carlo Using Gaussian Processes MCMCpack Markov Chain Monte Carlo (MCMC) Package MCMCprecision Precision of Discrete Parameters in Transdimensional MCMC MCPModPack Simulation-Based Design and Analysis of Dose-Finding Trials MCSimMod Working with 'MCSim' Models MD2sample Various Methods for the Two Sample Problem in D>1 Dimensions MDCcure Martingale Dependence Tools and Testing for Mixture Cure Models MDDC Modified Detecting Deviating Cells Algorithm in Pharmacovigilance MDFS MultiDimensional Feature Selection MDP2 Markov Decision Processes (MDPs) MDgof Various Methods for the Goodness-of-Fit Problem in D>1 Dimensions MESS Miscellaneous Esoteric Statistical Scripts MFPCA Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains MFSD Multivariate Functional Spatial Data MGDrivE Mosquito Gene Drive Explorer MGL Module Graphical Lasso MGMM Missingness-Aware Gaussian Mixture Models MGSDA Multi-Group Sparse Discriminant Analysis MHD Metric Halfspace Depth MHTmult Multiple Hypotheses Testing for Multiple Families/Groups Structure MICsplines The Computing of Monotonic Spline Bases and Constrained Least-Squares Estimates MJMbamlss Multivariate Joint Models with 'bamlss' MLBC Bias Correction Methods for Models Using Synthetic Data MLEcens Computation of the MLE for Bivariate Interval Censored Data MLZ Mean Length-Based Estimators of Mortality using TMB MM4LMM Inference of Linear Mixed Models Through MM Algorithm MMGFM Multi-Study Multi-Modality Generalized Factor Model MNARclust Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models MNP Fitting the Multinomial Probit Model MOLHD Multiple Objective Latin Hypercube Design MOutliers Multivariate Outlier Detection Methods MPBoost Treatment Allocation in Clinical Trials by the Maximal Procedure MPCR Multi Precision Computing MPSEM Modelling Phylogenetic Signals using Eigenvector Maps MPTinR Analyze Multinomial Processing Tree Models MR.RGM Fitting Multivariate Bidirectional Mendelian Randomization Networks Using Bayesian Directed Cyclic Graphical Models MRCE Multivariate Regression with Covariance Estimation MRIreduce ROI-Based Transformation of Neuroimages into High-Dimensional Data Frames MSCMT Multivariate Synthetic Control Method Using Time Series MSCquartets Analyzing Gene Tree Quartets under the Multi-Species Coalescent MSEtool Management Strategy Evaluation Toolkit MSGARCH Markov-Switching GARCH Models MSIMST Bayesian Monotonic Single-Index Regression Model with the Skew-T Likelihood MSTest Hypothesis Testing for Markov Switching Models MSclassifR Automated Classification of Mass Spectra MSinference Multiscale Inference for Nonparametric Time Trend(s) MSnbase Base Functions and Classes for Mass Spectrometry and Proteomics MTLR Survival Prediction with Multi-Task Logistic Regression MTS All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models MVR Mean-Variance Regularization MVT Estimation and Testing for the Multivariate t-Distribution MVar Multivariate Analysis MVar.pt Analise multivariada (brazilian portuguese) MachineShop Machine Learning Models and Tools MagmaClustR Clustering and Prediction using Multi-Task Gaussian Processes with Common Mean ManifoldOptim An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization ManlyMix Manly Mixture Modeling and Model-Based Clustering MarZIC Marginal Mediation Effects with Zero-Inflated Compositional Mediator MarginalMaxTest Max-Type Test for Marginal Correlation with Bootstrap MassSpecWavelet Peak Detection for Mass Spectrometry data using wavelet-based algorithms MasterBayes Maximum Likelihood and Markov Chain Monte Carlo (MCMC) Methods for Pedigree Reconstruction and Analysis MatchIt Nonparametric Preprocessing for Parametric Causal Inference Matching Multivariate and Propensity Score Matching with Balance Optimization MatrixCorrelation Matrix Correlation Coefficients MatrixExtra Extra Methods for Sparse Matrices MaxPro Maximum Projection Designs MazamaRollUtils Efficient Rolling Functions MediaK Calculate MeDiA_K Distance MedianaDesigner Power and Sample Size Calculations for Clinical Trials MendelianRandomization Mendelian Randomization Package MetaHD A Multivariate Meta-Analysis Model for High-Dimensional Data MetaSKAT Meta Analysis for SNP-Set (Sequence) Kernel Association Test MethScope Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding MetricGraph Random Fields on Metric Graphs Mhorseshoe Approximate Algorithm for Horseshoe Prior MicroMoB Discrete Time Simulation of Mosquito-Borne Pathogen Transmission MicrobiomeStat Statistical Methods for Microbiome Compositional Data MinTriadic Extension to the 'Lolog' Package for 'Triadic' Network Statistics MiscMath Miscellaneous Mathematical Tools MissCP Change Point Detection with Missing Values MixLFA Mixture of Longitudinal Factor Analysis Methods MixMatrix Classification with Matrix Variate Normal and t Distributions MixSim Simulating Data to Study Performance of Clustering Algorithms MixedIndTests Tests of Randomness and Tests of Independence MixfMRI Mixture fMRI Clustering Analysis MixtureFitting Fitting of Univariate Mixture Distributions to Data using Various Approaches MoTBFs Learning Hybrid Bayesian Networks using Mixtures of Truncated Basis Functions ModelMetrics Rapid Calculation of Model Metrics MomTrunc Moments of Folded and Doubly Truncated Multivariate Distributions MonoPoly Functions to Fit Monotone Polynomials MonotonicityTest Nonparametric Bootstrap Test for Regression Monotonicity Morpho Calculations and Visualisations Related to Geometric Morphometrics MortCast Estimation and Projection of Age-Specific Mortality Rates MuChPoint Multiple Change Point MuFiMeshGP Multi-Fidelity Emulator for Computer Experiments with Tunable Fidelity Levels MultNonParam Multivariate Nonparametric Methods MultOrdRS Model Multivariate Ordinal Responses Including Response Styles MultSurvTests Permutation Tests for Multivariate Survival Analysis MultiBD Multivariate Birth-Death Processes MultiCOAP High-Dimensional Covariate-Augmented Overdispersed Multi-Study Poisson Factor Model MultiFit Multiscale Fisher's Independence Test for Multivariate Dependence MultiLCIRT Multidimensional Latent Class Item Response Theory Models MultiModalR Fast Bayesian Probability Estimation for Multimodal Categorical Data MultiRFM High-Dimensional Multi-Study Robust Factor Model MultiStatM Multivariate Statistical Methods MultiscaleDTM Multi-Scale Geomorphometric Terrain Attributes MultivariateRandomForest Models Multivariate Cases Using Random Forests N2R Fast and Scalable Approximate k-Nearest Neighbor Search Methods using 'N2' Library NAM Nested Association Mapping NBPSeq Negative Binomial Models for RNA-Sequencing Data NCutYX Clustering of Omics Data of Multiple Types with a Multilayer Network Representation NLPwavelet Bayesian Wavelet Analysis Using Non-Local Priors NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) NNS Nonlinear Nonparametric Statistics NPBayesImputeCat Non-Parametric Bayesian Multiple Imputation for Categorical Data NPCirc Nonparametric Circular Methods NPflow Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data NSM3 Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition NScluster Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models NUSS Mixed N-Grams and Unigram Sequence Segmentation NestMRMC Single Reader Between-Cases AUC Estimator in Nested Data NetDA Network-Based Discriminant Analysis Subject to Multi-Label Classes NetMix Dynamic Mixed-Membership Network Regression Model NetPreProc Network Pre-Processing and Normalization NetRep Permutation Testing Network Module Preservation Across Datasets NetVAR Network Structures in VAR Models NetworkChange Bayesian Package for Network Changepoint Analysis NetworkDistance Distance Measures for Networks NetworkInference Inferring Latent Diffusion Networks NlinTS Models for Non Linear Causality Detection in Time Series Nmix Bayesian Inference on Univariate Normal Mixtures NoSleepR Prevent System Sleep During Long R Tasks NonlinearDiD Staggered Difference-in-Differences with Nonlinear Outcomes NormPsy Normalisation of Psychometric Tests Numero Statistical Framework to Define Subgroups in Complex Datasets OBsMD Objective Bayesian Model Discrimination in Follow-Up Designs OCNet Optimal Channel Networks ODRF Oblique Decision Random Forest for Classification and Regression OPSR Ordered Probit Switching Regression ORION Ordinal Relations OSFD Output Space-Filling Design OTclust Mean Partition, Uncertainty Assessment, Cluster Validation and Visualization Selection for Cluster Analysis OceanView Visualisation of Oceanographic Data and Model Output OmicFlow Fast and Efficient (Automated) Analysis of Sparse Omics Data OpenCL Interface allowing R to use OpenCL OpenImageR An Image Processing Toolkit OpenMx Extended Structural Equation Modelling Opt5PL Optimal Designs for the 5-Parameter Logistic Model OptCirClust Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible OptGS Near-Optimal Group-Sequential Designs for Continuous Outcomes OptHedging Estimation of value and hedging strategy of call and put options. OptSurvCutR Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with 'OptSurvCutR' OptimalBinningWoE Optimal Binning and Weight of Evidence Framework for Modeling Orcs Omnidirectional R Code Snippets OutcomeWeights Outcome Weights of Treatment Effect Estimators OwenQ Owen Q-Function PAC Partition-Assisted Clustering and Multiple Alignments of Networks PAFit Generative Mechanism Estimation in Temporal Complex Networks PAGE Predictor-Assisted Graphical Models under Error-in-Variables PAGFL Joint Estimation of Latent Groups and Group-Specific Coefficients in (Time-Varying) Panel Data Models PAMmisc Miscellaneous Functions for Passive Acoustic Analysis PANACEA Personalized Network-Based Anti-Cancer Therapy Evaluation PANPRSnext Building PRS Models Based on Summary Statistics of GWAs PAutilities Streamline Physical Activity Research PBSddesolve Solver for Delay Differential Equations PBSmapping Mapping Fisheries Data and Spatial Analysis Tools PBSmodelling GUI Tools Made Easy: Interact with Models and Explore Data PCMBaseCpp Fast Likelihood Calculation for Phylogenetic Comparative Models PCMRS Model Response Styles in Partial Credit Models PCObw Bandwidth Selector with Penalized Comparison to Overfitting Criterion PCpluS Piecewise Constant Plus Smooth Regression PDEnaiveBayes Plausible Naive Bayes Classifier Using PDE PDFEstimator Multivariate Nonparametric Probability Density Estimator PDSCE Positive Definite Sparse Covariance Estimators PEPBVS Bayesian Variable Selection using Power-Expected-Posterior Prior PGRdup Discover Probable Duplicates in Plant Genetic Resources Collections PHSMM Penalised Maximum Likelihood Estimation for Hidden Semi-Markov Models PINSPlus Clustering Algorithm for Data Integration and Disease Subtyping PJFM Variational Inference for High-Dimensional Joint Frailty Model PKI Public Key Infrastucture for R Based on the X.509 Standard PKPDsim Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations PLFD Portmanteau Local Feature Discrimination for Matrix-Variate Data PLNmodels Poisson Lognormal Models PMA Penalized Multivariate Analysis PMCMRplus Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended POMaSPU Adaptive Association Tests for Multiple Phenotypes using Proportional Odds Model (POM-aSPU) PONG2 KIR Genotype Imputation and Model Training from SNP Array Data POSetR Partially Ordered Sets in R POT Generalized Pareto Distribution and Peaks Over Threshold PP Person Parameter Estimation PPMR Probabilistic Two Sample Mendelian Randomization PPMiss Copula-Based Estimator for Long-Range Dependent Processes under Missing Data PPRL Privacy Preserving Record Linkage PPSFS Partial Profile Score Feature Selection in High-Dimensional Generalized Linear Interaction Models PPforest Projection Pursuit Classification Forest PPtreeExt Projection Pursuit Classification Tree Extensions PPtreeViz Projection Pursuit Classification Tree Visualization PRDA Conduct a Prospective or Retrospective Design Analysis PRECAST Embedding and Clustering with Alignment for Spatial Omics Datasets PRIMAL Parametric Simplex Method for Sparse Learning PRIMEplus Study Design for Immunotherapy Clinical Trials PROJ Generic Coordinate System Transformations Using 'PROJ' PROsetta Linking Patient-Reported Outcomes Measures PRTree Probabilistic Regression Trees PReMiuM Dirichlet Process Bayesian Clustering, Profile Regression PSGD Projected Subset Gradient Descent PSPI Propensity Score Predictive Inference for Generalizability PSPManalysis Analysis of Physiologically Structured Population Models PUGMM Parsimonious Ultrametric Gaussian Mixture Models PUlasso High-Dimensional Variable Selection with Presence-Only Data PWEALL Design and Monitoring of Survival Trials Accounting for Complex Situations PanelCount Random Effects and/or Sample Selection Models for Panel Count Data PanelMatch Matching Methods for Causal Inference with Time-Series Cross-Sectional Data PanelSelect Panel Sample Selection Models ParamHelpers Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning PartialNetwork Estimating Peer Effects Using Partial Network Data PeakError Compute the Label Error of Peak Calls PeakSegDP Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data PeakSegDisk Disk-Based Constrained Change-Point Detection PeakSegJoint Joint Peak Detection in Several ChIP-Seq Samples PeakSegOptimal Optimal Segmentation Subject to Up-Down Constraints PearsonDS Pearson Distribution System PenCoxFrail Regularization in Cox Frailty Models Peptides Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences PerfMeas Performance Measures for Ranking and Classification Tasks PerformanceAnalytics Econometric Tools for Performance and Risk Analysis PhaseType Inference for Phase-Type Distributions PheVis Automatic Phenotyping of Electronic Health Record at Visit Resolution PhylogeneticEM Automatic Shift Detection using a Phylogenetic EM Pijavski Global Univariate Minimization PlayerRatings Dynamic Updating Methods for Player Ratings Estimation PoDBAY Vaccine Efficacy Estimation Package PoissonBinomial Efficient Computation of Ordinary and Generalised Poisson Binomial Distributions PoissonMultinomial The Poisson-Multinomial Distribution PoissonPCA Poisson-Noise Corrected PCA PolynomF Polynomials in R PortfolioAnalytics Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios PottsUtils Utility Functions of the Potts Models PoweR Computation of Power and Level Tables for Hypothesis Tests PreciseSums Accurate Floating Point Sums and Products ProFAST Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction ProTrackR2 Manipulate and Play 'ProTracker' Modules ProbSVMs Probabilistic Support Vector Machines ProbitSpatial Probit with Spatial Dependence, SAR, SEM and SARAR Models ProcData Process Data Analysis ProfileGLMM Bayesian Profile Regression using Generalised Linear Mixed Models ProjectionBasedClustering Projection Based Clustering PropClust Propensity Clustering and Decomposition Pursuit Projection Pursuit PwrGSD Power in a Group Sequential Design QCA Qualitative Comparative Analysis QF Density, Cumulative and Quantile Functions of Quadratic Forms QFASA Quantitative Fatty Acid Signature Analysis QHScrnomo Construct Nomograms for Competing Risks Regression Models QR QR Factorization without Pivoting QRM Provides R-Language Code to Examine Quantitative Risk Management Concepts QTL.gCIMapping QTL Genome-Wide Composite Interval Mapping QTL.gCIMapping.GUI QTL Genome-Wide Composite Interval Mapping with Graphical User Interface QTLRel Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees QZ Generalized Eigenvalues and QZ Decomposition Qest Quantile-Based Estimator QregBB Block Bootstrap Methods for Quantile Regression in Time Series QsRutils R Functions Useful for Community Ecology Qtools Utilities for Quantiles QuadratiK Collection of Methods Constructed using Kernel-Based Quadratic Distances QuanDA Quantile-Based Discriminant Analysis for High-Dimensional Imbalanced Classification QuantRegGLasso Adaptively Weighted Group Lasso for Semiparametric Quantile Regression Models QuantileModels Estimation of Different Quantile Related Models QuantilePeer Quantile Peer Effect Models Quartet Comparison of Phylogenetic Trees Using Quartet and Split Measures QuickJSR Interface for the 'QuickJS-NG' Lightweight 'JavaScript' Engine Qval The Q-Matrix Validation Methods Framework R2BayesX Estimate Structured Additive Regression Models with 'BayesX' R2D2ordinal Implements Pseudo-R2D2 Prior for Ordinal Regression R2sample Various Methods for the Two Sample Problem RAINBOWR Genome-Wide Association Study with SNP-Set Methods RAMP Regularized Generalized Linear Models with Interaction Effects RANKS Ranking of Nodes with Kernelized Score Functions RANN Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric RApiDatetime R API for 'Date' and 'Datetime' RApiSerialize R API Serialization RAppArmor Bindings to AppArmor and Security Related Linux Tools RBF Robust Backfitting RBGL An interface to the BOOST graph library RBesT R Bayesian Evidence Synthesis Tools RCALI Calculation of the Integrated Flow of Particles Between Polygons RCSF Airborne LiDAR Filtering Method Based on Cloth Simulation RCTRecruit Non-Parametric Recruitment Prediction for Randomized Clinical Trials RClickhouse 'Yandex Clickhouse' Interface for R with Basic 'dplyr' Support RCurl General Network (HTTP/FTP/...) Client Interface for R RDM Quantify Dependence using Rearranged Dependence Measures RDP The Ramer-Douglas-Peucker Algorithm RDS Respondent-Driven Sampling RDSsamplesize RDS Sample Size Estimation and Power Calculation RDieHarder R Interface to the 'DieHarder' RNG Test Suite REddyProc Post Processing of (Half-)Hourly Eddy-Covariance Measurements REndo Fitting Linear Models with Endogenous Regressors using Latent Instrumental Variables RFIF Fast Iterative Filtering (FIF) with Portable FFT Backend RGBM LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network Reconstruction RGMM Robust Mixture Model RGN Robust-Gauss Newton (RGN) Optimization of Sum-of-Squares Objective Function RGeode Geometric Density Estimation RHRV Heart Rate Variability Analysis of ECG Data RI2by2 Randomization Inference for Treatment Effects on a Binary Outcome RITCH Parser for the ITCH Protocol RInSp R Individual Specialization RInside C++ Classes to Embed R in C++ (and C) Applications RJSONIO Serialize R Objects to JSON RJafroc Artificial Intelligence Systems and Observer Performance RLRsim Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models RLT Reinforcement Learning Trees RLumCarlo Monte-Carlo Methods for Simulating Luminescence Phenomena RLumModel Solving Ordinary Differential Equations to Understand Luminescence RMCC Airborne LiDAR Filtering Method Based on Multiscale Curvature RMCLab Lab for Matrix Completion and Imputation of Discrete Rating Data RMFM Robust Matrix Factor Model RMKdiscrete Sundry Discrete Probability Distributions RMM Revenue Management Modeling RMSNumpress 'Rcpp' Bindings to Native C++ Implementation of MS Numpress RMSS Robust Multi-Model Subset Selection RMVL Mappable Vector Library for Handling Large Datasets RMariaDB Database Interface and MariaDB Driver RMixtCompIO Minimal Interface of the C++ 'MixtComp' Library for Mixture Models with Heterogeneous and (Partially) Missing Data RMySQL Database Interface and 'MySQL' Driver for R RNOmni Rank Normal Transformation Omnibus Test RNetCDF Interface to 'NetCDF' Datasets RNewsflow Tools for Comparing Text Messages Across Time and Media RNifti Fast R and C++ Access to NIfTI Images RNiftyReg Image Registration Using the 'NiftyReg' Library ROC utilities for ROC, with microarray focus RODBC ODBC Database Access ROI.plugin.qpoases 'qpOASES' Plugin for the 'R' Optimization Infrastructure ROKET Optimal Transport-Based Kernel Regression ROTS Reproducibility-Optimized Test Statistic ROptSpace Matrix Reconstruction from a Few Entries RPEGLMEN Gamma and Exponential Generalized Linear Models with Elastic Net Penalty RPatternJoin String Similarity Joins for Hamming and Levenshtein Distances RPesto Phylogenetic Estimation of Shifts in the Tempo of Origination RPhosFate Soil and Chemical Substance Emission and Transport Model RPostgreSQL R Interface to the 'PostgreSQL' Database System RPostgres C++ Interface to PostgreSQL RProtoBuf R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3) RProtoBufLib C++ headers and static libraries of Protocol buffers RPtests Goodness of Fit Tests for High-Dimensional Linear Regression Models RQuantLib R Interface to the 'QuantLib' Library RRF Regularized Random Forest RRI Residual Randomization Inference for Regression Models RSC Robust and Sparse Correlation Matrix RSEIS Seismic Time Series Analysis Tools RSKC Robust Sparse K-Means RSNNS Neural Networks using the Stuttgart Neural Network Simulator (SNNS) RSO Ridge Selection Operator for Sparse Linear Regression RSQLite SQLite Interface for R RSSL Implementations of Semi-Supervised Learning Approaches for Classification RSTr Gibbs Samplers for Discrete Bayesian Spatiotemporal Models RScelestial Scelestial: Steiner Tree Based Single-Cell Lineage Tree Inference RSclient Client for Rserve RSiena Siena - Simulation Investigation for Empirical Network Analysis RSpectra Solvers for Large-Scale Eigenvalue and SVD Problems RStoolbox Remote Sensing Data Analysis RTCC Detecting Trait Clustering in Environmental Gradients RTL Risk Tool Library - Trading, Risk, Analytics for Commodities RTMB 'R' Bindings for 'TMB' RTSA 'Trial Sequential Analysis' for Error Control and Inference in Sequential Meta-Analyses RTextTools Automatic Text Classification via Supervised Learning RTransferEntropy Measuring Information Flow Between Time Series with Shannon and Renyi Transfer Entropy RTriangle Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator RVCompare Compare Real Valued Random Variables RWDataPlyr Read and Manipulate Data from 'RiverWare' RWNN Random Weight Neural Networks RWiener Wiener Process Distribution Functions RZigZag Zig-Zag Sampler RZooRoH Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data Racmacs Antigenic Cartography Macros RadEro Cs-137 Conversion Model Radviz Project Multidimensional Data in 2D Space RandomForestsGLS Random Forests for Dependent Data RankAggSIgFUR Polynomially Bounded Rank Aggregation under Kemeny's Axiomatic Approach RankAggreg Weighted Rank Aggregation Rankcluster Model-Based Clustering for Multivariate Partial Ranking Data Rapi Interface for Multiple Data Providers 'EDDS' and 'FRED' RapidFuzz String Similarity Computation Using 'RapidFuzz' RaschSampler Rasch Sampler Ravages Rare Variant Analysis and Genetic Simulations RavenR Raven Hydrological Modelling Framework R Support and Analysis Rbeast Bayesian Change-Point Detection and Time Series Decomposition Rblpapi R Interface to 'Bloomberg' Rborist Extensible, Parallelizable Implementation of the Random Forest Algorithm Rcatch22 Calculation of 22 CAnonical Time-Series CHaracteristics Rcpp Seamless R and C++ Integration RcppAlgos High Performance Tools for Combinatorics and Computational Mathematics RcppAnnoy 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors RcppArmadillo 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library RcppArray 'Rcpp' Meets 'C++' Arrays RcppBDT 'Rcpp' Bindings for the Boost Date_Time Library RcppBessel Bessel Functions Rcpp Interface RcppBigIntAlgos Factor Big Integers with the Parallel Quadratic Sieve RcppBlaze 'Rcpp' Integration for the 'Blaze' High-Performance 'C++' Math Library RcppCCTZ 'Rcpp' Bindings for the 'CCTZ' Library RcppCNPy Read-Write Support for 'NumPy' Files via 'Rcpp' RcppCWB 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB') RcppClassic Deprecated 'classic' 'Rcpp' 'API' RcppClassicExamples Examples using 'RcppClassic' to Interface R and C++ RcppColMetric Efficient Column-Wise Metric Computation Against Common Vector RcppColors Color Mappings and 'C++' Header Files for Color Conversion RcppDE Global Optimization by Differential Evolution in C++ RcppDPR 'Rcpp' Implementation of Dirichlet Process Regression RcppDist 'Rcpp' Integration of Additional Probability Distributions RcppDynProg 'Rcpp' Dynamic Programming RcppEigen 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library RcppEnsmallen Header-Only C++ Mathematical Optimization Library for 'Armadillo' RcppExamples Examples using 'Rcpp' to Interface R and C++ RcppFarmHash Interface to the Google 'FarmHash' Family of Hash Functions RcppFastAD 'Rcpp' Bindings to 'FastAD' Auto-Differentiation RcppFastFloat 'Rcpp' Bindings for the 'fast_float' Header-Only Library for Number Parsing RcppGSL 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices RcppGetconf 'Rcpp' Interface for Querying System Configuration Variables RcppGreedySetCover Greedy Set Cover RcppHMM Rcpp Hidden Markov Model RcppHNSW 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors RcppHungarian Solves Minimum Cost Bipartite Matching Problems RcppInt64 'Rcpp'-Based Helper Functions to Pass 'Int64' and 'nanotime' Values Between 'R' and 'C++' RcppJagger An R Wrapper for Jagger RcppML Rcpp Machine Learning Library RcppMagicEnum 'Rcpp' Bindings to 'Magic Enum' 'C++' 'Enum' Support RcppMeCab 'rcpp' Wrapper for 'mecab' Library RcppMsgPack 'MsgPack' C++ Header Files and Interface Functions for R RcppNLoptExample 'Rcpp' Package Illustrating Header-Only Access to 'NLopt' RcppNumerical 'Rcpp' Integration for Numerical Computing Libraries RcppParallel Parallel Programming Tools for 'Rcpp' RcppPlanc Parallel Low-Rank Approximation with Nonnegativity Constraints RcppQuantuccia R Bindings to the Calendaring Functionality of 'QuantLib' RcppRedis 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library RcppRoll Efficient Rolling / Windowed Operations RcppSMC Rcpp Bindings for Sequential Monte Carlo RcppSimdJson 'Rcpp' Bindings for the 'simdjson' Header-Only Library for 'JSON' Parsing RcppSpdlog R and C++ Interfaces to 'spdlog' C++ Header Library for Logging RcppTN Rcpp-Based Truncated Normal Distribution RNG and Family RcppTOML 'Rcpp' Bindings to Parser for "Tom's Obvious Markup Language" RcppThread R-Friendly Threading in C++ RcppTskit 'R' Access to the 'tskit C' API RcppUUID Generating Universally Unique Identificators RcppXsimd Xsimd C++ Header-Only Library Files RcppXts Interface the 'xts' API via 'Rcpp' RcppZiggurat 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations Rcsdp R Interface to the CSDP Semidefinite Programming Library Rdimtools Dimension Reduction and Estimation Methods Rdisop Decomposition of Isotopic Patterns Rdsdp R Interface to DSDP Semidefinite Programming Library ReAD Powerful Replicability Analysis of Genome-Wide Association Studies ReIns Functions from "Reinsurance: Actuarial and Statistical Aspects" ReVAMP Interface to 'Vamp' Audio Analysis Plugins ReacTran Reactive Transport Modelling in 1d, 2d and 3d RealVAMS Multivariate VAM Fitting RecAssoRules Recursive Mining for Frequent Pattern and Confident Association Rules Recocrop Estimating Environmental Suitability for Plants RecordLinkage Record Linkage Functions for Linking and Deduplicating Data Sets RefBasedMI Reference-Based Imputation for Longitudinal Clinical Trials with Protocol Deviation RespirAnalyzer Analysis Functions of Respiratory Data RestRserve A Framework for Building HTTP API Rfast A Collection of Efficient and Extremely Fast R Functions Rfast2 A Collection of Efficient and Extremely Fast R Functions II Rfit Rank-Based Estimation for Linear Models Rfmtool Fuzzy Measure Tools Rforestry Random Forests, Linear Trees, and Gradient Boosting for Inference and Interpretability Rfuzzycoco Provides an R Interface to the 'FuzzyCoCo' C++ Library and Extends It Rglpk R/GNU Linear Programming Kit Interface Rgof 1d Goodness of Fit Tests Rgraphviz Provides plotting capabilities for R graph objects RhpcBLASctl Control the Number of Threads on 'BLAS' Rhtslib HTSlib high-throughput sequencing library as an R package RiemBase Functions and C++ Header Files for Computation on Manifolds Riemann Learning with Data on Riemannian Manifolds Rirt Data Analysis and Parameter Estimation Using Item Response Theory Rlabkey Data Exchange Between R and 'LabKey' Server Rlibeemd Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN) Rlibkdv A Versatile Kernel Density Visualization Library for Geospatial Analytics (Heatmap) Rlinsolve Iterative Solvers for (Sparse) Linear System of Equations Rlof R Parallel Implementation of Local Outlier Factor(LOF) Rmalschains Continuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains) RmecabKo Korean Text Analysis with 'MeCab' Rmixmod Classification with Mixture Modelling Rmodule Automated Markov Chain Monte Carlo for Arbitrarily Structured Correlation Matrices Rmpfr Interface R to MPFR - Multiple Precision Floating-Point Reliable Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) Rnanoflann Extremely Fast Nearest Neighbor Search Rnmr1D Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra RoBMA Robust Bayesian Meta-Analyses RoBSA Robust Bayesian Survival Analysis RobExtremes Optimally Robust Estimation for Extreme Value Distributions RobGARCHBoot Robust Bootstrap Forecast Densities for GARCH Models RobKF Innovative and/or Additive Outlier Robust Kalman Filtering RobRegression Robust Multivariate Regression RobStatTM Robust Statistics: Theory and Methods RobustAFT Truncated Maximum Likelihood Fit and Robust Accelerated Failure Time Regression for Gaussian and Log-Weibull Case RobustBayesianCopas Robust Bayesian Copas Selection Model RobustCalibration Robust Calibration of Imperfect Mathematical Models RobustGaSP Robust Gaussian Stochastic Process Emulation RobustLPA Robust Latent Profile Analysis Rogue Identify Rogue Taxa in Sets of Phylogenetic Trees Rook HTTP Web Server for R Ropj Import Origin(R) Project Files RoughSets Data Analysis Using Rough Set and Fuzzy Rough Set Theories RoundAndRound Plot Objects Moving in Orbits Rparadox Read Paradox Database Files Rpcop Principal Curves of Oriented Points Rphylopars Phylogenetic Comparative Tools for Missing Data and Within-Species Variation Rpoppler PDF Tools Based on Poppler RprobitB Bayesian Probit Choice Modeling Rquefts Quantitative Evaluation of the Native Fertility of Tropical Soils Rserve Versatile R Server RsimdDispatch Runtime 'SIMD' Dispatch Templates for 'C' Code in 'R' Packages Rsolnp General Non-Linear Optimization Rsomoclu Somoclu Rssa A Collection of Methods for Singular Spectrum Analysis Rsubbotools Fast Estimation of Subbottin and AEP Distributions (Generalized Error Distribution) Rsymphony SYMPHONY in R Rtinycc Builds the 'TinyCC' Command-Line Interface and Library for 'C' Scripting in 'R' Rtsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation Rttf2pt1 'ttf2pt1' Program Rtwobitlib '2bit' 'C' Library RuHere Flags Spatial Errors in Biological Collection Data Using Specialists' Information Runuran R Interface to the 'UNU.RAN' Random Variate Generators Rvcg Manipulations of Triangular Meshes Based on the 'VCGLIB' API Rvoterdistance Voter Distance to Polling Locations Rwave Time-Frequency Analysis of 1-D Signals Rwbo Run the 'Open-WBO' MaxSAT Solver Rwofost WOFOST Crop Growth Simulation Model Ryacas R Interface to the 'Yacas' Computer Algebra System S4Arrays Foundation of array-like containers in Bioconductor S4Vectors Foundation of vector-like and list-like containers in Bioconductor S7 An Object Oriented System Meant to Become a Successor to S3 and S4 SAFEPG A Novel SAFE Model for Predicting Climate-Related Extreme Losses SAGMM Clustering via Stochastic Approximation and Gaussian Mixture Models SALES The (Adaptive) Elastic Net and Lasso Penalized Sparse Asymmetric Least Squares (SALES) and Coupled Sparse Asymmetric Least Squares (COSALES) using Coordinate Descent and Proximal Gradient Algorithms SAM Sparse Additive Modelling SAMGEP A Semi-Supervised Method for Prediction of Phenotype Event Times SAMtool Stock Assessment Methods Toolkit SANple Fitting Shared Atoms Nested Models via Markov Chains Monte Carlo SANvi Fitting Shared Atoms Nested Models via Variational Bayes SAPP Statistical Analysis of Point Processes SAR Smart Adaptive Recommendations SATS Signature Analyzer for Targeted Sequencing SBMTrees Longitudinal Sequential Imputation and Prediction with Bayesian Trees Mixed-Effects Models for Longitudinal Data SBmedian Scalable Bayes with Median of Subset Posteriors SCEPtER Stellar CharactEristics Pisa Estimation gRid SCEPtERbinary Stellar CharactEristics Pisa Estimation gRid for Binary Systems SCORNET Semi-Supervised Calibration of Risk with Noisy Event Times SChangeBlock Spatial Structural Change Detection by an Analysis of Variability Between Blocks of Observations SDALGCP2 Discrete Log-Gaussian Cox Processes for Aggregated Disease Counts SDMtune Species Distribution Model Selection SEERaBomb SEER and Atomic Bomb Survivor Data Analysis Tools SEL Semiparametric Elicitation SELF A Structural Equation Embedded Likelihood Framework for Causal Discovery SFDesign Space-Filling Designs SGDinference Inference with Stochastic Gradient Descent SGL Fit a GLM (or Cox Model) with a Combination of Lasso and Group Lasso Regularization SGPR Sparse Group Penalized Regression for Bi-Level Variable Selection SHT Statistical Hypothesis Testing Toolbox SIBER Stable Isotope Bayesian Ellipses in R SIGN Similarity Identification in Gene Expression SILGGM Statistical Inference of Large-Scale Gaussian Graphical Model in Gene Networks SIMEXBoost Boosting Method for High-Dimensional Error-Prone Data SIMplyBee 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes SIRmcmc Compartmental Susceptible-Infectious-Recovered (SIR) Model of Community and Household Infection SIS Sure Independence Screening SIT Association Measurement Through Sliced Independence Test (SIT) SITH A Spatial Model of Intra-Tumor Heterogeneity SK4FGA Scott-Knott for Forensic Glass Analysis SKAT SNP-Set (Sequence) Kernel Association Test SKFCPD Fast Online Changepoint Detection for Temporally Correlated Data SLGP Spatial Logistic Gaussian Process for Field Density Estimation SLHD Maximin-Distance (Sliced) Latin Hypercube Designs SLOPE Sorted L1 Penalized Estimation SMASH Subclone Multiplicity Allocation and Somatic Heterogeneity SMR Externally Studentized Midrange Distribution SMUT Multi-SNP Mediation Intersection-Union Test SNPRelate Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data SNPassoc SNPs-Based Whole Genome Association Studies SNPkit S4 Tools for Reading and Organizing Genetic Data SNSeg Self-Normalization(SN) Based Change-Point Estimation for Time Series SOMMD Self Organising Maps for the Analysis of Molecular Dynamics Data SPACO Spatial Component Analysis for Spatial Sequencing Data SPECIES Statistical Package for Species Richness Estimation SPSP Selection by Partitioning the Solution Paths SPlit Split a Dataset for Training and Testing SQLFormatteR Format SQL Queries SSGL Spike-and-Slab Group Lasso for Group-Regularized Generalized Linear Models SSLASSO The Spike-and-Slab LASSO SSN2 Spatial Modeling on Stream Networks SSOSVM Stream Suitable Online Support Vector Machines STAREG An Empirical Bayes Approach for Replicability Analysis Across Two Studies STARTS Functions for the STARTS Model STARTdesign Single to Double Arm Transition Design for Phase II Clinical Trials STB Simultaneous Tolerance Bounds SVDNF Discrete Nonlinear Filtering for Stochastic Volatility Models SVG Spatially Variable Genes Detection Methods for Spatial Transcriptomics SamplingBigData Sampling Methods for Big Data ScaleSpikeSlab Scalable Spike-and-Slab Scalelink Create Scale Linkage Scores ScatterDensity Density Estimation and Visualization of 2D Scatter Plots ScoreEB Score Test Integrated with Empirical Bayes for Association Study SearchTrees Spatial Search Trees SelectBoost.beta Stability-Selection via Correlated Resampling for Beta-Regression Models SelectBoost.gamlss Stability-Selection via Correlated Resampling for 'GAMLSS' Models SelfControlledCaseSeries Self-Controlled Case Series SemiCompRisks Hierarchical Models for Parametric and Semi-Parametric Analyses of Semi-Competing Risks Data SenSpe Estimating Specificity at Controlled Sensitivity, or Vice Versa SensIAT Sensitivity Analysis for Irregular Assessment Times SeqKat Detection of Kataegis SequenceSpikeSlab Exact Bayesian Model Selection Methods for the Sparse Normal Sequence Model Seurat Tools for Single Cell Genomics SeuratObject Data Structures for Single Cell Data ShiftConvolvePoibin Exactly Computing the Tail of the Poisson-Binomial Distribution ShortRead FASTQ input and manipulation ShrinkCovMat Shrinkage Covariance Matrix Estimators ShrinkageTrees Bayesian Tree Ensembles for Survival Analysis and Causal Inference SiFINeT Single Cell Feature Identification with Network Topology SiMRiv Simulating Multistate Movements in River/Heterogeneous Landscapes SiPhyNetwork A Phylogenetic Simulator for Reticulate Evolution Sieve Nonparametric Estimation by the Method of Sieves Signac Analysis of Single-Cell Chromatin Data SimBIID Simulation-Based Inference Methods for Infectious Disease Models SimEUCartelLaw Simulation of Legal Exemption System for European Cartel Law SimInf A Framework for Data-Driven Stochastic Disease Spread Simulations SimJoint Simulate Joint Distribution SimReg Similarity Regression SimTOST Sample Size Estimation for Bio-Equivalence Trials Through Simulation SingleR Reference-Based Single-Cell RNA-Seq Annotation SmartSVA Fast and Robust Surrogate Variable Analysis SmokingHistoryGenerator R Package for the Smoking History Generator SmoothHazard Estimation of Smooth Hazard Models for Interval-Censored Data SnowballC Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library Sobol4R Sobol Indices for Models with Fixed and Stochastic Parameters SoftBart Implements the SoftBart Algorithm SoundexBR Phonetic-Coding for Portuguese SoyNAM Soybean Nested Association Mapping Dataset SpTe2M Nonparametric Modeling and Monitoring of Spatio-Temporal Data SpaCCI Spatially Aware Cell-Cell Interaction Analysis SpaCOAP High-Dimensional Spatial Covariate-Augmented Overdispersed Poisson Factor Model SpaTopic Topic Inference to Identify Tissue Architecture in Multiplexed Images SpaceTimeBSS Blind Source Separation for Multivariate Spatio-Temporal Data SparseArray High-performance sparse data representation and manipulation in R SparseChol Sparse Matrix C++ Classes Including Sparse Cholesky LDL Decomposition of Symmetric Matrices SparseICA Sparse Independent Component Analysis SparseLPM The Sparse Latent Position Model for Nonnegative Interaction Data SparseM Sparse Linear Algebra SparseTSCGM Sparse Time Series Chain Graphical Models SpatMCA Regularized Spatial Maximum Covariance Analysis SpatPCA Regularized Principal Component Analysis for Spatial Data SpatialBSS Blind Source Separation for Multivariate Spatial Data SpatialEpi Methods and Data for Spatial Epidemiology SpatialExtremes Modelling Spatial Extremes SpatialGEV Fit Spatial Generalized Extreme Value Models SpatialInference Tools for Statistical Inference with Geo-Coded Data SpatialKDE Kernel Density Estimation for Spatial Data SpatialNP Multivariate Nonparametric Methods Based on Spatial Signs and Ranks SpatialPack Tools for Assessment the Association Between Two Spatial Processes SpatialTools Tools for Spatial Data Analysis Spbsampling Spatially Balanced Sampling SpeTestNP Non-Parametric Tests of Parametric Specifications SpecsVerification Forecast Verification Routines for Ensemble Forecasts of Weather and Climate SplitGLM Split Generalized Linear Models SplitReg Split Regularized Regression Sshaped Nonparametric, Tuning-Free Estimation of S-Shaped Functions StMoSim Quantile-Quantile Plot with Several Gaussian Simulations StanHeaders C++ Header Files for Stan StatRec A Statistical Method for Multi-Item Rating and Recommendation Problems StealLikeBayes A Compendium of Bayesian Statistical Routines Written in 'C++' StempCens Spatio-Temporal Estimation and Prediction for Censored/Missing Responses StepwiseTest Multiple Testing Method to Control Generalized Family-Wise Error Rate and False Discovery Proportion StereoMorph Stereo Camera Calibration and Reconstruction StochBlock Stochastic Blockmodeling of One-Mode and Linked Networks StormR Analyzing the Behaviour of Wind Generated by Tropical Storms and Cyclones StrainRanking Ranking of Pathogen Strains StrathE2E2 End-to-End Marine Food Web Model StratifiedSampling Different Methods for Stratified Sampling StuteTest Stute (1997) Linearity Test SubTS Positive Tempered Stable Distributions and Related Subordinators SuperExactTest Exact Test and Visualization of Multi-Set Intersections SuperGauss Superfast Likelihood Inference for Stationary Gaussian Time Series SuperRanker Sequential Rank Agreement SuperpixelImageSegmentation Superpixel Image Segmentation SuppDists Supplementary Distributions SurfRough Calculate Surface/Image Texture Indexes SurrogateBMA Flexible Evaluation of Surrogate Markers with Bayesian Model Averaging SurrogateParadoxTest Empirical Testing of Surrogate Paradox Assumptions SurrogateRegression Surrogate Outcome Regression Analysis SurvEval Methods for the Evaluation of Survival Models SurvivalClusteringTree Clustering Analysis Using Survival Tree and Forest Algorithms SymTS Symmetric Tempered Stable Distributions SyncRNG A Synchronized Tausworthe RNG for R and Python SynchWave Synchrosqueezed Wavelet Transform T4cluster Tools for Cluster Analysis T4transport Tools for Computational Optimal Transport TAG Transformed Additive Gaussian Processes TAM Test Analysis Modules TAQMNGR Manage Tick-by-Tick Transaction Data TBRDist Rearrangement Distances Between Phylogenetic Trees TCHazaRds Tropical Cyclone (Hurricane, Typhoon) Spatial Hazard Modelling TCIU Spacekime Analytics, Time Complexity and Inferential Uncertainty TDA Statistical Tools for Topological Data Analysis TDAkit Toolkit for Topological Data Analysis TDApplied Machine Learning and Inference for Topological Data Analysis TDAstats Pipeline for Topological Data Analysis TDAvec Vector Summaries of Persistence Diagrams TDboost A Boosted Tweedie Compound Poisson Model TFMPvalue Efficient and Accurate P-Value Computation for Position Weight Matrices TFRE A Tuning-Free Robust and Efficient Approach to High-Dimensional Regression TFunHDDC Clustering of Functional Data via Mixtures of t-Distributions TICM Testing the Validity of the Independent Component Model Assumption TIMP Fitting Separable Nonlinear Models in Spectroscopy and Microscopy TLMoments Calculate TL-Moments and Convert Them to Distribution Parameters TMB Template Model Builder: A General Random Effect Tool Inspired by 'ADMB' TMTI Too Many, Too Improbable (TMTI) Test Procedures TPmsm Estimation of Transition Probabilities in Multistate Models TSDFGS Training Set Determination for Genomic Selection TSEntropies Time Series Entropies TSHRC Two Stage Hazard Rate Comparison TSLA Tree-Guided Rare Feature Selection and Logic Aggregation TSP Infrastructure for the Traveling Salesperson Problem TSSS Time Series Analysis with State Space Model TSrepr Time Series Representations TTR Technical Trading Rules TTR.PGM Thornley Transport Resistance Plant Growth Model TULIP A Toolbox for Linear Discriminant Analysis with Penalties TUWmodel Lumped/Semi-Distributed Hydrological Model for Education Purposes TapeS Tree Taper Curves and Sorting Based on 'TapeR' TauStar Efficient Computation and Testing of the Bergsma-Dassios Sign Covariance TensorClustering Model-Based Tensor Clustering TensorMCMC Tensor Regression with Stochastic Low-Rank Updates TestCor FWER and FDR Controlling Procedures for Multiple Correlation Tests TestDesign Optimal Test Design Approach to Fixed and Adaptive Test Construction TestsSymmetry Tests for Symmetry when the Center of Symmetry is Unknown TexExamRandomizer Personalizes and Randomizes Exams Written in 'LaTeX' TiPS Trajectories and Phylogenies Simulator Tinflex A Universal Non-Uniform Random Number Generator TopKLists Inference, Aggregation and Visualization for Top-K Ranked Lists TraMineR Trajectory Miner: a Sequence Analysis Toolkit TraMineRextras TraMineR Extension Transition Characterise Transitions in Test Result Status in Longitudinal Studies TreeBUGS Hierarchical Multinomial Processing Tree Modeling TreeDimensionTest Trajectory Presence and Heterogeneity in Multivariate Data TreeDist Calculate and Map Distances Between Phylogenetic Trees TreeSearch Phylogenetic Analysis with Discrete Character Data TreeTools Create, Modify and Analyse Phylogenetic Trees TrialEmulation Causal Analysis of Observational Time-to-Event Data TrialSimulator Clinical Trial Simulator TrialSize R Functions for Chapter 3,4,6,7,9,10,11,12,14,15 of Sample Size Calculation in Clinical Research TrioSGL Trio Model with a Combination of Lasso and Group Lasso Regularization TruncatedNormal Truncated Multivariate Normal and Student Distributions TunePareto Multi-Objective Parameter Tuning for Classifiers TwoStepSDFM Estimate a Sparse Mixed Frequency Gaussian Factor Model Using a Two-Step Procedure TwoWayFEWeights Estimation of the Weights Attached to the Two-Way Fixed Effects Regressions UAHDataScienceSF Interactive Statistical Learning Functions UComp Automatic Univariate Time Series Modelling of many Kinds UPCM Uncertainty in Partial Credit Models Umatrix Visualization of Structures in High-Dimensional Data UniExactFunTest Uniform Exact Functional Tests for Contingency Tables Upsilon Another Test of Association for Count Data V8 Embedded JavaScript and WebAssembly Engine for R VARSELECTEXPOSURE Variable Selection Methods Including an Exposure Variable VARtests Bootstrap Tests for Cointegration and Autocorrelation in VARs VBLPCM Variational Bayes Latent Position Cluster Model for Networks VBel Variational Bayes for Fast and Accurate Empirical Likelihood Inference VC2copula Extend the 'copula' Package with Families and Models from 'VineCopula' VCA Variance Component Analysis VCBART Fit Varying Coefficient Models with Bayesian Additive Regression Trees VEwaningVariant Vaccine Efficacy Over Time - Variant Aware VGAM Vector Generalized Linear and Additive Models VGAMextra Additions and Extensions of the 'VGAM' Package VIC5 The Variable Infiltration Capacity (VIC) Hydrological Model VICatMix Variational Mixture Models for Clustering Categorical Data VIGoR Variational Bayesian Inference for Genome-Wide Regression VIM Visualization and Imputation of Missing Values VLMC Variable Length Markov Chains ('VLMC') Models VMDecomp Variational Mode Decomposition VPdtw Variable Penalty Dynamic Time Warping VarSelLCM Variable Selection for Model-Based Clustering of Mixed-Type Data Set with Missing Values VariantAnnotation Annotation of Genetic Variants VeccTMVN Multivariate Normal Probabilities using Vecchia Approximation VectorForgeML High-Performance Machine Learning Framework with C++ Acceleration VeryLargeIntegers Store and Operate with Arbitrarily Large Integers VineCopula Statistical Inference of Vine Copulas WARDEN Workflows for Health Technology Assessments in R using Discrete EveNts WGCNA Weighted Correlation Network Analysis WH Enhanced Implementation of Whittaker-Henderson Smoothing WLreg Regression Analysis Based on Win Loss Endpoints WOAkMedoids Whale Optimization Algorithm for K-Medoids Clustering WPKDE Weighted Piecewise Kernel Density Estimation WRI Wasserstein Regression and Inference WSPsignal Weibull Shape Parameter Tests for Signal Detection WaveSampling Weakly Associated Vectors (WAVE) Sampling Waypoint Convert, Validate, Format and Print Geographic Coordinates and Waypoints WebGestaltR Gene Set Analysis Toolkit WebGestaltR WeibullR Weibull Analysis for Reliability Engineering WeightSVM Subject Weighted Support Vector Machines WeightedCluster Clustering of Weighted Data WeightedTreemaps Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical Data WhiteLabRt Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting WienR Derivatives of the First-Passage Time Density and Cumulative Distribution Function, and Random Sampling from the (Truncated) First-Passage Time Distribution WinRatio Win Ratio for Prioritized Outcomes and 95% Confidence Interval WinsCRT Win Statistics Inference for Cluster-Randomized Trials WpProj Linear p-Wasserstein Projections XDNUTS Discontinuous Hamiltonian Monte Carlo with Varying Trajectory Length XML Tools for Parsing and Generating XML Within R and S-Plus XNomial Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities XOMultinom Exact Distributions of Some Functions of the Ordered Multinomial Counts XVector Foundation of external vector representation and manipulation in Bioconductor XYomics Analysis of Sex Differences in Omics Data for Complex Diseases YPInterimTesting Interim Monitoring Using Adaptively Weighted Log-Rank Test in Clinical Trials YatchewTest Yatchew (1997), De Chaisemartin & D'Haultfoeuille (2024) Linearity Test ZIPBayes Bayesian Methods in the Analysis of Zero-Inflated Poisson Model ZVCV Zero-Variance Control Variates a5R 'A5' Discrete Global Grid System aRtsy Generative Art with 'ggplot2' abcel Empirical Likelihood-Based Approximate Bayesian Computation abclass Angle-Based Classification abcpp Shared C++ Backend for Approximate Bayesian Computation abcrf Approximate Bayesian Computation via Random Forests abctools Tools for ABC Analyses aberrance Detect Aberrant Behavior in Test Data abess Fast Best Subset Selection abn Modelling Multivariate Data with Additive Bayesian Networks abtest Bayesian A/B Testing abundant High-Dimensional Principal Fitted Components and Abundant Regression acc Exploring Accelerometer Data acebayes Optimal Bayesian Experimental Design using the ACE Algorithm acepack ACE and AVAS for Selecting Multiple Regression Transformations actigraph.sleepr Detect Periods of Sleep and Non-Wear in 'ActiGraph' Data actuar Actuarial Functions and Heavy Tailed Distributions adaR A Fast 'WHATWG' Compliant URL Parser adapt3 Adaptive Dynamics and Community Matrix Model Projections adaptIVPT Adaptive Bioequivalence Design for In-Vitro Permeation Tests adaptivetau Tau-Leaping Stochastic Simulation adbcdrivermanager 'Arrow' Database Connectivity ('ADBC') Driver Manager adbcpostgresql 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver adbcsqlite 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver ade4 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences adegenet Exploratory Analysis of Genetic and Genomic Data adehabitatHR Home Range Estimation adehabitatHS Analysis of Habitat Selection by Animals adehabitatLT Analysis of Animal Movements adehabitatMA Tools to Deal with Raster Maps adelie Group Lasso and Elastic Net Solver for Generalized Linear Models adephylo Exploratory Analyses for the Phylogenetic Comparative Method adespatial Multivariate Multiscale Spatial Analysis adestr Estimation in Optimal Adaptive Two-Stage Designs adfExplorer Access and Manipulate Amiga Disk Files adheRenceRX Assess Medication Adherence from Pharmaceutical Claims Data adimpro Adaptive Smoothing of Digital Images adj Lightweight Adjacency Lists adjSURVCI Parameter and Adjusted Probability Estimation for Right-Censored Data adjclust Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix adjoin Constructing Adjacency Matrices Based on Spatial and Feature Similarity adlift An Adaptive Lifting Scheme Algorithm admisc Adrian Dusa's Miscellaneous admix Package Admix for Admixture (aka Contamination) Models admixr2 Aggregate Data Modelling adpss Design and Analysis of Locally or Globally Efficient Adaptive Designs ads Spatial Point Patterns Analysis affxparser Affymetrix File Parsing SDK affy Methods for Affymetrix Oligonucleotide Arrays affyPLM Methods for fitting probe-level models affyio Tools for parsing Affymetrix data files aftPenCDA Estimating Penalized AFT Models via Coordinate Descent aftgee Accelerated Failure Time Model with Generalized Estimating Equations aftsem Semiparametric Accelerated Failure Time Model afttest Model Diagnostics for Accelerated Failure Time Models agcounts Calculate 'ActiGraph' Counts from Accelerometer Data agop Aggregation Operators and Preordered Sets agregR Bayesian State-Space Aggregation of Brazilian Presidential Polls ahaz Regularization for Semiparametric Additive Hazards Regression ahocorasick Fast Multi-Pattern String Matching with the 'Aho-Corasick' Algorithm aiRthermo Atmospheric Thermodynamics and Visualization aifeducation Artificial Intelligence for Education aihuman Experimental Evaluation of Algorithm-Assisted Human Decision-Making airGR Suite of GR Hydrological Models for Precipitation-Runoff Modelling akima Interpolation of Irregularly and Regularly Spaced Data alakazam Immunoglobulin Clonal Lineage and Diversity Analysis alcyon Spatial Network Analysis almanac Tools for Working with Recurrence Rules alpaca Fit GLM's with High-Dimensional k-Way Fixed Effects alphabetr Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells alphashape3d Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud alqrfe Adaptive Lasso Quantile Regression with Fixed Effects alternativeROC Alternative and Fast ROC Analysis amap Another Multidimensional Analysis Package ambient A Generator of Multidimensional Noise ambit Simulation and Estimation of Ambit Processes ameras Analyze Multiple Exposure Realizations in Association Studies amorem Augmented Modelling of Relational Events ampir Predict Antimicrobial Peptides amsSim Adaptive Multilevel Splitting for Option Simulation and Pricing anMC Compute High Dimensional Orthant Probabilities analogue Analogue and Weighted Averaging Methods for Palaeoecology aniSNA Statistical Network Analysis of Animal Social Networks anomaly Detecting Anomalies in Data anominate Alpha-NOMINATE Ideal Point Estimator anticlust Subset Partitioning via Anticlustering antiword Extract Text from Microsoft Word Documents anytime Anything to 'POSIXct' or 'Date' Converter aorsf Accelerated Oblique Random Forests apcf Adapted Pair Correlation Function apcluster Affinity Propagation Clustering ape Analyses of Phylogenetics and Evolution aphid Analysis with Profile Hidden Markov Models aphylo Statistical Inference and Prediction of Annotations in Phylogenetic Trees apollo Tools for Choice Model Estimation and Application approxOT Approximate and Exact Optimal Transport Methods arcgisgeocode A Robust Interface to ArcGIS 'Geocoding Services' arcgisplaces Search for POIs using ArcGIS 'Places Service' arcgisrouting Access the ArcGIS Routing and Network Analysis Services arcgisutils R-ArcGIS Bridge Utility Functions archive Multi-Format Archive and Compression Support arcopt Adaptive Regularization using Cubics for Optimization arcpbf Process ArcGIS Protocol Buffer FeatureCollections area Calculate Area of Triangles and Polygons arfima Fractional ARIMA (and Other Long Memory) Time Series Modeling argus Random Variate Generator for the Argus Distribution aricode Efficient Computations of Standard Clustering Comparison Measures arima2 Likelihood Based Inference for ARIMA Modeling arkhaia Archaeological and Historical Analysis armspp Adaptive Rejection Metropolis Sampling (ARMS) via 'Rcpp' arrApply Apply a Function to a Margin of an Array arrangements Fast Generators and Iterators for Permutations, Combinations, Integer Partitions and Compositions arrow Integration to 'Apache' 'Arrow' ars Adaptive Rejection Sampling artma Automatic Replication Tools for Meta-Analysis arules Mining Association Rules and Frequent Itemsets arulesCBA Classification Based on Association Rules arulesSequences Mining Frequent Sequences asciicast Create 'Ascii' Screen Casts from R Scripts ash David Scott's ASH Routines ashr Methods for Adaptive Shrinkage, using Empirical Bayes askpass Password Entry Utilities for R, Git, and SSH asmbPLS Predicting and Classifying Patient Phenotypes with Multi-Omics Data aspline Spline Regression with Adaptive Knot Selection assist A Suite of R Functions Implementing Spline Smoothing Techniques asteRisk Computation of Satellite Position aster Aster Models aster2 Aster Models astgrepr Parse and Manipulate R Code astrochron A Computational Tool for Astrochronology astronomyengine R Bindings to the 'Astronomy Engine' C Library atakrig Area-to-Area Kriging audio Audio Interface for R augSIMEX Analysis of Data with Mixed Measurement Error and Misclassification in Covariates aum Area Under Minimum of False Positives and Negatives autoFRK Automatic Fixed Rank Kriging automerge R Bindings for 'Automerge' 'CRDT' Library autometric Background Resource Logging autothresholdr An R Port of the 'ImageJ' Plugin 'Auto Threshold' av Working with Audio and Video in R avar Allan Variance awdb Query the USDA NWCC Air and Water Database REST API aws Adaptive Weights Smoothing awsMethods Class and Methods Definitions for Packages 'aws', 'adimpro', 'fmri', 'dwi' b32 Fast and Vectorized Base32 Encoding b64 Fast and Vectorized Base 64 Engine bWGR Bayesian Whole-Genome Regression babelmixr2 Use 'nlmixr2' to Interact with Open Source and Commercial Software backbone Extracts the Backbone from Networks backports Reimplementations of Functions Introduced Since R-3.0.0 baclava Bayesian Analysis of Cancer Latency with Auxiliary Variable Augmentation bacontrees Bayesian Context Trees for Discrete Sequence Data badp Bayesian Averaging for Dynamic Panels bage Bayesian Estimation and Forecasting of Age-Specific Rates baggingbwsel Bagging Bandwidth Selection in Kernel Density and Regression Estimation bain Bayes Factors for Informative Hypotheses bakR Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets baldur Bayesian Hierarchical Modeling for Label-Free Proteomics balnet Pathwise Estimation of Covariate Balancing Propensity Scores bama High Dimensional Bayesian Mediation Analysis bamlss Bayesian Additive Models for Location, Scale, and Shape (and Beyond) bamm Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM) bamp Bayesian Age-Period-Cohort Modeling and Prediction bamsignals Extract read count signals from bam files banditpam Almost Linear-Time k-Medoids Clustering bark Bayesian Additive Regression Kernels bartXViz Visualization of BART and BARP using SHAP bartcs Bayesian Additive Regression Trees for Confounder Selection basad Bayesian Variable Selection with Shrinking and Diffusing Priors base64enc Tools for 'base64' Encoding base64url Fast and URL-Safe Base64 Encoder and Decoder basefun Infrastructure for Computing with Basis Functions baseline Baseline Correction of Spectra bases Basis Expansions for Regression Modeling basicspace Recovering a Basic Space from Issue Scales baskexact Analytical Calculation of Basket Trial Operating Characteristics batchelor Single-Cell Batch Correction Methods batchmix Semi-Supervised Bayesian Mixture Models Incorporating Batch Correction batchtools Tools for Computation on Batch Systems batman Convert Categorical Representations of Logicals to Actual Logicals bayMDS Bayesian Multidimensional Scaling and Choice of Dimension bayesCureRateModel Bayesian Cure Rate Modeling for Time-to-Event Data bayesDP Implementation of the Bayesian Discount Prior Approach for Clinical Trials bayesDccGarch Methods and Tools for Bayesian Dynamic Conditional Correlation GARCH(1,1) Model bayesEO Bayesian Smoothing of Remote Sensing Image Classification bayesGARCH Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations bayesImageS Bayesian Methods for Image Segmentation using a Potts Model bayesLife Bayesian Projection of Life Expectancy bayesPO Bayesian Inference for Presence-Only Data bayesPop Probabilistic Population Projection bayesQR Bayesian Quantile Regression bayesQRsurvey Bayesian Quantile Regression Models for Complex Survey Data Analysis bayesSSM Bayesian Methods for State Space Models bayesSurv Bayesian Survival Regression with Flexible Error and Random Effects Distributions bayesTFR Bayesian Fertility Projection bayesWatch Bayesian Change-Point Detection for Process Monitoring with Fault Detection bayescount Power Calculations and Bayesian Analysis of Count Distributions and FECRT Data using MCMC bayesefa Bayesian Exploratory Factor Analysis bayesianETAS Bayesian Estimation of the Temporal and Spatio-Temporal ETAS Models for Earthquake Occurrences bayesianVARs MCMC Estimation of Bayesian Vectorautoregressions bayeslist Bayesian Analysis of List Experiments with Prior Information bayeslm Efficient Sampling for Gaussian Linear Regression with Arbitrary Priors bayesm Bayesian Inference for Marketing/Micro-Econometrics bayesmove Non-Parametric Bayesian Analyses of Animal Movement baygel Bayesian Shrinkage Estimators for Precision Matrices in Gaussian Graphical Models bayou Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies bbdetection Identification of Bull and Bear States of the Market bbk Client for Central Bank APIs bbknnR Perform Batch Balanced KNN in R bbl Boltzmann Bayes Learner bbmix Bayesian Model for Genotyping using RNA-Seq bbotk Black-Box Optimization Toolkit bcROCsurface Bias-Corrected Methods for Estimating the ROC Surface of Continuous Diagnostic Tests bcf Causal Inference using Bayesian Causal Forests bclogit Conditional Logistic Regression bcp Bayesian Analysis of Change Point Problems bcpa Behavioral Change Point Analysis of Animal Movement bcrypt 'Blowfish' Key Derivation and Password Hashing bcv Cross-Validation for the SVD (Bi-Cross-Validation) bda Binned Data Analysis bdrc Bayesian Discharge Rating Curves bdsm Bayesian Dynamic Systems Modeling bdsmatrix Routines for Block Diagonal Symmetric Matrices bdsvd Block Structure Detection Using Singular Vectors beachmat Compiling Bioconductor to Handle Each Matrix Type beam Fast Bayesian Inference in Large Gaussian Graphical Models beastt Bayesian Evaluation, Analysis, and Simulation Software Tools for Trials beeswarm The Bee Swarm Plot, an Alternative to Stripchart beezdemand Behavioral Economic Easy Demand belg Boltzmann Entropy of a Landscape Gradient bench High Precision Timing of R Expressions bennu Bayesian Estimation of Naloxone Kit Number Under-Reporting bespatial Boltzmann Entropy for Spatial Data bestglm Best Subset GLM and Regression Utilities betaBayes Bayesian Beta Regression betareg Beta Regression betaregscale Beta Regression for Interval-Censored Scale-Derived Outcomes betategarch Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH Models beyondWhittle Bayesian Spectral Inference for Time Series bfast Breaks for Additive Season and Trend bfp Bayesian Fractional Polynomials bggum Bayesian Estimation of Generalized Graded Unfolding Model Parameters bgms Bayesian Analysis of Networks of Binary and/or Ordinal Variables bgumbel Bimodal Gumbel Distribution bgw Bunch-Gay-Welsch Statistical Estimation bhetGP Bayesian Heteroskedastic Gaussian Processes bhpm Bayesian Hierarchical Poisson Models for Multiple Grouped Outcomes with Clustering bife Binary Choice Models with Fixed Effects bigANNOY Approximate k-Nearest Neighbour Search for 'bigmemory' Matrices with Annoy bigGP Distributed Gaussian Process Calculations bigKNN Exact Search and Graph Construction for 'bigmemory' Matrices bigPCAcpp Principal Component Analysis for 'bigmemory' Matrices bigPLSR Partial Least Squares Regression Models with Big Matrices bigPLScox Partial Least Squares for Cox Models with Big Matrices bigQF Quadratic Forms in Large Matrices bigReg Generalized Linear Models (GLM) for Large Data Sets bigSurvSGD Big Survival Analysis Using Stochastic Gradient Descent bigalgebra 'BLAS' and 'LAPACK' Routines for Native R Matrices and 'big.matrix' Objects biganalytics Utilities for 'big.matrix' Objects from Package 'bigmemory' bigdatadist Distances for Machine Learning and Statistics in the Context of Big Data bigergm Fit, Simulate, and Diagnose Hierarchical Exponential-Family Models for Big Networks biglasso Extending Lasso Model Fitting to Big Data biglm Bounded Memory Linear and Generalized Linear Models biglmm Bounded Memory Linear and Generalized Linear Models bigmemory Manage Massive Matrices with Shared Memory and Memory-Mapped Files bignum Arbitrary-Precision Integer and Floating-Point Mathematics bigreadr Read Large Text Files bigrquery An Interface to Google's 'BigQuery' 'API' bigrquerystorage An Interface to Google's 'BigQuery Storage' API bigsnpr Analysis of Massive SNP Arrays bigsparser Sparse Matrix Format with Data on Disk bigsplines Smoothing Splines for Large Samples bigstatsr Statistical Tools for Filebacked Big Matrices bigtabulate Table, Apply, and Split Functionality for Matrix and 'big.matrix' Objects bigtcr Nonparametric Analysis of Bivariate Gap Time with Competing Risks bigtime Sparse Estimation of Large Time Series Models bigutilsr Utility Functions for Large-scale Data bild A Package for BInary Longitudinal Data binaryGP Fit and Predict a Gaussian Process Model with (Time-Series) Binary Response binaryRL Reinforcement Learning Tools for Two-Alternative Forced Choice Tasks bindrcpp An 'Rcpp' Interface to Active Bindings binom Binomial Confidence Intervals for Several Parameterizations binpackr Fast 1d Bin Packing binsegRcpp Efficient Implementation of Binary Segmentation binspp Bayesian Inference for Neyman-Scott Point Processes bio3d Biological Structure Analysis bioacoustics Analyse Audio Recordings and Automatically Extract Animal Vocalizations bioimagetools Tools for Microscopy Imaging biomartr Genomic Data Retrieval bioregion Comparison of Bioregionalization Methods biosensors.usc Distributional Data Analysis Techniques for Biosensor Data biovizBase Basic graphic utilities for visualization of genomic data. bipartite Visualising Bipartite Networks and Calculating Some (Ecological) Indices biplotEZ EZ-to-Use Biplots birdie Bayesian Instrumental Regression for Disparity Estimation bit Classes and Methods for Fast Memory-Efficient Boolean Selections bit64 A S3 Class for Vectors of 64bit Integers bitops Bitwise Operations bitriad Triadic Analysis of Affiliation Networks biwavelet Conduct Univariate and Bivariate Wavelet Analyses blackbox Black Box Optimization and Exploration of Parameter Space blaster Native R Implementation of an Efficient BLAST-Like Algorithm blatent Bayesian Latent Variable Models blavaan Bayesian Latent Variable Analysis blindrecalc Blinded Sample Size Recalculation bliss Bayesian Functional Linear Regression with Sparse Step Functions blockCV Spatial and Environmental Blocking for K-Fold and LOO Cross-Validation blockForest Block Forests: Random Forests for Blocks of Clinical and Omics Covariate Data blockTools Block, Assign, and Diagnose Potential Interference in Randomized Experiments blockmodeling Generalized and Classical Blockmodeling of Valued Networks blockmodels Latent and Stochastic Block Model Estimation by a 'V-EM' Algorithm blorr Tools for Developing Binary Logistic Regression Models blosc Compress and Decompress Data Using the 'BLOSC' Library blox Block Diagonal Matrix Approximation bluster Clustering Algorithms for Bioconductor blvim Boltzmann–Lotka–Volterra Interaction Model bmixture Bayesian Estimation for Finite Mixture of Distributions bnclassify Learning Discrete Bayesian Network Classifiers from Data bnlearn Bayesian Network Structure Learning, Parameter Learning and Inference bnnSurvival Bagged k-Nearest Neighbors Survival Prediction bnstruct Bayesian Network Structure Learning from Data with Missing Values boids4R Reynolds-Style Boids and Swarm Simulation bonsaiforest Shrinkage Based Forest Plots boodd Functions for the Book "Bootstrap for Dependent Data, with an R Package" boodist Some Distributions from the 'Boost' Library and More boostmath 'R' Bindings for the 'Boost' Math Functions bootCT Bootstrapping the ARDL Tests for Cointegration bootUR Bootstrap Unit Root Tests bootruin A Bootstrap Test for the Probability of Ruin in the Classical Risk Process bootstrap Functions for the Book "An Introduction to the Bootstrap" borrowr Estimate Causal Effects with Borrowing Between Data Sources box Write Reusable, Composable and Modular R Code bpAcc Blood Pressure Device Accuracy Evaluation: Statistical Considerations bpgmm Bayesian Model Selection Approach for Parsimonious Gaussian Mixture Models bpnreg Bayesian Projected Normal Regression Models for Circular Data bpr Fitting Bayesian Poisson Regression bpvars Forecasting with Bayesian Panel Vector Autoregressions bqmm Bayesian Multilevel Quantile Regression bqtl Bayesian QTL Mapping Toolkit braggR Calculate the Revealed Aggregator of Probability Predictions bravo Bayesian Screening and Variable Selection breakfast Methods for Fast Multiple Change-Point/Break-Point Detection and Estimation breathteststan Stan-Based Fit to Gastric Emptying Curves brglm Bias Reduction in Binomial-Response Generalized Linear Models brglm2 Bias Reduction in Generalized Linear Models brif A Tree and Forest Tool for Classification and Regression brio Basic R Input Output brmsmargins Bayesian Marginal Effects for 'brms' Models brnn Bayesian Regularization for Feed-Forward Neural Networks broadcast Broadcasted Array Operations Like 'NumPy' broman Karl Broman's R Code brotli A Compression Format Optimized for the Web brunnermunzel (Permuted) Brunner-Munzel Test bsamGP Bayesian Spectral Analysis Models using Gaussian Process Priors bsearchtools Binary Search Tools bsnsing Build Decision Trees with Optimal Multivariate Splits bspline B-Spline Interpolation and Regression bssm Bayesian Inference of Non-Linear and Non-Gaussian State Space Models bsts Bayesian Structural Time Series bsvarSIGNs Bayesian SVARs with Sign, Zero, and Narrative Restrictions bsvars Bayesian Estimation of Structural Vector Autoregressive Models bsynth Bayesian Synthetic Control btb Beyond the Border - Kernel Density Estimation for Urban Geography bunsen Marginal Survival Estimation with Covariate Adjustment bvarnet Bayesian Estimation of Dynamic VAR Models using STAN bvars Bayesian Forecasting with Large Vector Autoregressions bvarsv Bayesian Analysis of a Vector Autoregressive Model with Stochastic Volatility and Time-Varying Parameters bvartools Bayesian Inference of Vector Autoregressive and Error Correction Models bvhar Bayesian Vector Heterogeneous Autoregressive Modeling bvls The Stark-Parker algorithm for bounded-variable least squares bwd Backward Procedure for Change-Point Detection bws Bayesian Weighted Sums bytescircle Statistics About Bytes Contained in a File as a Circle Plot bzinb Bivariate Zero-Inflated Negative Binomial Model Estimator c212 Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes) c3dr Read and Write C3D Motion Capture Files cIRT Choice Item Response Theory cSEM Composite-Based Structural Equation Modeling cTMed Continuous-Time Mediation caRamel Automatic Calibration by Evolutionary Multi Objective Algorithm caTools Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc cachem Cache R Objects with Automatic Pruning calba Efficient Neighborhood Basal Area Metrics for Trees calcite Bindings to the Calcite Design System 'JavaScript' Component Library calculus High Dimensional Numerical and Symbolic Calculus calibrationband Calibration Bands capr Covariate Assisted Principal Regression capybara Fast and Memory Efficient Fitting of Linear Models with High-Dimensional Fixed Effects carSurv Correlation-Adjusted Regression Survival (CARS) Scores carat Covariate-Adaptive Randomization for Clinical Trials carbondate Calibration and Summarisation of Radiocarbon Dates caret Classification and Regression Training cartogramR Continuous Cartogram cartographer Turn Place Names into Map Data cartography Thematic Cartography carts Simulation-Based Assessment of Covariate Adjustment in Randomized Trials cash Discrete Choice and Competitive Reactions: End-to-End Simulation castor Efficient Phylogenetics on Large Trees cat Analysis and Imputation of Categorical-Variable Datasets with Missing Values catIrt Simulate IRT-Based Computerized Adaptive Tests catSurv Computerized Adaptive Testing for Survey Research catch Covariate-Adjusted Tensor Classification in High-Dimensions catdap Categorical Data Analysis Program Package catlearn Formal Psychological Models of Categorization and Learning catsim Binary and Categorical Image Similarity Index caugi Causal Graph Interface cauphy Trait Evolution on Phylogenies Using the Cauchy Process causalDT Causal Distillation Trees causalOT Optimal Transport Weights for Causal Inference causalSLSE Semiparametric Least Squares Inference for Causal Effects caviarpd Cluster Analysis via Random Partition Distributions cayleyR Cayley Graph Analysis for Permutation Puzzles cba Clustering for Business Analytics cbbinom Continuous Analog of a Beta-Binomial Distribution cbinom Continuous Analog of a Binomial Distribution ccLRforR Case-Control Likelihood Ratio (ccLR) ccaPP (Robust) Canonical Correlation Analysis via Projection Pursuit cccp Cone Constrained Convex Problems cclust Convex Clustering Methods and Clustering Indexes ccrtm Coupled Chain Radiative Transfer Models cctools Tools for the Continuous Convolution Trick in Nonparametric Estimation cdcsis Conditional Distance Correlation Based Feature Screening and Conditional Independence Inference cdlTools Tools to Download and Work with USDA Cropscape Data cdlsim Simulation of Cropland Data Layer Products from the USDA celestial Collection of Common Astronomical Conversion Routines and Functions cellWise Analyzing Data with Cellwise Outliers cenROC Estimating Time-Dependent ROC Curve and AUC for Censored Data censo2022arg Extraction and Analysis of 2022 Argentina Census Microdata from REDATAM Databases cepreader Read 'CEP' and Legacy 'CANOCO' Files cequre Censored Quantile Regression & Monotonicity-Respecting Restoring ceser Cluster Estimated Standard Errors cgAUC Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it. cglasso Conditional Graphical LASSO for Gaussian Graphical Models with Censored and Missing Values cgmguru Advanced Continuous Glucose Monitoring Analysis with High-Performance C++ Backend cgvR Interactive 3D Visualization of Large Cayley Graphs via Vulkan changepoint Methods for Changepoint Detection changepoint.np Methods for Nonparametric Changepoint Detection changepointGA Changepoint Detection via Modified Genetic Algorithms changepointTests Change Point Tests for Joint Distributions and Copulas changepoints A Collection of Change-Point Detection Methods cheapr Simple Functions to Save Time and Memory checkglobals Static Analysis of R-Code Dependencies checkmate Fast and Versatile Argument Checks cheddar Analysis and Visualisation of Ecological Communities chillR Statistical Methods for Phenology Analysis in Temperate Fruit Trees chngpt Estimation and Hypothesis Testing for Threshold Regression choicer Discrete Choice Models for Economic Applications chomper A Comprehensive Hit or Miss Probabilistic Entity Resolution Model chopthin The Chopthin Resampler chouca A Stochastic Cellular Automaton Engine chron Chronological Objects which Can Handle Dates and Times ciflyr Reachability-Based Primitives for Graphical Causal Inference cifmodeling Visualization and Polytomous Modeling of Survival and Competing Risks cinterpolate Interpolation From C circlus Clustering and Simulation of Spherical Cauchy and PKBD Models circular Circular Statistics circumplex Analysis and Visualization of Circular Data cit Causal Inference Test cladoRcpp C++ Implementations of Phylogenetic Cladogenesis Calculations clarabel Interior Point Conic Optimization Solver classInt Choose Univariate Class Intervals cld2 Google's Compact Language Detector 2 cld3 Google's Compact Language Detector 3 cleancall C Resource Cleanup via Exit Handlers clevr Clustering and Link Prediction Evaluation in R clhs Conditioned Latin Hypercube Sampling cli Helpers for Developing Command Line Interfaces clifford Arbitrary Dimensional Clifford Algebras clinfun Clinical Trial Design and Data Analysis Functions clinical Analysis of Clinical Data clinpubr Clinical Publication clmstan Cumulative Link Models with 'CmdStanR' clock Date-Time Types and Tools clogitL1 Fitting Exact Conditional Logistic Regression with Lasso and Elastic Net Penalties clogitboost Boosting Conditional Logit Model cloneRate Estimate Growth Rates from Phylogenetic Trees clubpro Classification Using Binary Procrustes Rotation clue Cluster Ensembles clusrank Wilcoxon Rank Tests for Clustered Data clustAnalytics Cluster Evaluation on Graphs clustTMB Spatio-Temporal Finite Mixture Model using 'TMB' clusterCrit Clustering Indices clusterGGM Sparse Gaussian Graphical Modeling with Variable Clustering clusterMI Cluster Analysis with Missing Values by Multiple Imputation clusterSim Searching for Optimal Clustering Procedure for a Data Set clustering.sc.dp Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint clustermq Evaluate Function Calls on HPC Schedulers (SLURM, LSF, SGE, GCS, OCS, PBS, Torque) clustord Cluster Ordinal Data via Proportional Odds or Ordered Stereotype clustur Clustering cmbClust Conditional Mixture Modeling and Model-Based Clustering cmfrec Collective Matrix Factorization for Recommender Systems cmpp Direct Parametric Inference for the Cumulative Incidence Function in Competing Risks cmprsk Subdistribution Analysis of Competing Risks cmprskQR Analysis of Competing Risks Using Quantile Regressions cmpsR R Implementation of Congruent Matching Profile Segments Method cmstatrExt More Statistical Methods for Composite Material Data cmtkr Wrapper for the Computational Morphometry Toolkit ('CMTK') Library cna Causal Modeling with Coincidence Analysis cnaOpt Optimizing Consistency and Coverage in Configurational Causal Modeling cnum Chinese Numerals Processing coFAST Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment coRanking Co-Ranking Matrix coala A Framework for Coalescent Simulation coalescentMCMC MCMC Algorithms for the Coalescent cobin Cobin and Micobin Regression Models for Continuous Proportional Data cobs Constrained B-Splines (Sparse Matrix Based) coconots Convolution-Closed Models for Count Time Series cocons Covariate-Based Covariance Functions for Nonstationary Spatial Modeling coda.base A Basic Set of Functions for Compositional Data Analysis codep Multiscale Codependence Analysis coenoflex Gradient-Based Coenospace Vegetation Simulator coga Convolution of Gamma Distributions coglasso Collaborative Graphical Lasso - Multi-Omics Network Reconstruction coin Conditional Inference Procedures in a Permutation Test Framework cola A Framework for Consensus Partitioning cold Count Longitudinal Data collapse Advanced and Fast Data Transformation collections High Performance Container Data Types collpcm Collapsed Latent Position Cluster Model for Social Networks colorednoise Simulate Temporally Autocorrelated Populations colorfast Fast Conversion of R Colors to Color Component Values and Native Packed Integer Format colorspace A Toolbox for Manipulating and Assessing Colors and Palettes colourvalues Assigns Colours to Values comat Creates Co-Occurrence Matrices of Spatial Data combiter Combinatorics Iterators comets Covariance Measure Tests for Conditional Independence commonmark High Performance CommonMark and Github Markdown Rendering in R comparator Comparison Functions for Clustering and Record Linkage compareC Compare Two Correlated C Indices with Right-Censored Survival Outcome compas Conformational Manipulations of Protein Atomic Structures comperank Ranking Methods for Competition Results complex Time Series Analysis and Forecasting Using Complex Variables complexlm Linear Fitting for Complex Valued Data compositions Compositional Data Analysis conMItion Conditional Mutual Information Estimation for Multi-Omics Data conTree Contrast Trees and Boosting condSURV Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data coneproj Primal or Dual Cone Projections with Routines for Constrained Regression conleyreg Estimations using Conley Standard Errors conos Clustering on Network of Samples conquer Convolution-Type Smoothed Quantile Regression conquestr An R Package to Extend 'ACER ConQuest' constrainedKriging Constrained, Covariance-Matching Constrained and Universal Point or Block Kriging constructive Display Idiomatic Code to Construct Most R Objects contfrac Continued Fractions cooltools Practical Tools for Scientific Computations and Visualizations coop Co-Operation: Fast Covariance, Correlation, and Cosine Similarity Operations copCAR Fitting the copCAR Regression Model for Discrete Areal Data cophescan Adaptation of the Coloc Method for PheWAS copre Tools for Nonparametric Martingale Posterior Sampling copula Multivariate Dependence with Copulas corMLPE Correlation Structures for Symmetric Relational Data corTESTsrd Significance Testing of Rank Cross-Correlations under SRD cord Community Estimation in G-Models via CORD corels R Binding for the 'Certifiably Optimal RulE ListS (Corels)' Learner coresynth Fast and Unified Synthetic Control Methods corpustools Managing, Querying and Analyzing Tokenized Text corrRF Clustered Random Forests for Optimal Prediction and Inference of Clustered Data corrselect Correlation-Based and Model-Based Predictor Pruning cosimmr Fast Fitting of Stable Isotope Mixing Models with Covariates cossonet Sparse Nonparametric Regression for High-Dimensional Data costsensitive Cost-Sensitive Multi-Class Classification countSTAR Flexible Modeling of Count Data countdata The Beta-Binomial Test for Count Data countsplit Splitting a Count Matrix into Independent Folds coupling Analysis of Coupling Coordination Degree couplr Optimal Pairing and Matching via Linear Assignment covBM Brownian Motion Processes for 'nlme'-Models covafillr Local Polynomial Regression of State Dependent Covariates in State-Space Models covercorr Coverage Correlation Coefficient and Testing for Independence covglasso Sparse Covariance Matrix Estimation covr Test Coverage for Packages coxerr Cox Regression with Dependent Error in Covariates coxme Mixed Effects Cox Models coxphf Cox Regression with Firth's Penalized Likelihood coxphw Weighted Estimation in Cox Regression coxrobust Fit Robustly Proportional Hazards Regression Model coxsei Fitting a CoxSEI Model coxstream Memory-Efficient Cox Proportional Hazards via Streaming Newton-Raphson cp1919 Radio Observations of the Pulse Profiles and Dispersion Measures of Twelve Pulsars cplm Compound Poisson Linear Models cpm Sequential and Batch Change Detection Using Parametric and Nonparametric Methods cpop Detection of Multiple Changes in Slope in Univariate Time-Series cpp11bigwig Read bigWig and bigBed Files cpp11qpdf Split, Combine and Compress PDF Files cppRouting Algorithms for Routing and Solving the Traffic Assignment Problem cppSim Fast and Memory Efficient Spatial Interaction Models cppcontainers 'C++' Standard Template Library Containers cppdoubles Fast Relative Comparisons of Floating Point Numbers in 'C++' cpr Control Polygon Reduction cqrReg Quantile, Composite Quantile Regression and Regularized Versions craftgrn Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks cramer Multivariate Nonparametric Cramer-Test for the Two-Sample-Problem crandep Network Analysis of Dependencies of CRAN Packages crawl Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data crc32c Cyclic Redundancy Check with CPU-Specific Acceleration crch Censored Regression with Conditional Heteroscedasticity crctStepdown Univariate Analysis of Cluster Trials with Multiple Outcomes creditr Credit Default Swaps credule Credit Default Swap Functions crimCV Group-Based Modelling of Longitudinal Data crqa Unidimensional and Multidimensional Methods for Recurrence Quantification Analysis crrSC Competing Risks Regression for Stratified and Clustered Data crs Categorical Regression Splines cryptorng Access System Cryptographic Pseudorandom Number Generators csaw ChIP-Seq Analysis with Windows cstab Selection of Number of Clusters via Normalized Clustering Instability csvread Fast Specialized CSV File Loader ct Integrated Camera-Trap Data Management and Analysis ctgt Closed Testing with Globaltest for Pathway Analysis ctl Correlated Trait Locus Mapping ctmcd Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data cts Continuous Time Autoregressive Models ctsem Continuous Time Structural Equation Modelling ctsmTMB Continuous Time Stochastic Modelling using Template Model Builder ctypesio Read and Write Standard 'C' Types from Files, Connections and Raw Vectors cubature Adaptive Multivariate Integration over Hypercubes cubfits Codon Usage Bias Fits cubicBsplines Computation of a Cubic B-Spline Basis and Its Derivatives cubing Rubik's Cube Solving cuda.ml R Interface for the RAPIDS cuML Suite of Libraries curl A Modern and Flexible Web Client for R curvHDR Filtering of Flow Cytometry Samples curveDepth Tukey Curve Depth and Distance in the Space of Curves cusna Native GPU-Accelerated Simulation and Estimation of Network Models cusp Cusp-Catastrophe Model Fitting Using Maximum Likelihood cutpointr Determine and Evaluate Optimal Cutpoints in Binary Classification Tasks cvLM Cross-Validation for Linear and Ridge Regression Models cvasi Calibration, Validation, and Simulation of TKTD Models cxreg Complex-Valued Lasso and Complex-Valued Graphical Lasso cytometree Automated Cytometry Gating and Annotation dBlockmodeling Deterministic Blockmodeling of Signed, One-Mode and Two-Mode Networks dHSIC Independence Testing via Hilbert Schmidt Independence Criterion dMrs Competing Risk in Dependent Net Survival Analysis dRiftDM Estimating (Time-Dependent) Drift Diffusion Models dada2 Accurate, high-resolution sample inference from amplicon sequencing data dang 'Dang' Associated New Goodies dann Discriminant Adaptive Nearest Neighbor Classification data.sketches Probabilistic Streaming Data Sketches data.table Extension of `data.frame` data4health A Practical Workflow for Health Data Wrangling datafsm Estimating Finite State Machine Models from Data datasusr Fast Access to Brazilian Public Health Data from 'DATASUS' datazoom.amazonia Simplify Access to Data from the Amazon Region date Functions for Handling Dates datefixR Standardize Dates in Different Formats or with Missing Data dateutils Date Utils datey Exact Date and Duration Arithmetic on an Annual Grid dauphin Compact Standard for Australian Phone Numbers dawai Discriminant Analysis with Additional Information dbMatrix Database-Backed Matrix Classes and Operations dbarts Discrete Bayesian Additive Regression Trees Sampler dblcens Compute the NPMLE of Distribution Function from Doubly Censored Data, Plus the Empirical Likelihood Ratio for F(T) dbmss Distance-Based Measures of Spatial Structures dbnR Dynamic Bayesian Network Learning and Inference dbscan Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms dcce Dynamic Common Correlated Effects Estimation for Panel Data dccmidas DCC Models with GARCH and GARCH-MIDAS Specifications in the Univariate Step, RiskMetrics, Moving Covariance and Scalar and Diagonal BEKK Models dccpp Fast Computation of Distance Correlations dcifer Genetic Relatedness Between Polyclonal Infections dcm2 Calculating the M2 Model Fit Statistic for Diagnostic Classification Models dcorBSS Distance-Correlation Based Methods for Blind Source Separation and Dependence Analysis dcortools Providing Fast and Flexible Functions for Distance Correlation Analysis dcov A Fast Implementation of Distance Covariance dcsvm Density Convoluted Support Vector Machines dcurver Utility Functions for Davidian Curves ddModel The Decision Diffusion Model ddalpha Depth-Based Classification and Calculation of Data Depth ddc Distance Density Clustering Algorithm dde Solve Delay Differential Equations ddsPLS Data-Driven Sparse Partial Least Squares deBif Bifurcation Analysis of Ordinary Differential Equation Systems deSolve Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE') deadwood Outlier Detection via Trimming of Mutual Reachability Minimum Spanning Trees deal Learning Bayesian Networks with Mixed Variables decido Bindings for 'Mapbox' Ear Cutting Triangulation Library declared Functions for Declared Missing Values decompr Global Value Chain Decomposition decor Retrieve Code Decorations decorrelate Decorrelation Projection Scalable to High Dimensional Data deductive Data Correction and Imputation Using Deductive Methods deepSTRAPP Test for Differences in Diversification Rates over Time deepgp Bayesian Deep Gaussian Processes using MCMC defm Estimation and Simulation of Multi-Binary Response Models deforestable Classify RGB Images into Forest or Non-Forest deform Spatial Deformation and Dimension Expansion Gaussian Processes degreenet Models for Skewed Count Distributions Relevant to Networks delarr Lazy Delayed Arrays with Fused Execution deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation denim Generate and Simulate Deterministic Compartmental Models densEstBayes Density Estimation via Bayesian Inference Engines densityClust Clustering by Fast Search and Find of Density Peaks densityratio Distribution Comparison Through Density Ratio Estimation densvis Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction depcache Cache R Expressions, Taking Their Dependencies into Account depcoeff Dependency Coefficients depthR Multivariate Depth Functions for General Dimension descr Descriptive Statistics deseats Data-Driven Locally Weighted Regression for Trend and Seasonality in TS desla Desparsified Lasso Inference for Time Series detectRUNS Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes detrendr Detrend Images devEMF EMF Graphics Output Device devianLM Detecting Extremal Values in a Normal Linear Model devoid A Graphic Device that Does Nothing dexter Data Management and Analysis of Tests dfcomb Phase I/II Adaptive Dose-Finding Design for Combination Studies dfms Dynamic Factor Models dfmta Phase I/II Adaptive Dose-Finding Design for MTA dfphase1 Phase I Control Charts (with Emphasis on Distribution-Free Methods) dfsaneacc Accelerated Derivative-Free Method for Large-Scale Nonlinear Systems of Equations dga Capture-Recapture Estimation using Bayesian Model Averaging dggridR Discrete Global Grids dglars Differential Geometric Least Angle Regression dgof Discrete Goodness-of-Fit Tests dhmeasures Digital History Measures diagis Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling diceR Diverse Cluster Ensemble in R dicepro Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization diffIRT Diffusion IRT Models for Response and Response Time Data diffcp Differentiating Through Cone Programs diffmatchpatch String Diff, Match, and Patch Utilities diffobj Diffs for R Objects digest Create Compact Hash Digests of R Objects dimRed A Framework for Dimensionality Reduction dina Bayesian Estimation of DINA Model dipm Depth Importance in Precision Medicine (DIPM) Method dipsaus A Dipping Sauce for Data Analysis and Visualizations diptest Hartigan's Dip Test Statistic for Unimodality - Corrected disaggregation Disaggregation Modelling disclapmix Discrete Laplace Mixture Inference using the EM Algorithm disclapmix2 Mixtures of Discrete Laplace Distributions using Numerical Optimisation discretefit Simulated Goodness-of-Fit Tests for Discrete Distributions dismo Species Distribution Modeling dispRity Measuring Disparity dispeRse Simulation of Demic Diffusion with Environmental Constraints dissimilarities Creating, Manipulating, and Subsetting "dist" Objects distances Tools for Distance Metrics distantia Advanced Toolset for Efficient Time Series Dissimilarity Analysis distcomp Computations over Distributed Data without Aggregation distops Usual Operations for Distance Matrices in R distory Distance Between Phylogenetic Histories distr Object Oriented Implementation of Distributions distrEx Extensions of Package 'distr' divDyn Diversity Dynamics using Fossil Sampling Data diveMove Dive Analysis and Calibration divent Entropy Partitioning to Measure Diversity diversitree Comparative 'Phylogenetic' Analyses of Diversification diversityForest Innovative Complex Split Procedures in Random Forests Through Candidate Split Sampling divest Get Images Out of DICOM Format Quickly divo Tools for Analysis of Diversity and Similarity in Biological Systems dixon Nearest Neighbour Contingency Table Analysis dixonTest Dixon's Ratio Test for Outlier Detection dlib Allow Access to the 'Dlib' C++ Library dlm Bayesian and Likelihood Analysis of Dynamic Linear Models dlmtree Bayesian Treed Distributed Lag Models dmbc Model Based Clustering of Binary Dissimilarity Measurements dng Distributions and Gradients dnn Deep Neural Network Tools for Probability and Statistic Models doRedis 'Foreach' Parallel Adapter Using the 'Redis' Database doc2vec Distributed Representations of Sentences, Documents and Topics docopulae Optimal Designs for Copula Models documentosbr Validate Brazilian Administrative Registers - Valida Documentos dodgr Distances on Directed Graphs dormancy Detection and Analysis of Dormant Patterns in Data dosearch Causal Effect Identification from Multiple Incomplete Data Sources dotCall64 Enhanced Foreign Function Interface Supporting Long Vectors doubcens Survivor Function Estimation for Doubly Interval-Censored Failure Time Data dparser Port of 'Dparser' Package dpcc Dynamic Programming for Convex Clustering dpcid Differential Partial Correlation IDentification dplR Dendrochronology Program Library in R dplyr A Grammar of Data Manipulation dpseg Piecewise Linear Segmentation by Dynamic Programming dqrng Fast Pseudo Random Number Generators dracor Decode Draco Format 3D Mesh Data drclust Simultaneous Clustering and (or) Dimensionality Reduction dream Dynamic Relational Event Analysis and Modeling drf Distributional Random Forests drgee Doubly Robust Generalized Estimating Equations drogonR High-Performance HTTP Server for R via 'Drogon' dropout Handling Incomplete Responses in Survey Data Analysis drrglm Doubly Regularized Matrix-Variate Regression drugDemand Drug Demand Forecasting dscore D-Score for Child Development dsem Dynamic Structural Equation Models dslice Dynamic Slicing dsn Data Source Name and Description Helpers for Use with 'GDAL' dsp Dynamic Shrinkage Process and Change Point Detection dspline Tools for Computations with Discrete Splines dtametaTMB Diagnostic Test Accuracy Meta-Analysis using Template Model Builder dti Analysis of Diffusion Weighted Imaging (DWI) Data dtrSurv Dynamic Treatment Regimes for Survival Analysis dtts 'data.table' Time-Series dtw Dynamic Time Warping Algorithms dtwclust Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance dualtrees Decimated and Undecimated 2D Complex Dual-Tree Wavelet Transform duckdb DBI Package for the DuckDB Database Management System dwdradar Read Binary Radar Files from 'DWD' (German Weather Service) dynConfiR Dynamic Models for Confidence and Response Time Distributions dynaTree Dynamic Trees for Learning and Design dynatop An Implementation of Dynamic TOPMODEL Hydrological Model in R dynmix Estimation of Dynamic Finite Mixtures dynr Dynamic Models with Regime-Switching dynsbm Dynamic Stochastic Block Models dynsurv Dynamic Models for Survival Data dynutils Common Functionality for the 'dynverse' Packages e1071 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien e2tree Explainable Ensemble Trees eBsc "Empirical Bayes Smoothing Splines with Correlated Errors" eCAR Eigenvalue CAR Models eClosure Methods Based on the e-Closure Principle eDITH Model Transport of Environmental DNA in River Networks eDMA Dynamic Model Averaging with Grid Search eDNAjoint Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework eFCM Exponential Factor Copula Model eNchange Ensemble Methods for Multiple Change-Point Detection eRm Extended Rasch Modeling eaf Plots of the Empirical Attainment Function eam Evidence Accumulation Models earth Multivariate Adaptive Regression Splines earthtide Parallel Implementation of 'ETERNA 3.40' for Prediction and Analysis of Earth Tides easyVerification Ensemble Forecast Verification for Large Data Sets ebTobit Empirical Bayesian Tobit Matrix Estimation ebdbNet Empirical Bayes Estimation of Dynamic Bayesian Networks ebmstate Empirical Bayes Multi-State Cox Model ecespa Functions for Spatial Point Pattern Analysis echelon The Echelon Analysis and the Detection of Spatial Clusters using Echelon Scan Method echoice2 Choice Models with Economic Foundation echos Echo State Networks for Time Series Modeling and Forecasting eco Ecological Inference in 2x2 Tables ecodist Dissimilarity-Based Functions for Ecological Analysis ecodive Parallel and Memory-Efficient Ecological Diversity Metrics ecolMod "A Practical Guide to Ecological Modelling - Using R as a Simulation Platform" ecolRxC Ecological Inference of RxC Tables by Latent Structure Approaches economiccomplexity Computational Methods for Economic Complexity ecotraj Ecological Trajectory Analysis ecp Non-Parametric Multiple Change-Point Analysis of Multivariate Data ecr Evolutionary Computation in R eddington Compute a Cyclist's Eddington Number edgeR Empirical Analysis of Digital Gene Expression Data in R edgebundle Algorithms for Bundling Edges in Networks and Visualizing Flow and Metro Maps edgemodelr Local Large Language Model Inference Engine edina Bayesian Estimation of an Exploratory Deterministic Input, Noisy and Gate Model edlibR R Integration for Edlib, the C/C++ Library for Exact Pairwise Sequence Alignment using Edit (Levenshtein) Distance eds eds: Low-level reader for Alevin EDS format ef Modelling Framework for the Estimation of Salmonid Abundance effectplots Effect Plots eglhmm Extended Generalised Linear Hidden Markov Models eha Event History Analysis eiPack Ecological Inference and Higher-Dimension Data Management eicm Explicit Interaction Community Models eimpute Efficiently Impute Large Scale Incomplete Matrix einsum Einstein Summation eive An Algorithm for Reducing Errors-in-Variable Bias in Simple and Multiple Linear Regressions elcf4R Electricity Load Curves Forecasting at Individual Level elfDistr Kumaraswamy Complementary Weibull Geometric (Kw-CWG) Probability Distribution elgbd Empirical Likelihood for General Block Designs ellipsis Tools for Working with ... elmNNRcpp The Extreme Learning Machine Algorithm elo Ranking Teams by Elo Rating and Comparable Methods elrm Exact Logistic Regression via MCMC elsa Entropy-Based Local Indicator of Spatial Association emBayes Robust Bayesian Variable Selection via Expectation-Maximization emIRT EM Algorithms for Estimating Item Response Theory Models emcAdr Evolutionary Version of the Metropolis-Hastings Algorithm emdist Earth Mover's Distance emoa Evolutionary Multiobjective Optimization Algorithms empichar Evaluates the Empirical Characteristic Function for Multivariate Samples emplik Empirical Likelihood Ratio for Censored/Truncated Data encharter Enhanced Office Open XML Charting for 'openxlsx2' enderecobr Padronizador de Endereços Brasileiros (Brazilian Addresses Standardizer) endogeneity Recursive Two-Stage Models to Address Endogeneity endorse Bayesian Measurement Models for Analyzing Endorsement Experiments energy E-Statistics: Multivariate Inference via the Energy of Data energymethod Two-Sample Test of many Functional Means using the Energy Method enerscape Compute Energy Landscapes enmpa Ecological Niche Modeling using Presence-Absence Data enrichit 'C++' Implementations of Functional Enrichment Analysis enviPat Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry envnames Keep Track of User-Defined Environment Names epanet2toolkit Call 'EPANET' Functions to Simulate Pipe Networks epicR Evaluation Platform in Chronic Obstructive Pulmonary Disease epigrowthfit Nonlinear Mixed Effects Models of Epidemic Growth epinet Epidemic/Network-Related Tools epinetr Epistatic Network Modelling with Forward-Time Simulation epiphy Analysis of Plant Disease Epidemics epiworldR Fast Agent-Based Epi Models epizootic Spatially Explicit Population Models of Disease Transmission in Wildlife eplusr A Toolkit for Using Whole Building Simulation Program 'EnergyPlus' epm EcoPhyloMapper equalCovs Testing the Equality of Two Covariance Matrices equateMultiple Equating of Multiple Forms equivalence Provides Tests and Graphics for Assessing Tests of Equivalence erah Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics eratosthenes Archaeological Synchronism erboost Nonparametric Multiple Expectile Regression via ER-Boost ergm Fit, Simulate and Diagnose Exponential-Family Models for Networks ergm.count Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges ergm.ego Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data ergm.multi Fit, Simulate and Diagnose Exponential-Family Models for Multiple or Multilayer Networks ergm.rank Fit, Simulate and Diagnose Exponential-Family Models for Rank-Order Relational Data ergm.sign Exponential-Family Models for Signed Networks ergmclust Exponential-Family Random Graph Models for Network Clustering ergmgp Tools for Modeling ERGM Generating Processes ergmito Exponential Random Graph Models for Small Networks ernest A Toolkit for Nested Sampling ernm Exponential-Family Random Network Models errum Exploratory Reduced Reparameterized Unified Model Estimation esaddle Extended Empirical Saddlepoint Density Approximations eseis Environmental Seismology Toolbox esemifar Smoothing Long-Memory Time Series esmprep Data Preparation During and After the Use of the Experience Sampling Methodology (ESM) espadon Easy Study of Patient DICOM Data in Oncology esreg Joint Quantile and Expected Shortfall Regression ess Efficient Stepwise Selection in Decomposable Models essHist The Essential Histogram estimatr Fast Estimators for Design-Based Inference etasFLP Mixed FLP and ML Estimation of ETAS Space-Time Point Processes for Earthquake Description ethiodate Working with Ethiopian Dates etm Empirical Transition Matrix eulerr Area-Proportional Euler and Venn Diagrams eurodata Fast and Easy Eurostat Data Import and Search evalR Evaluation of Unverified Code evd Functions for Extreme Value Distributions evdbayes Bayesian Analysis in Extreme Value Theory eventglm Regression Models for Event History Outcomes evesim Evolution Emulator: Species Diversification under an Evolutionary Relatedness Dependent Scenario evgam Generalised Additive Extreme Value Models evinf Inference with Extreme Value Inflated Count Data evitaicossa Antiassociative Algebra evolqg Evolutionary Quantitative Genetics evtree Evolutionary Learning of Globally Optimal Trees ewens Ewens Distribution ewp An Empirical Model for Underdispersed Count Data exactRankTests Exact Distributions for Rank and Permutation Tests exactextractr Fast Extraction from Raster Datasets using Polygons exametrika Test Theory Analysis and Biclustering excursions Excursion Sets and Contour Credibility Regions for Random Fields exdex Estimation of the Extremal Index exdqlm Extended Dynamic Quantile Linear Models exif Read EXIF Metadata from JPEGs expSBM An Exponential Stochastic Block Model for Interaction Lengths expectreg Expectile and Quantile Regression experiment R Package for Designing and Analyzing Randomized Experiments expertsurv Incorporate Expert Opinion with Parametric Survival Models expint Exponential Integral and Incomplete Gamma Function expm Matrix Exponential, Log, 'etc' expperm Computing Expectations and Marginal Likelihoods for Permutations extBatchMarking Extended Batch Marking Models extraDistr Additional Univariate and Multivariate Distributions extrememix Bayesian Estimation of Extreme Value Mixture Models extremis Statistics of Extremes exuber Econometric Analysis of Explosive Time Series eyelinkReader Import Gaze Data for EyeLink Eye Tracker fBasics Rmetrics - Markets and Basic Statistics fChange Functional Change Point Detection and Analysis fDMA Dynamic Model Averaging and Dynamic Model Selection for Continuous Outcomes fEGarch SM/LM EGARCH & GARCH, VaR/ES Backtesting & Dual LM Extensions fGarch Rmetrics - Autoregressive Conditional Heteroskedastic Modelling fHMM Fitting Hidden Markov Models to Financial Data fICA Classical, Reloaded and Adaptive FastICA Algorithms fNonlinear Rmetrics - Nonlinear and Chaotic Time Series Modelling fRLR Fit Repeated Linear Regressions fUnitRoots Rmetrics - Modelling Trends and Unit Roots fabMix Overfitting Bayesian Mixtures of Factor Analyzers with Parsimonious Covariance and Unknown Number of Components fabPrediction Compute FAB (Frequentist and Bayes) Conformal Prediction Intervals fabia FABIA: Factor Analysis for Bicluster Acquisition fable Forecasting Models for Tidy Time Series fable.intermittent Forecasting Models for Intermittent Time Series factor256 Use Raw Vectors to Minimize Memory Consumption of Factors factorana Factor Model Estimation with Latent Variables factorstochvol Bayesian Estimation of (Sparse) Latent Factor Stochastic Volatility Models fad Factor Analysis for Data falcon Finding Allele-Specific Copy Number in Next-Generation Sequencing Data falconx Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data fanc Penalized Likelihood Factor Analysis via Nonconvex Penalty fangs Feature Allocation Neighborhood Greedy Search Algorithm fansi ANSI Control Sequence Aware String Functions far Modelization for Functional AutoRegressive Processes farff A Faster 'ARFF' File Reader and Writer farver High Performance Colour Space Manipulation fasano.franceschini.test Fasano-Franceschini Test: A Multivariate Kolmogorov-Smirnov Two-Sample Test fastAFT Fast Regression for the Accelerated Failure Time (AFT) Model fastGHQuad Fast 'Rcpp' Implementation of Gauss-Hermite Quadrature fastGLCM 'GLCM' Texture Features fastICA FastICA Algorithms to Perform ICA and Projection Pursuit fastJT Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies fastLISA Fast Local Indicators of Spatial Association (LISA) fastLink Fast Probabilistic Record Linkage with Missing Data fastLogisticRegressionWrap Fast Logistic Regression Wrapper fastM Fast Computation of Multivariate M-Estimators fastMatMR High-Performance Matrix Market File Operations fastPLS A Fast Implementation of Partial Least Square fastQR Fast QR Decomposition and Update fastText Efficient Learning of Word Representations and Sentence Classification fastTextR An Interface to the 'fastText' Library fastTopics Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data fastVoteR Efficient Voting Methods for Committee Selection fastWavelets Compute Maximal Overlap Discrete Wavelet Transform (MODWT) and À Trous Discrete Wavelet Transform fastadi Self-Tuning Data Adaptive Matrix Imputation fastbeta Fast Approximation of Time-Varying Infectious Disease Transmission Rates fastcluster Fast Hierarchical Clustering Routines for R and 'Python' fastcox Lasso and Elastic-Net Penalized Cox's Regression in High Dimensions Models using the Cocktail Algorithm fastcpd Fast Change Point Detection via Sequential Gradient Descent fastei Methods for ''A Fast Alternative for the R x C Ecological Inference Case'' fasterize Fast Polygon to Raster Conversion fastgeojson High-Performance 'GeoJSON' and 'JSON' Serialization fastglm Fast and Stable Fitting of Generalized Linear Models using 'RcppEigen' fastglmpca Fast Algorithms for Generalized Principal Component Analysis fastkmedoids Faster K-Medoids Clustering Algorithms: FastPAM, FastCLARA, FastCLARANS fastkqr A Fast Algorithm for Kernel Quantile Regression fastliu Fast Functions for Liu Regression with Regularization Parameter and Statistics fastlpr Fast Local Polynomial Regression and Kernel Density Estimation fastmap Fast Data Structures fastmatch Fast 'match()' Function fastmatrix Fast Computation of some Matrices Useful in Statistics fastmit Fast Mutual Information Based Independence Test fastplyr Fast Alternatives to 'tidyverse' Functions fastpng Read and Write PNG Files with Configurable Decoder/Encoder Options fastpolicytree Constructs Policy Trees from Covariate and Reward Data fastpos Finds the Critical Sequential Point of Stability for a Pearson Correlation fastqq Faster Generation of Quantile Quantile Plots with Large Samples fastrc Fast Reverse Complement of DNA and RNA Sequences fasttime Fast Utility Function for Time Parsing and Conversion fasttreeid Identifies Parameters in a Tree-Shaped SCM fastymd Fast Utilities for Year Month Day Objects fb4package 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend fbati Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families fbroc Fast Algorithms to Bootstrap Receiver Operating Characteristics Curves fcaR Formal Concept Analysis fcci Feldman-Cousins Confidence Intervals fcl A Financial Calculator fclust Fuzzy Clustering fcros A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations fda.usc Functional Data Analysis and Utilities for Statistical Computing fdaMixed Functional Data Analysis in a Mixed Model Framework fdaPDE Physics-Informed Spatial and Functional Data Analysis fdaSP Sparse Functional Data Analysis Methods fdacluster Joint Clustering and Alignment of Functional Data fdaconcur Concurrent Regression and History Index Models for Functional Data fdadensity Functional Data Analysis for Density Functions by Transformation to a Hilbert Space fdaoutlier Outlier Detection Tools for Functional Data Analysis fdapace Functional Data Analysis and Empirical Dynamics fdarep Two-Dimensional FPCA, Marginal FPCA, and Product FPCA for Repeated Functional Data fdasrvf Elastic Functional Data Analysis fddm Fast Implementation of the Diffusion Decision Model fdesigns Optimal Experimental Designs for Dynamic/Functional Models fdrtool Estimation of (Local) False Discovery Rates and Higher Criticism feather R Bindings to the Feather 'API' fechner Fechnerian Scaling of Discrete Object Sets fect Fixed Effects Counterfactual Estimators fedmatch Fast, Flexible, and User-Friendly Record Linkage Methods ff Memory-Efficient Storage of Large Data on Disk and Fast Access Functions fftw Fast FFT and DCT Based on the FFTW Library fftwtools Wrapper for 'FFTW3' Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms fgsea Fast Gene Set Enrichment Analysis fiber S7 Data Structures for Diffusion MRI Tractography fiberLD Fiber Length Determination fido Bayesian Multinomial Logistic Normal Regression fields Tools for Spatial Data filearray File-Backed Array for Out-of-Memory Computation filehash Simple Key-Value Database filelock Portable File Locking filling Matrix Completion, Imputation, and Inpainting Methods finalsize Calculate the Final Size of an Epidemic fingerPro Unmixing Model Framework fingerprint Functions to Operate on Binary Fingerprint Data finity Test for Finiteness of Moments in a Distribution fio Friendly Input-Output Analysis fishMod Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models fishmethods Fishery Science Methods and Models fixes Staggered DiD Tools: Event Studies and ATT Aggregation fixest Fast Fixed-Effects Estimations flam Fits Piecewise Constant Models with Data-Adaptive Knots flan FLuctuation ANalysis on Mutation Models flankr Implementing Computational Models of Attentional Selectivity flare Family of Lasso Regression flashClust Implementation of Fast Hierarchical Clustering fletcher Compute Fletcher Checksums (16, 32, and 64 Bit) flexBART A More Flexible BART Model flexBCF Fast & Flexible Implementation of Bayesian Causal Forests flexCountReg Estimation of a Variety of Count Regression Models flexclust Flexible Cluster Algorithms flexiblas 'FlexiBLAS' API Interface flexlsx Exporting 'flextable' to 'xlsx' Files flexpolyline Flexible Polyline Encoding flexrsurv Flexible Relative Survival Analysis flexsurv Flexible Parametric Survival and Multi-State Models flexurba Construct Flexible Urban Delineations flint Fast Library for Number Theory flintyR Simple and Flexible Tests of Sample Exchangeability flip Multivariate Permutation Tests flipr Flexible Inference via Permutations in R float 32-Bit Floats flock Process Synchronization Using File Locks flownet Transport Modeling: Network Processing, Route Enumeration, and Traffic Assignment flsa Path Algorithm for the General Fused Lasso Signal Approximator fluidsynth Read and Play Digital Music (MIDI) flying Simulation of Bird Flight Range fmds Multidimensional Scaling Development Kit fmdu (Restricted) [external] Multidimensional Unfolding fmesher Triangle Meshes and Related Geometry Tools fmri Analysis of fMRI Experiments fmriAR Fast AR and ARMA Noise Whitening for Functional MRI (fMRI) Design and Data fmrihrf Hemodynamic Response Functions for fMRI Data Analysis fmrs Variable Selection in Finite Mixture of AFT Regression and FMR Models fmtr Easily Apply Formats to Data fntl Numerical Tools for 'Rcpp' and Lambda Functions focus Online Changepoint Detection in Univariate and Multivariate Data Streams folda Forward Stepwise Discriminant Analysis with Pillai's Trace footBayes Fitting Bayesian and MLE Football Models forecast Forecasting Functions for Time Series and Linear Models forensim Interpretation of Forensic DNA Mixtures forestBalance Balancing Confounder Distributions with Forest Energy Balancing forestControl Approximate False Positive Rate Control in Selection Frequency for Random Forest fourierin Computes Numeric Fourier Integrals fozziejoin Utilities for Joining Dataframes with Inexact Matching fpROC Fast Partial Receiver Operating Characteristic (ROC) Test for Ecological Niche Modeling fpeek Check Text Files Content at a Glance fplot Automatic Distribution Graphs Using Formulas fpod Read and Process 'FPOD' and 'CPOD' Data fpop Segmentation using Optimal Partitioning and Function Pruning fpopw Weighted Segmentation using Functional Pruning and Optimal Partioning fpow Computing the Noncentrality Parameter of the Noncentral F Distribution frab How to Add Two R Tables fracdiff Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models fractional Vulgar Fractions in R fracture Convert Decimals to Fractions frailtyEM Fitting Frailty Models with the EM Algorithm frailtyMMpen Efficient Algorithm for High-Dimensional Frailty Model frailtySurv General Semiparametric Shared Frailty Model frailtypack Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints free Flexible Regularized Estimating Equations freealg The Free Algebra freestiler Create Vector Tiles from Spatial Data fromo Fast Robust Moments frontier Stochastic Frontier Analysis frontiles Partial Frontier Efficiency Analysis frontmatter Parse Front Matter from Documents froth Emulate a 'Forth' Programming Environment fru A Blazing Fast Implementation of Random Forest fs Cross-Platform File System Operations Based on 'libuv' fso Fuzzy Set Ordination fssg Parametric Survival Modeling in Bulk fst Lightning Fast Serialization of Data Frames fstcore R Bindings to the 'Fstlib' Library funMoDisco Motif Discovery in Functional Data funbootband Simultaneous Prediction and Confidence Bands for Time Series Data func2vis Clean and Visualize Over Expression Results from 'ConsensusPathDB' funcharts Functional Control Charts fuser Fused Lasso for High-Dimensional Regression over Groups fuzzyRankTests Fuzzy Rank Tests and Confidence Intervals fuzzystring Fast Fuzzy String Joins for Data Frames gCat Graph-Based Two-Sample Tests for Categorical Data gKRLS Generalized Kernel Regularized Least Squares gMCP Graph Based Multiple Comparison Procedures gMCPLite Lightweight Graph Based Multiple Comparison Procedures gMWT Generalized Mann-Whitney Type Tests gRain Bayesian Networks gRbase A Package for Graphical Modelling in R gRc Inference in Graphical Gaussian Models with Edge and Vertex Symmetries gRim Graphical Interaction Models gadjid Graph Adjustment Identification Distances for Causal Graphs galamm Generalized Additive Latent and Mixed Models gam Generalized Additive Models gamesGA Genetic Algorithm for Sequential Symmetric Games gamlr Gamma Lasso Regression gamlss Generalized Additive Models for Location Scale and Shape gamlss.dist Distributions for Generalized Additive Models for Location Scale and Shape gammSlice Generalized Additive Mixed Model Analysis via Slice Sampling gamsel Fit Regularization Path for Generalized Additive Models gamselBayes Bayesian Generalized Additive Model Selection gamstransfer A Data Interface Between 'GAMS' and R ganDataModel Build a Metric Subspaces Data Model for a Data Source ganGenerativeData Generate Generative Data for a Data Source gap Genetic Analysis Package garchx Flexible and Robust GARCH-X Modelling gaselect Genetic Algorithm (GA) for Variable Selection from High-Dimensional Data gasper Graph Signal Processing gaston Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models gausscov The Gaussian Covariate Method for Variable Selection gbeta Generalized Beta and Beta Prime Distributions gbm Generalized Boosted Regression Models gbm3 Generalized Boosted Regression Models gcKrig Analysis of Geostatistical Count Data using Gaussian Copulas gcdnet The (Adaptive) LASSO and Elastic Net Penalized Least Squares, Logistic Regression, Hybrid Huberized Support Vector Machines, Squared Hinge Loss Support Vector Machines and Expectile Regression using a Fast Generalized Coordinate Descent Algorithm gclm Graphical Continuous Lyapunov Models gcmr Gaussian Copula Marginal Regression gcrma Background Adjustment Using Sequence Information gctsc Gaussian and Student-t Copula Models for Count Time Series gdalcubes Earth Observation Data Cubes from Satellite Image Collections gdalraster Bindings to 'GDAL' gdm Generalized Dissimilarity Modeling gdpc Generalized Dynamic Principal Components gdsfmt R Interface to CoreArray Genomic Data Structure (GDS) Files gdtools Font Metrics and Font Management Utilities for R Graphics gdverse Analysis of Spatial Stratified Heterogeneity gdxtools Manipulate 'GDX' Files gear Geostatistical Analysis in R gedi2 Gene Expression Decomposition and Integration gee Generalized Estimation Equation Solver geeVerse A Comprehensive Analysis of High Dimensional Longitudinal Data geepack Generalized Estimating Equation Package geer Bias-Reduced and Penalized Generalized Estimating Equations geigen Calculate Generalized Eigenvalues, the Generalized Schur Decomposition and the Generalized Singular Value Decomposition of a Matrix Pair with Lapack geiger Analysis of Evolutionary Diversification gek Gradient-Enhanced Kriging gelnet Generalized Elastic Nets gemtc Network Meta-Analysis Using Bayesian Methods gen3sis General Engine for Eco-Evolutionary Simulations genSurv Generating Multi-State Survival Data gena Genetic Algorithm and Particle Swarm Optimization genefilter genefilter: methods for filtering genes from high-throughput experiments genepi Genetic Epidemiology Design and Inference genepop Population Genetic Data Analysis Using Genepop genie Fast, Robust, and Outlier Resistant Hierarchical Clustering genieclust Genie: Fast and Robust Hierarchical Clustering genio Genetics Input/Output Functions genlasso Path Algorithm for Generalized Lasso Problems genodds Generalised Odds Ratios genscore Generalized Score Matching Estimators gensvm A Generalized Multiclass Support Vector Machine geoBayes Analysis of Geostatistical Data using Bayes and Empirical Bayes Methods geoR Analysis of Geostatistical Data geoarrow Extension Types for Spatial Data for Use with 'Arrow' geocmeans Implementing Methods for Spatial Fuzzy Unsupervised Classification geocomplexity Mitigating Spatial Bias Through Geographical Complexity geodist Fast, Dependency-Free Geodesic Distance Calculations geodiv Methods for Calculating Gradient Surface Metrics geographiclib Access to 'GeographicLib' geogrid Turn Geospatial Polygons into Regular or Hexagonal Grids geohashTools Tools for Working with Geohashes geojsonR A GeoJson Processing Toolkit geojsonsf GeoJSON to Simple Feature Converter geokmeans A Collection of Fast, Exact and Eco-Friendly k-Means Clustering Algorithms geomander Geographic Tools for Studying Gerrymandering geometries Convert Between R Objects and Geometric Structures geometry Mesh Generation and Surface Tessellation geommc Geometric Markov Chain Sampling geos Open Source Geometry Engine ('GEOS') R API geosphere Spherical Trigonometry geostatsp Geostatistical Modelling with Likelihood and Bayes gert Simple Git Client for R getPass Masked User Input getip 'IP' Address 'Lookup' gettz Get the Timezone Information ggbrain Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax ggdist Visualizations of Distributions and Uncertainty ggdmc Cognitive Models ggdmcHeaders 'C++' Headers for 'ggdmc' Package ggdmcLikelihood Likelihood Computation for 'ggdmc' Package ggdmcModel Model Builders for 'ggdmc' Package ggdmcPrior Prior Probability Functions of the Standard and Truncated Distribution ggforce Accelerating 'ggplot2' ggip Data Visualization for IP Addresses and Networks ggiraph Make 'ggplot2' Graphics Interactive gglasso Group Lasso Penalized Learning Using a Unified BMD Algorithm gglinedensity Make DenseLines Heatmaps with 'ggplot2' ggmlR 'GGML' Tensor Operations for Machine Learning ggpointdensity A Cross Between a 2D Density Plot and a Scatter Plot ggraph An Implementation of Grammar of Graphics for Graphs and Networks ggrepel Automatically Position Non-Overlapping Text Labels with 'ggplot2' ggsql Grammar of Graphics for SQL ggwordcloud A Word Cloud Geom for 'ggplot2' ghcm Functional Conditional Independence Testing with the GHCM ghyp Generalized Hyperbolic Distribution and Its Special Cases gibasa An Alternative 'Rcpp' Wrapper of 'MeCab' gicf Penalised Likelihood Estimation of a Covariance Matrix gif Graphical Independence Filtering gifski Highest Quality GIF Encoder gigg Group Inverse-Gamma Gamma Shrinkage for Sparse Regression with Grouping Structure giniVarCI Gini Indices, Variances and Confidence Intervals for Finite and Infinite Populations ginormal Generalized Inverse Normal Distribution Density and Generation git2r Provides Access to Git Repositories gjam Generalized Joint Attribute Modeling gkmSVM Gapped-Kmer Support Vector Machine gkwdist Generalized Kumaraswamy Distribution Family gkwreg Generalized Kumaraswamy Regression Models for Bounded Data glasso Graphical Lasso: Estimation of Gaussian Graphical Models glassoFast Fast Graphical LASSO glca An R Package for Multiple-Group Latent Class Analysis glcm Calculate Textures from Grey-Level Co-Occurrence Matrices (GLCMs) gld Estimation and Use of the Generalised (Tukey) Lambda Distribution glinternet Learning Interactions via Hierarchical Group-Lasso Regularization glinvci Phylogenetic Comparative Methods with Uncertainty Estimates gllm Generalised log-Linear Model gllvm Generalized Linear Latent Variable Models glm.deploy 'C' and 'Java' Source Code Generator for Fitted Glm Objects glmGamPoi Fit a Gamma-Poisson Generalized Linear Model glmSTARMA (Double) Generalized Linear Models for Spatio-Temporal Data glmbayes Bayesian Generalized Linear Models (IID Samples) glmlep Fit GLM with LEP-Based Penalized Maximum Likelihood glmm Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation glmmEP Generalized Linear Mixed Model Analysis via Expectation Propagation glmmLasso Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation glmmML Generalized Linear Models with Clustering glmmTMB Generalized Linear Mixed Models using Template Model Builder glmmrBase Monte Carlo Maximum Likelihood and Analysis of Generalised Linear Mixed Models glmmrOptim Approximate Optimal Experimental Designs Using Generalised Linear Mixed Models glmmsel Generalised Linear Mixed Model Selection glmnet Lasso and Elastic-Net Regularized Generalized Linear Models glmpath L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model glmtlp Generalized Linear Models with Truncated Lasso Penalty globalKinhom Inhomogeneous K- And Pair Correlation Functions Using Global Estimators globalOptTests Objective functions for benchmarking the performance of global optimization algorithms globpso Swarm Intelligence Optimization glow Make Plots that Glow glue Interpreted String Literals gmGeostats Geostatistics for Compositional Analysis gmm Generalized Method of Moments and Generalized Empirical Likelihood gmp Multiple Precision Arithmetic gmtFD General Multiple Tests for Univariate and Multivariate Functional Data gmvjoint Joint Models of Survival and Multivariate Longitudinal Data gmwmx Estimate Functional and Stochastic Parameters of Linear Models with Correlated Residuals gmwmx2 Estimate Functional and Stochastic Parameters of Linear Models with Correlated Residuals and Missing Data gnlm Generalized Nonlinear Regression Models gnm Generalized Nonlinear Models goat Gene Set Analysis Using the Gene Set Ordinal Association Test gofCopula Goodness-of-Fit Tests for Copulae gofar Generalized Co-Sparse Factor Regression goffda Goodness-of-Fit Tests for Functional Data goftest Classical Goodness-of-Fit Tests for Univariate Distributions goldfish Statistical Network Models for Dynamic Network Data goldilocks Goldilocks Adaptive Trial Designs for Time-to-Event Endpoints googlePolylines Encoding Coordinates into 'Google' Polylines governor Speed Limiter to Control Rate of Execution of Loops gower Gower's Distance gpboost Combining Tree-Boosting with Gaussian Process and Mixed Effects Models gpcp Genomic Prediction of Cross Performance gplite General Purpose Gaussian Process Modelling gplm Generalized Partial Linear Models (GPLM) gps General P-Splines gpss Gaussian Processes for Social Science grainscape Landscape Connectivity, Habitat, and Protected Area Networks grandR Comprehensive Analysis of Nucleotide Conversion Sequencing Data graph graph: A package to handle graph data structures graphicalEvidence Graphical Evidence graphicalVAR Graphical VAR for Experience Sampling Data graphlayouts Additional Layout Algorithms for Network Visualizations graphpcor Models for Correlation Matrices Based on Graphs graphql A GraphQL Query Parser grasps Groupwise Regularized Adaptive Sparse Precision Solution grattan Australian Tax Policy Analysis grattanInflators Inflators for Australian Policy Analysis gravmagsubs Gravitational and Magnetic Attraction of 3-D Vertical Rectangular Prisms greed Clustering and Model Selection with the Integrated Classification Likelihood greeks Sensitivities of Prices of Financial Options and Implied Volatilities greenR Green Index Quantification, Analysis and Visualization greencrab.toolkit Run 'Stan' Models to Interpret Green Crab Monitoring Assessments gremlin Mixed-Effects REML Incorporating Generalized Inverses gretel Generalized Path Analysis for Social Networks greybox Toolbox for Model Building and Forecasting grf Generalized Random Forests gridOT Approximate Optimal Transport Between Two-Dimensional Grids gridmicrotex Native 'LaTeX' Math Rendering for Grid Graphics gridtext Improved Text Rendering Support for 'Grid' Graphics groc Generalized Regression on Orthogonal Components groupedSurv Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function grouprar Group Response Adaptive Randomization for Clinical Trials grove Wavelet Functional ANOVA Through Markov Groves growth Multivariate Normal and Elliptically-Contoured Repeated Measurements Models growthrates Estimate Growth Rates from Experimental Data grpCox Penalized Cox Model for High-Dimensional Data with Grouped Predictors grpSLOPE Group Sorted L1 Penalized Estimation grpnet Group Elastic Net Regularized GLMs and GAMs grpreg Regularization Paths for Regression Models with Grouped Covariates grpsel Group Subset Selection grumpy Read 'NumPy' '.npy' and '.npz' Files grwat River Hydrograph Separation and Analysis gsDesign Group Sequential Design gsDesign2 Group Sequential Design with Non-Constant Effect gsEasy Gene Set Enrichment Analysis in R gsaot Compute Global Sensitivity Analysis Indices Using Optimal Transport gscounts Group Sequential Designs with Negative Binomial Outcomes gsignal Signal Processing gsisdecoder High Efficient Functions to Decode NFL Player IDs gsl Wrapper for the Gnu Scientific Library gslnls GSL Multi-Start Nonlinear Least-Squares Fitting gss General Smoothing Splines gstat Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation gsw Gibbs Sea Water Functions gte Generalized Turnbull's Estimator gtfs2gps Converting Transport Data from GTFS Format to GPS-Like Records gtfsrealtime Read GTFS-Realtime Files into Data Frames gtfsrouter Routing with 'GTFS' (General Transit Feed Specification) Data gtfstools General Transit Feed Specification (GTFS) Editing and Analysing Tools gtools Various R Programming Tools gwpcormapper Geographically Weighted Partial Correlation Mapper h3lib Exposes the 'Uber' 'H3' Library to R Packages h3o H3 Geospatial Indexing System h3r Hexagonal Hierarchical Geospatial Indexing System h5lite Simplified 'HDF5' Interface hSDM Hierarchical Bayesian Species Distribution Models hahmmr Haplotype-Aware Hidden Markov Model for RNA hal9001 The Scalable Highly Adaptive Lasso handwriter Handwriting Analysis in R hann Hopfield Artificial Neural Networks hans Haversines are not Slow hapassoc Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous harmony Fast, Sensitive, and Accurate Integration of Single Cell Data hashmapR Fast, Vectorized Hashmap hashr Hash R Objects to Integers Fast havel Visualize and Tabulate 'R' Package Dependencies haven Import and Export 'SPSS', 'Stata' and 'SAS' Files hawkes Hawkes process simulation and calibration toolkit hawkesbow Estimation of Hawkes Processes from Binned Observations hbal Hierarchically Regularized Entropy Balancing hbamr Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan' hbmem Hierarchical Bayesian Analysis of Recognition Memory hclust1d Hierarchical Clustering of Univariate (1d) Data hdbayes Bayesian Analysis of Generalized Linear Models with Historical Data hdbcp Bayesian Change Point Detection for High-Dimensional Data hdbinseg Change-Point Analysis of High-Dimensional Time Series via Binary Segmentation hdf5lib Headers and Static Libraries for 'HDF5' hdf5r Interface to the 'HDF5' Binary Data Format hdflex High-Dimensional Aggregate Density Forecasts hdme High-Dimensional Regression with Measurement Error hdnom Benchmarking and Visualization Toolkit for Penalized Cox Models hdpGLM Hierarchical Dirichlet Process Generalized Linear Models hdqr Fast Algorithm for Penalized Quantile Regression hdrcde Highest Density Regions and Conditional Density Estimation hdsvm Fast Algorithm for Support Vector Machine hdtg Generate Samples from Multivariate Truncated Normal Distributions healthbR Access Brazilian Public Health Data healthyAddress Convert Addresses to Standard Inputs heatindex Calculating Heat Stress heatwaveR Detect Heatwaves and Cold-Spells heck Highly Performant String Case Converter hellorust Minimal Examples of Using Rust Code in R hermiter Efficient Sequential and Batch Estimation of Univariate and Bivariate Probability Density Functions and Cumulative Distribution Functions along with Quantiles (Univariate) and Nonparametric Correlation (Bivariate) hesim Health Economic Simulation Modeling and Decision Analysis hetGP Heteroskedastic Gaussian Process Modeling and Design under Replication heterogen Spatial Functions for Heterogeneity and Climate Variability heumilkr Heuristic Capacitated Vehicle Routing Problem Solver hexDensity Fast Kernel Density Estimation with Hexagonal Grid hexbin Hexagonal Binning Routines hexify Equal-Area Hex Grids on the 'Snyder' 'ISEA' 'Icosahedron' hgm Holonomic Gradient Method and Gradient Descent hgwrr Hierarchical and Geographically Weighted Regression hhdynamics Fitting Household Transmission Model to Estimate Household Transmission Dynamics of Influenza hhsmm Hidden Hybrid Markov/Semi-Markov Model Fitting hibayes Individual-Level, Summary-Level and Single-Step Bayesian Regression Model hierNest Penalized Regression with Hierarchical Nested Parameterization Structure hierNet A Lasso for Hierarchical Interactions hierarchicalSets Set Data Visualization Using Hierarchies highOrderPortfolios Design of High-Order Portfolios Including Skewness and Kurtosis highfrequency Tools for Highfrequency Data Analysis highlight Syntax Highlighter highs 'HiGHS' Optimization Solver hilbertSimilarity Hilbert Similarity Index for High Dimensional Data hint Tools for Hypothesis Testing Based on Hypergeometric Intersection Distributions hipread Read Hierarchical Fixed Width Files hisse Hidden State Speciation and Extinction histmdl A Most Informative Histogram-Like Model hitandrun "Hit and Run" and "Shake and Bake" for Sampling Uniformly from Convex Shapes hkevp Spatial Extreme Value Analysis with the Hierarchical Model of Reich and Shaby (2012) hlt Higher-Order Item Response Theory hmcdm Hidden Markov Cognitive Diagnosis Models for Learning hmde Hierarchical Methods for Differential Equations hmm.discnp Hidden Markov Models with Discrete Non-Parametric Observation Distributions hmmTMB Fit Hidden Markov Models using Template Model Builder hommel Methods for Closed Testing with Simes Inequality, in Particular Hommel's Method hood2net Create a Language Network from Neighborhoods of Words hopit Hierarchical Ordered Probit Models with Application to Reporting Heterogeneity houba Manipulation of (Large) Memory-Mapped Objects (Vectors, Matrices and Arrays) hpa Distributions Hermite Polynomial Approximation hqreg Regularization Paths for Lasso or Elastic-Net Penalized Huber Loss Regression and Quantile Regression hrqglas Group Variable Selection for Quantile and Robust Mean Regression hrt Heteroskedasticity Robust Testing hsphase Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data hsrecombi Estimation of Recombination Rate and Maternal LD in Half-Sibs hsstan Hierarchical Shrinkage Stan Models for Biomarker Selection htetree Causal Inference with Tree-Based Machine Learning Algorithms htmltools Tools for HTML hts Hierarchical and Grouped Time Series htsr Hydro-Meteorology Time-Series httk High-Throughput Toxicokinetics httpgd A 'HTTP' Server Graphics Device httpuv HTTP and WebSocket Server Library huge High-Dimensional Undirected Graph Estimation humaniformat A Parser for Human Names humanleague Synthetic Population Generator hunspell High-Performance Stemmer, Tokenizer, and Spell Checker hutilscpp Miscellaneous Functions in C++ hydrotoolbox Hydrological Tools for Handling Hydro-Meteorological Data Records hyper2 The Hyperdirichlet Distribution, Mark 2 hypergeo2 Generalized Hypergeometric Function with Tunable High Precision hypergraph.sizing Hypergraph-Based Sizing Function for Generalised Linear Step-Up Method hypervolume High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls hystar Fit the Hysteretic Threshold Autoregressive Model iAR Irregularly Observed Autoregressive Models iBST Improper Bagging Survival Tree iCellR Analyzing High-Throughput Single Cell Sequencing Data iClusterVB Fast Integrative Clustering and Feature Selection for High Dimensional Data iDIFr Intersectional Differential Item Functioning Analysis iDOVE Durability of Vaccine Efficacy Against SARS-CoV-2 Infection iGraphMatch Tools for Graph Matching iNEXT Interpolation and Extrapolation for Species Diversity iNEXT.3D Interpolation and Extrapolation for Three Dimensions of Biodiversity iapws Formulations of the International Association for the Properties of Water and Steam ibdsegments Identity by Descent Probability in Pedigrees ibdsim2 Simulation of Chromosomal Regions Shared by Family Members ibm Individual Based Models in R ibmcraftr Toolkits to Develop Individual-Based Models in Infectious Disease ibr Iterative Bias Reduction ibs Integral of B-Spline Functions iccbeta Multilevel Model Intraclass Correlation for Slope Heterogeneity icenReg Regression Models for Interval Censored Data icensmis Study Design and Data Analysis in the Presence of Error-Prone Diagnostic Tests and Self-Reported Outcomes ichimoku Visualization and Tools for Ichimoku Kinko Hyo Strategies iclogcondist Log-Concave Distribution Estimation with Interval-Censored Data icmstate Interval Censored Multi-State Models icosa Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra icr Compute Krippendorff's Alpha idar Individual Diversity-Area Relationships idefix Efficient Designs for Discrete Choice Experiments idiffomix Integrated Differential Analysis of Multi Omics Data using a Joint Mixture Model ieTest Indirect Effects Testing Methods in Mediation Analysis ieeeround Functions to Set and Get the IEEE Rounding Mode ifctools Italian Fiscal Code ('Codice Fiscale') Utilities ifit Simulation-Based Fitting of Parametric Models with Minimum Prior Information ifs Iterated Function Systems igcop Computational Tools for the IG and IGL Copula Families iglm Regression under Interference in Connected Populations igraph Network Analysis and Visualization igrf International Geomagnetic Reference Field ijtiff Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files ilabelled Simple Handling of Labelled Data illuminaio Parsing Illumina Microarray Output Files image.CannyEdges Implementation of the Canny Edge Detector for Images image.ContourDetector Implementation of the Unsupervised Smooth Contour Line Detection for Images image.CornerDetectionF9 Find Corners in Digital Images with FAST-9 image.CornerDetectionHarris Implementation of the Harris Corner Detection for Images image.LineSegmentDetector Detect Line Segments in Images image.Otsu Otsu's Image Segmentation Method image.binarization Binarize Images for Enhancing Optical Character Recognition image.libfacedetection Convolutional Neural Network for Face Detection imager Image Processing Library Based on 'CImg' imagerExtra Extra Image Processing Library Based on 'imager' imaginarycss Tools for Studying Imaginary Cognitive Social Structure imagine IMAGing engINEs, Tools for Application of Image Filters to Data Matrices imbibe A Pipe-Friendly Image Calculator immer Item Response Models for Multiple Ratings immunarch Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R imp4p Imputation for Proteomics impARI Improving Permutation-Based All-Resolutions Inference ('impARI') impactflu Quantification of Population-Level Impact of Vaccination impactr Mechanical Loading Prediction Through Accelerometer Data impute impute: Imputation for microarray data imputeMulti Imputation Methods for Multivariate Multinomial Data imputeTS Time Series Missing Value Imputation imt Impact Measurement Toolkit imuGAP Immunity: Geographic and Age-Based Projection imuf Estimate Orientation of an Inertial Measurement Unit inca Integer Calibration incgraph Incremental Graphlet Counting for Network Optimisation incubate Parametric Time-to-Event Analysis with Variable Incubation Phases indelmiss Insertion Deletion Analysis While Accounting for Possible Missing Data indexthis Quick Indexation india Influence Diagnostics in Statistical Models inferCSN Inferring Cell-Specific Gene Regulatory Network inferr Inferential Statistics influenceR Software Tools to Quantify Structural Importance of Nodes in a Network influential Identification and Classification of the Most Influential Nodes infocausality Information-Theoretic Measure of Causality infotheo Information-Theoretic Measures infoxtr Information-Theoretic Measures for Revealing Variable Interactions inlabru Bayesian Latent Gaussian Modelling using INLA and Extensions inplace In-place Operators for R instantiate Pre-Compiled 'CmdStan' Models in R Packages intRegGOF Integrated Regression Goodness of Fit intRinsic Likelihood-Based Intrinsic Dimension Estimators interep Interaction Analysis of Repeated Measure Data interflex Estimation, Diagnostics and Visualization of Conditional Marginal Effects interleave Converts Tabular Data to Interleaved Vectors interp Interpolation Methods interpolators Some Interpolation Methods interpret Fit Interpretable Machine Learning Models interprocess Mutexes, Semaphores, and Message Queues intervalaverage Time-Weighted Averaging for Interval Data intervalpsych Analyzing Interval Data in Psychometrics intervals Tools for Working with Points and Intervals intkrige A Numerical Implementation of Interval-Valued Kriging intmap Ordered Containers with Integer Keys intrinsicFRP An R Package for Factor Model Asset Pricing intsurv Integrative Survival Modeling invgamstochvol Obtains the Log Likelihood for an Inverse Gamma Stochastic Volatility Model ionet Network Analysis for Input-Output Tables iotarelr Iota Inter Coder Reliability for Content Analysis iotools I/O Tools for Streaming ipaddress Data Analysis for IP Addresses and Networks ipfp Fast Implementation of the Iterative Proportional Fitting Procedure in C ipft Indoor Positioning Fingerprinting Toolset ipmr Integral Projection Models ipred Improved Predictors iprior Regression Modelling using I-Priors ipsecr Spatially Explicit Capture-Recapture by Inverse Prediction iq Protein Quantification in Mass Spectrometry-Based Proteomics irace Iterated Racing for Automatic Algorithm Configuration irlba Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices irls Generalised Linear Models via Iteratively Reweighted Least Squares ironseed Improved Random Number Generator Seeding irt Item Response Theory and Computerized Adaptive Testing Functions irtoys A Collection of Functions Related to Item Response Theory (IRT) isa2 The Iterative Signature Algorithm isingLenzMC Monte Carlo for Classical Ising Model island Stochastic Island Biogeography Theory Made Easy islasso The Induced Smoothed Lasso isnullptr Check if an 'externalptr' is a Null Pointer iso8601 Working with ISO8601 Dates and Times isoband Generate Isolines and Isobands from Regularly Spaced Elevation Grids isocir Isotonic Inference for Circular Data isocubes Voxel Data Visualization with Isometric Cubes isodistrreg Isotonic Distributional Regression (IDR) isotree Isolation-Based Outlier Detection isva Independent Surrogate Variable Analysis itdr Integral Transformation Methods for SDR in Regression iterLap Approximate Probability Densities by Iterated Laplace Approximations itmsa Information-Theoretic Measures for Spatial Association itp The Interpolate, Truncate, Project (ITP) Root-Finding Algorithm ivdoctr Ensures Mutually Consistent Beliefs When Using IVs ivtools Instrumental Variables ivx Robust Econometric Inference jSDM Joint Species Distribution Models jaccard Testing Similarity Between Binary Datasets using Jaccard/Tanimoto Coefficients jackalope A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator jacobi Jacobi Theta Functions and Related Functions jfa Statistical Methods for Auditing jgd JSON Graphics Device jinjar Template Engine Inspired by 'Jinja' jlview Zero-Copy Julia to R Array Bridge via ALTREP jmatrix Read from/Write to Disk Matrices with any Data Type in a Binary Format jmcm Joint Mean-Covariance Models using 'Armadillo' and S4 jmotif Time Series Analysis Toolkit Based on Symbolic Aggregate Discretization, i.e. SAX jmvconnect Connect to the 'jamovi' Statistical Spreadsheet joineRML Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes jointDiag Joint Approximate Diagonalization of a Set of Square Matrices jointseg Joint Segmentation of Multivariate (Copy Number) Signals jomo Multilevel Joint Modelling Multiple Imputation jpeg Read and write JPEG images jqr Client for 'jq', a 'JSON' Processor jrSiCKLSNMF Multimodal Single-Cell Omics Dimensionality Reduction jsonify Convert Between 'R' Objects and Javascript Object Notation (JSON) jsonlite A Simple and Robust JSON Parser and Generator for R jti Junction Tree Inference jumps Hodrick-Prescott Filter with Jumps junctions The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages kSamples K-Sample Rank Tests and their Combinations kalmanfilter Kalman Filter kamila Methods for Clustering Mixed-Type Data kanjistat A Statistical Framework for the Analysis of Japanese Kanji Characters kappalab Non-Additive Measure and Integral Manipulation Functions kazaam Tools for Tall Distributed Matrices kbal Kernel Balancing kcpRS Kernel Change Point Detection on the Running Statistics kde1d Univariate Kernel Density Estimation kdecopula Kernel Smoothing for Bivariate Copula Densities kdevine Multivariate Kernel Density Estimation with Vine Copulas kendallknight Efficient Implementation of Kendall's Correlation Coefficient Computation kerSeg New Kernel-Based Change-Point Detection kergp Gaussian Process Laboratory kernda Kernel Discriminant Analysis kerndwd Distance Weighted Discrimination (DWD) and Kernel Methods kernelboot Smoothed Bootstrap and Random Generation from Kernel Densities kernlab Kernel-Based Machine Learning Lab kernreg Nadaraya-Watson Kernel Regression keyATM Keyword Assisted Topic Models keyclust A Model for Semi-Supervised Keyword Extraction from Word Embedding Models keylist Lightweight List Extensions that Enforce Unique Keys keyperm Keyword Analysis Using Permutation Tests keypress Wait for a Key Press in a Terminal keyring Access the System Credential Store from R kgrams Classical k-gram Language Models kimfilter Kim Filter kissmig a Keep It Simple Species Migration Model kit Data Manipulation Functions Implemented in C kkmeans Fast Implementations of Kernel K-Means kknn Weighted k-Nearest Neighbors kmBlock k-Means Like Blockmodeling of One-Mode and Linked Networks kmc Kaplan-Meier Estimator with Constraints for Right Censored Data -- a Recursive Computational Algorithm kmeRtone Multi-Purpose and Flexible k-Meric Enrichment Analysis Software kmer Fast K-Mer Counting and Clustering for Biological Sequence Analysis knn.covertree An Accurate kNN Implementation with Multiple Distance Measures knnmi k-Nearest Neighbor Mutual Information Estimator kohonen Supervised and Unsupervised Self-Organising Maps krige Geospatial Kriging with Metropolis Sampling kriging Ordinary Kriging krm Kernel Based Regression Models ks Kernel Smoothing ksNN K* Nearest Neighbors Algorithm ksm Kernel Density Estimation for Random Symmetric Positive Definite Matrices kstMatrix Basic Functions in Knowledge Space Theory Using Matrix Representation ktaucenters Robust Clustering Procedures ktweedie 'Tweedie' Compound Poisson Model in the Reproducing Kernel Hilbert Space kvh Read/Write Files in Key-Value-Hierarchy Format kyotil Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies kza Kolmogorov-Zurbenko Adaptive Filters l0ara Sparse Generalized Linear Model with L0 Approximation for Feature Selection l1spectral An L1-Version of the Spectral Clustering laGP Local Approximate Gaussian Process Regression labdsv Ordination and Multivariate Analysis for Ecology lacm Latent Autoregressive Count Models lacunr Fast 3D Lacunarity for Voxel Data lakhesis Consensus Seriation for Binary Data lamW Lambert-W Function lamle Maximum Likelihood Estimation of Latent Variable Models landscapeR Categorical Landscape Simulation Facility landscapemetrics Landscape Metrics for Categorical Map Patterns landscapetools Landscape Utility Toolbox landsepi Landscape Epidemiology and Evolution languageserver Language Server Protocol lars Least Angle Regression, Lasso and Forward Stagewise latentcor Fast Computation of Latent Correlations for Mixed Data latentnet Latent Position and Cluster Models for Statistical Networks later Utilities for Scheduling Functions to Execute Later with Event Loops lavaSearch2 Tools for Model Specification in the Latent Variable Framework lavacreg Latent Variable Count Regression Models lazyeval Lazy (Non-Standard) Evaluation lazymatrix Perform Complex Matrix Operations Symbolically on Sparse Matrices lbaModel The Linear Ballistic Accumulation Model lbfgs Limited-memory BFGS Optimization lbfgsb3c Limited Memory BFGS Minimizer with Bounds on Parameters with optim() 'C' Interface lcmm Extended Mixed Models Using Latent Classes and Latent Processes lconnect Simple Tools to Compute Landscape Connectivity Metrics lcopula Liouville Copulas lda Collapsed Gibbs Sampling Methods for Topic Models lddmm Longitudinal Drift-Diffusion Mixed Models (LDDMM) ldmppr Estimate and Simulate from Location Dependent Marked Point Processes ldsep Linkage Disequilibrium Shrinkage Estimation for Polyploids ldt Automated Uncertainty Analysis leaderCluster Leader Clustering Algorithm leaps Regression Subset Selection learner Latent Space-Based Transfer Learning lefko3 Historical and Ahistorical Population Projection Matrix Analysis legion Forecasting Using Multivariate Models leidenAlg Implements the Leiden Algorithm via an R Interface leidenbase R and C/C++ Wrappers to Run the Leiden find_partition() Function lemna Lemna Ecotox Effect Model leontief Input-Output Analysis leptokurticMixture Implements Parsimonious Finite Mixtures of Multivariate Elliptical Leptokurtic-Normals lessSEM Non-Smooth Regularization for Structural Equation Models lest Vectorised Nested if-else Statements Similar to CASE WHEN in 'SQL' lexRankr Extractive Summarization of Text with the LexRank Algorithm lfa Logistic Factor Analysis for Categorical Data lfe Linear Group Fixed Effects lfl Linguistic Fuzzy Logic lfmm Latent Factor Mixed Models lgarch Simulation and Estimation of Log-GARCH Models lgspline Lagrangian Multiplier Smoothing Splines for Smooth Function Estimation lhs Latin Hypercube Samples libcoin Linear Test Statistics for Permutation Inference libdeflate DEFLATE Compression and Static Library libgeos Open Source Geometry Engine ('GEOS') C API libimath 'Imath' Computer Graphics Linear Algebra Static Library libipldr R Bindings to the 'Rust' 'IPLD' Library libopenexr Static Library and Headers for 'OpenEXR' Image I/O libr Libraries, Data Dictionaries, and a Data Step for R libstable4u Stable Distribution Functions...For You lifecontingencies Financial and Actuarial Mathematics for Life Contingencies lifepack Insurance Reserve Calculations lightAUC Fast AUC Computation lightgbm Light Gradient Boosting Machine limSolve Solving Linear Inverse Models lime Local Interpretable Model-Agnostic Explanations limma Linear Models for Microarray and Omics Data linERR Linear Excess Relative Risk Model lincom Linear Biomarker Combination: Empirical Performance Optimization linelistBayes Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches lineup Lining Up Two Sets of Measurements lineup2 Lining Up Two Sets of Measurements lingdist Fast Linguistic Distance and Alignment Computation lingmatch Linguistic Matching and Accommodation link2GI Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools lintools Manipulation of Linear Systems of (in)Equalities list Statistical Methods for the Item Count Technique and List Experiment lit Latent Interaction Testing for Genome-Wide Studies literanger Fast Serializable Random Forests Based on 'ranger' ljr Logistic Joinpoint Regression llamaR Interface for Large Language Models via 'llama.cpp' llmjson Repair Malformed JSON Strings llrem LLM Relational Event Models lm.br Linear Model with Breakpoint lmPerm Permutation Tests for Linear Models lmSubsets Exact Variable-Subset Selection in Linear Regression lmap Logistic Mapping lme4 Linear Mixed-Effects Models using 'Eigen' and S4 lmm Linear Mixed Models lmmprobe Sparse High-Dimensional Linear Mixed Modeling with a Partitioned Empirical Bayes ECM Algorithm lmom L-Moments lmomRFA Regional Frequency Analysis using L-Moments lmtest Testing Linear Regression Models lnmCluster Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data lnmixsurv Bayesian Mixture Log-Normal Survival Model lobstr Visualize R Data Structures with Trees locStra Fast Implementation of (Local) Population Stratification Methods localLLM Running Local LLMs with 'llama.cpp' Backend localScore Package for Sequence Analysis by Local Score localboot Local Bootstrap Methods for Various Networks localgauss Estimating Local Gaussian Parameters locfit Local Regression, Likelihood and Density Estimation locits Test of Stationarity and Localized Autocovariance locpol Kernel Local Polynomial Regression loder Dependency-Free Access to PNG Image Files logKDE Computing Log-Transformed Kernel Density Estimates for Positive Data logStirling2 Fast Stirling Numbers of the Second Kind logconcens Maximum Likelihood Estimation of a Log-Concave Density Based on Censored Data logcumulant Goodness-of-Fit Tests and Diagrams Based on Mellin Log-Cumulants loggit2 Easy-to-Use, Dependencyless Logger logicDT Identifying Interactions Between Binary Predictors logistf Firth's Bias-Reduced Logistic Regression logisticPCA Binary Dimensionality Reduction logitr Logit Models w/Preference & WTP Space Utility Parameterizations loglognorm Double Log Normal Distribution Functions logspline Routines for Logspline Density Estimation lokern Kernel Regression Smoothing with Local or Global Plug-in Bandwidth lolog Latent Order Logistic Graph Models longclust Model-Based Clustering and Classification for Longitudinal Data longevity Statistical Methods for the Analysis of Excess Lifetimes longitree Decision Tree Analysis for Longitudinal Measurement Data lorec LOw Rand and sparsE Covariance matrix estimation lotri A Simple Way to Specify Symmetric, Block Diagonal Matrices lowmemtkmeans Low Memory Use Trimmed K-Means lowpassFilter Lowpass Filtering lpSolve Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs lpSolveAPI R Interface to 'lp_solve' Version 5.5.2.0 lpcde Boundary Adaptive Local Polynomial Conditional Density Estimator lpirfs Local Projections Impulse Response Functions lpridge Local Polynomial (Ridge) Regression lpsymphony Symphony integer linear programming solver in R lqmm Linear Quantile Mixed Models lrstat Power and Sample Size Calculation for Non-Proportional Hazards and Beyond lsReg Performs Large Scale Regressions lsei Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints lsirm12pl Latent Space Item Response Model lslx Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares lsoda 'C++' Header Library for Ordinary Differential Equations lstar Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics ltsa Linear Time Series Analysis ltsk Local Time Space Kriging luajr 'LuaJIT' Scripting lubridate Make Dealing with Dates a Little Easier ludic Linkage Using Diagnosis Codes lulcc Land Use Change Modelling in R lumbermark Resistant Clustering via Chopping Up Mutual Reachability Minimum Spanning Trees lutz Look Up Time Zones of Point Coordinates lwgeom Bindings to Selected 'liblwgeom' Functions for Simple Features lzstring Wrapper for 'lz-string' 'C++' Library m2r Interface to 'Macaulay2' mBvs Bayesian Variable Selection Methods for Multivariate Data mDAG Inferring Causal Network from Mixed Observational Data Using a Directed Acyclic Graph mGSFPCA Estimate Functional Principal Components from Sparse Data mHMMbayes Multilevel Hidden Markov Models Using Bayesian Estimation mRMRe Parallelized Minimum Redundancy, Maximum Relevance (mRMR) mSimCC Micro Simulation Model for Cervical Cancer Prevention mable Maximum Approximate Bernstein/Beta Likelihood Estimation mactivate Multiplicative Activation maftools Summarize, Analyze and Visualize MAF Files magi MAnifold-Constrained Gaussian Process Inference magick Advanced Graphics and Image-Processing in R magree Implements the O'Connell-Dobson-Schouten Estimators of Agreement for Multiple Observers magrittr A Forward-Pipe Operator for R malan MAle Lineage ANalysis mandelbrot Generates Views on the Mandelbrot Set manifold Operations for Riemannian Manifolds manta Multivariate Asymptotic Non-Parametric Test of Association maotai Tools for Matrix Algebra, Optimization and Inference mapdata Extra Map Databases mapdeck Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl' mapi Mapping Averaged Pairwise Information mappoly Genetic Linkage Maps in Autopolyploids mapproj Map Projections maps Draw Geographical Maps mapscanner Print Maps, Draw on Them, Scan Them Back in maptpx MAP Estimation of Topic Models maq Multi-Armed Qini marble Robust Marginal Bayesian Variable Selection for Gene-Environment Interactions marcox Marginal Hazard Ratio Estimation in Clustered Failure Time Data marelac Tools for Aquatic Sciences marked Mark-Recapture Analysis for Survival and Abundance Estimation markerpen Marker Gene Detection via Penalized Principal Component Analysis markets Estimation Methods for Markets in Equilibrium and Disequilibrium markophylo Markov Chain Models for Phylogenetic Trees markovMSM Methods for Checking the Markov Condition in Multi-State Survival Data markovchain Easy Handling Discrete Time Markov Chains markovmix Mixture of Markov Chains with Support of Higher Orders and Multiple Sequences marqLevAlg A Parallelized General-Purpose Optimization Based on Marquardt-Levenberg Algorithm marquee Markdown Parser and Renderer for R Graphics mas Multi-Population Association Studies masc Simulate the Multi-Attribute Search and Choice (MASC) Model mase Model-Assisted Survey Estimators mashr Multivariate Adaptive Shrinkage mastif Mast Inference and Forecasting matchingMarkets Analysis of Stable Matchings matchingR Matching Algorithms in R and C++ mateable Assess Mating Potential in Space and Time matricks Useful Tricks for Matrix Manipulation matrixCorr Collection of Correlation, Agreement, and Reliability Estimators matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors) matrixdist Statistics for Matrix Distributions matrixprofiler Matrix Profile for R matrixset Creating, Manipulating and Annotating Matrix Ensemble maxbootR Efficient Bootstrap Methods for Block Maxima maxentcpp Maximum Entropy Species Distribution Modeling ('C++' Implementation) maxstablePCA Apply a PCA Like Procedure Suited for Multivariate Extreme Value Distributions maxstat Maximally Selected Rank Statistics mbbefd Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and Destruction Rate Modelling mbest Moment-Based Estimation for Hierarchical Models mboost Model-Based Boosting mccca Visualizing Class Specific Heterogeneous Tendencies in Categorical Data mcclust Process an MCMC Sample of Clusterings mcemGLM Maximum Likelihood Estimation for Generalized Linear Mixed Models mcen Multivariate Cluster Elastic Net mcga Machine Coded Genetic Algorithms for Real-Valued Optimization Problems mcglm Multivariate Covariance Generalized Linear Models mclm Mastering Corpus Linguistics Methods mclust Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation mclustAddons Addons for the 'mclust' Package mclustcomp Measures for Comparing Clusters mcmc Markov Chain Monte Carlo mcmcsae Markov Chain Monte Carlo Small Area Estimation mcmcse Monte Carlo Standard Errors for MCMC mco Multiple Criteria Optimization Algorithms and Related Functions mcr Method Comparison Regression mcrPioda Method Comparison Regression - Mcr Fork for M- And MM-Deming Regression md4r Markdown Parser Implemented using the 'MD4C' Library mda Mixture and Flexible Discriminant Analysis mdbr Work with Microsoft Access Files mdendro Extended Agglomerative Hierarchical Clustering mdgc Missing Data Imputation Using Gaussian Copulas mdmb Model Based Treatment of Missing Data meanShiftR A Computationally Efficient Mean Shift Implementation meanr Sentiment Analysis Scorer measles Measles Epidemiological Models measr Bayesian Psychometric Measurement Using 'Stan' meboot Maximum Entropy Bootstrap for Time Series medfate Mediterranean Forest Simulation medfateland Mediterranean Landscape Simulation melt Multiple Empirical Likelihood Tests meltt Matching Event Data by Location, Time and Type memisc Management of Survey Data and Presentation of Analysis Results memo Hashmaps and Memoization (in-Memory Caching of Repeated Computations) memshare Shared Memory Multithreading memuse Memory Estimation Utilities mergeGridR Grid-Based Number Merge Puzzle Simulation metaBMA Bayesian Model Averaging for Random and Fixed Effects Meta-Analysis metaRange Framework to Build Mechanistic and Metabolic Constrained Species Distribution Models metacart Meta-CART: A Flexible Approach to Identify Moderators in Meta-Analysis metacoder Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data metadynminer Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed' metadynminer3d Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed' metafolio Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization metapod Meta-Analyses on P-Values of Differential Analyses metarep Replicability-Analysis Tools for Meta-Analysis meteoland Landscape Meteorology Tools meteor Meteorological Data Manipulation methFuse Functional Segmentation of the Methylome mets Analysis of Multivariate Event Times mev Modelling of Extreme Values mewAvg A Fixed Memeory Moving Expanding Window Average mexhaz Mixed Effect Excess Hazard Models mfGARCH Mixed-Frequency GARCH Models mfrmr Estimation and Diagnostics for Many-Facet Measurement Models mgarchBEKK Simulating, Estimating and Diagnosing MGARCH (BEKK and mGJR) Processes mgc Multiscale Graph Correlation mgee2 Marginal Analysis of Misclassified Longitudinal Ordinal Data mgsub Safe, Multiple, Simultaneous String Substitution mgwrsar GWR, Mixed GWR with Spatial Autocorrelation and Multiscale GWR/GTWR (Top-Down Scale Approaches) mhazard Nonparametric and Semiparametric Methods for Multivariate Failure Time Data mhn The Modified Half-Normal Distribution mhpfilter Modified Hodrick-Prescott Filter with Optimal Smoothing Parameter Selection mhsmm Inference for Hidden Markov and Semi-Markov Models mhurdle Multiple Hurdle Tobit Models mice Multivariate Imputation by Chained Equations miceFast Fast Imputations Using 'Rcpp' and 'Armadillo' miceadds Some Additional Multiple Imputation Functions, Especially for 'mice' microbenchmark Accurate Timing Functions microseq Basic Biological Sequence Handling microsimulation Discrete Event Simulation in R and C++, with Tools for Cost-Effectiveness Analysis micsr Microeconometrics with R midasml Estimation and Prediction Methods for High-Dimensional Mixed Frequency Time Series Data midnight A 'tidymodels' Engine and Other Extensions for the 'midr' Package midr Learning from Black-Box Models by Maximum Interpretation Decomposition mig Multivariate Inverse Gaussian Distribution miic Learning Causal or Non-Causal Graphical Models Using Information Theory milorGWAS Mixed Logistic Regression for Genome-Wide Analysis Studies (GWAS) milr Multiple-Instance Logistic Regression with LASSO Penalty mime Map Filenames to MIME Types minMSE Implementation of the minMSE Treatment Assignment Method for One or Multiple Treatment Groups minerva Maximal Information-Based Nonparametric Exploration for Variable Analysis minet Mutual Information NETworks miniLNM Miniature Logistic-Normal Multinomial Models miniPCH Survival Distributions with Piece-Wise Constant Hazards minic Minimization Methods for Ill-Conditioned Problems minimaxALT Generate Optimal Designs of Accelerated Life Test using PSO-Based Algorithm minimaxApprox Minimax Approximation of Functions by Polynomials and Rational Functions minpack.lm R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds minqa Derivative-Free Optimization Algorithms by Quadratic Approximation minty Minimal Type Guesser mirt Multidimensional Item Response Theory mirtCAT Computerized Adaptive Testing with Multidimensional Item Response Theory miscF Miscellaneous Functions misclassGLM Computation of Generalized Linear Models with Misclassified Covariates Using Side Information misha Toolkit for Analysis of Genomic Data missDeaths Simulating and Analyzing Time to Event Data in the Presence of Population Mortality missSBM Handling Missing Data in Stochastic Block Models missoNet Joint Sparse Regression & Network Learning with Missing Data mistral Methods in Structural Reliability mix Estimation/Multiple Imputation for Mixed Categorical and Continuous Data mixAK Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering mixR Finite Mixture Modeling for Raw and Binned Data mixcat Mixed Effects Cumulative Link and Logistic Regression Models mixdir Cluster High Dimensional Categorical Datasets mixedBayes Bayesian Longitudinal Regularized Quantile Mixed Model mixedCCA Sparse Canonical Correlation Analysis for High-Dimensional Mixed Data mixedClust Co-Clustering of Mixed Type Data mixedMem Tools for Discrete Multivariate Mixed Membership Models mixgb Multiple Imputation Through 'XGBoost' mixl Simulated Maximum Likelihood Estimation of Mixed Logit Models for Large Datasets mixor Mixed-Effects Ordinal Regression Analysis mixsqp Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions mixtime Mixed Temporal Vectors and Operations mixtools Tools for Analyzing Finite Mixture Models mixture Mixture Models for Clustering and Classification mixvlmc Variable Length Markov Chains with Covariates mizer Dynamic Multi-Species Size Spectrum Modelling mkde 2D and 3D Movement-Based Kernel Density Estimates (MKDEs) ml Supervised Learning with Mandatory Splits and Seeds mlbench Machine Learning Benchmark Problems mlegp Maximum Likelihood Estimates of Gaussian Processes mlmc Multi-Level Monte Carlo mlogitBMA Bayesian Model Averaging for Multinomial Logit Models mlpack 'Rcpp' Integration for the 'mlpack' Library mlr Machine Learning in R mlr3learners Recommended Learners for 'mlr3' mlr3mbo Flexible Bayesian Optimization mlr3misc Helper Functions for 'mlr3' mlr3oml Connector Between 'mlr3' and 'OpenML' mlr3resampling Resampling Algorithms for 'mlr3' Framework mlrMBO Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions mlrv Long-Run Variance Estimation in Time Series Regression mlsbm Efficient Estimation of Bayesian SBMs & MLSBMs mlstm Multilevel Supervised Topic Models with Multiple Outcomes mlt Most Likely Transformations mlts Multilevel Latent Time Series Models with 'R' and 'Stan' mlumr Multilevel Unanchored Meta-Regression for Indirect Treatment Comparisons mmand Mathematical Morphology in Any Number of Dimensions mmap Map Pages of Memory mmapcharr Memory-Map Character Files mmcm Modified Maximum Contrast Method mmconvert Mouse Map Converter mmeta Multivariate Meta-Analysis mmpca Integrative Analysis of Several Related Data Matrices mmrm Mixed Models for Repeated Measures mmsample Multivariate Matched Sampling mniw The Matrix-Normal Inverse-Wishart Distribution mnlfa Moderated Nonlinear Factor Analysis mnorm Multivariate Normal Distribution mnormt The Multivariate Normal and t Distributions, and Their Truncated Versions mobsim Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes modeLLtest Compare Models with Cross-Validated Log-Likelihood modelSelection High-Dimensional Model Selection modernVA An Implementation of Two Modern Education-Based Value-Added Models modesto Modeling and Analysis of Stochastic Systems modsem Latent Interaction (and Moderation) Analysis in Structural Equation Models (SEM) mokken Conducts Mokken Scale Analysis mombf Model Selection with Bayesian Methods and Information Criteria momentfit Methods of Moments momentuHMM Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models mongolite Fast and Simple 'MongoDB' Client for R monolix2rx Converts 'Monolix' Models to 'rxode2' monomvn Estimation for MVN and Student-t Data with Monotone Missingness monoreg Bayesian Monotonic Regression Using a Marked Point Process Construction monotone Performs Monotone Regression monreg Nonparametric Monotone Regression moocore Core Mathematical Functions for Multi-Objective Optimization mop Mobility Oriented-Parity Metric mori Shared Memory for R Objects morpheus Estimate Parameters of Mixtures of Logistic Regressions morse Modelling Reproduction and Survival Data in Ecotoxicology morseTKTD Bayesian Inference of TKTD Models mosum Moving Sum Based Procedures for Changes in the Mean motif Local Pattern Analysis motmot Models of Trait Macroevolution on Trees mousetrap Process and Analyze Mouse-Tracking Data movMF Mixtures of von Mises-Fisher Distributions move Visualizing and Analyzing Animal Track Data moveHMM Animal Movement Modelling using Hidden Markov Models moveWindSpeed Estimate Wind Speeds from Bird Trajectories mp Multidimensional Projection Techniques mpactr Correction of Preprocessed MS Data mpath Regularized Linear Models mpmi Mixed-Pair Mutual Information Estimators mr.mashr Multiple Regression with Multivariate Adaptive Shrinkage mrMLM Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS mrMLM.GUI Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface mrbsizeR Scale Space Multiresolution Analysis of Random Signals mrddGlobal Global Testing for Multivariate Regression Discontinuity Designs mrf2d Markov Random Field Models for Image Analysis mrfDepth Depth Measures in Multivariate, Regression and Functional Settings mrfse Markov Random Field Structure Estimator mrgsolve Simulate from ODE-Based Models mritc MRI Tissue Classification mrtsSphere Multi-Resolution Thin-Plate Splines on the Sphere msPCA Sparse Principal Component Analysis with Multiple Principal Components msce Hazard of Multi-Stage Clonal Expansion Models msda Multi-Class Sparse Discriminant Analysis msde Bayesian Inference for Multivariate Stochastic Differential Equations msentropy Spectral Entropy for Mass Spectrometry Data msgps Degrees of Freedom of Elastic Net, Adaptive Lasso and Generalized Elastic Net msm Multi-State Markov and Hidden Markov Models in Continuous Time mssearchr Library Search Against Electron Ionization Mass Spectral Databases mstate Data Preparation, Estimation and Prediction in Multi-State Models mtdesign Mander and Thompson Designs muhaz Hazard Function Estimation in Survival Analysis mulea Enrichment Analysis Using Multiple Ontologies and False Discovery Rate multbxxc Auxiliary Routines for Influx Software multgee GEE Solver for Correlated Nominal or Ordinal Multinomial Responses multiRL Reinforcement Learning Tools for Multi-Armed Bandit multiScaleR Methods for Optimizing Scales of Effect multiblock Multiblock Data Fusion in Statistics and Machine Learning multibridge Evaluating Multinomial Order Restrictions with Bridge Sampling multicool Permutations of Multisets in Cool-Lex Order multilevLCA Estimates and Plots Single-Level and Multilevel Latent Class Models multilink Multifile Record Linkage and Duplicate Detection multimark Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks multimode Mode Testing and Exploring multinet Analysis and Mining of Multilayer Social Networks multinets Multilevel Networks Analysis multinomialLogitMix Clustering Multinomial Count Data under the Presence of Covariates multinomineq Bayesian Inference for Multinomial Models with Inequality Constraints multipleDL Addressing Detection Limits by Cumulative Probability Models (CPMs) multipleOutcomes Joint Covariance and Treatment-Effect Tests for Multiple Outcomes multiscape Multi-Objective Spatial Planning multispatialCCM Multispatial Convergent Cross Mapping multitaper Spectral Analysis Tools using the Multitaper Method multivar Penalized Estimation of Multiple-Subject Vector Autoregressive Models multivariance Measuring Multivariate Dependence Using Distance Multivariance multiview Cooperative Learning for Multi-View Analysis multtest Resampling-based multiple hypothesis testing mums2 Microbial Ecology by Tandem Mass Spectrometry muscle Multiple Sequence Alignment with MUSCLE muse Multiple Unobserved Sources of Error State Space Models mutualinf Computation and Decomposition of the Mutual Information Index mvLSW Multivariate, Locally Stationary Wavelet Process Estimation mvMAPIT Multivariate Genome Wide Marginal Epistasis Test mvMORPH Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data mvPot Multivariate Peaks-over-Threshold Modelling for Spatial Extreme Events mvabund Statistical Methods for Analysing Multivariate Abundance Data mvgam Multivariate (Dynamic) Generalized Additive Models mvgb Multivariate Probabilities of Scale Mixtures of Multivariate Normal Distributions via the Genz and Bretz (2002) QRSVN Method mvna Nelson-Aalen Estimator of the Cumulative Hazard in Multistate Models mvnfast Fast Multivariate Normal and Student's t Methods mvnimpute Simultaneously Impute the Missing and Censored Values mvnmle ML Estimation for Multivariate Normal Data with Missing Values mvord Multivariate Ordinal Regression Models mvp Fast Symbolic Multivariate Polynomials mvrsquared Compute the Coefficient of Determination for Vector or Matrix Outcomes mvst Bayesian Inference for the Multivariate Skew-t Model mvtnorm Multivariate Normal and t Distributions mwcsr Solvers for Maximum Weight Connected Subgraph Problem and Its Variants mx.crypto Matrix End-to-End Encryption Primitives mxsem Specify 'OpenMx' Models with a 'lavaan'-Style Syntax myTAI Evolutionary Transcriptomics mzR parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) n1qn1 Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS Optimization nQuack Predicting Ploidal Level from Sequence Data nVennR2 An Interface to 'nVenn2' nabor Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions nadiv (Non)Additive Genetic Relatedness Matrices nametagger Named Entity Recognition in Texts using 'NameTag' nandb Number and Brightness Image Analysis nanoarrow Interface to the 'nanoarrow' 'C' Library nanonext Lightweight Toolkit for Messaging, Concurrency and the Web nanoparquet Read and Write 'Parquet' Files nanotime Nanosecond-Resolution Time Support for R nara Native Raster Image Tools narray Subset- And Name-Aware Array Utility Functions naryn Native Access Medical Record Retriever for High Yield Analytics natcpp Fast C++ Primitives for the 'NeuroAnatomy Toolbox' nativeORT Native R 'ONNX' Runtime natural Estimating the Error Variance in a High-Dimensional Linear Model navigation Analyze the Impact of Sensor Error Modelling on Navigation Performance nbody Gravitational N-Body Simulation nbpMatching Functions for Optimal Non-Bipartite Matching ncdf4 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files ncvreg Regularization Paths for SCAD and MCP Penalized Regression Models ndjson Wicked-Fast Streaming 'JSON' ('ndjson') Reader ndl Naive Discriminative Learning neatRanges Tidy Up Date/Time Ranges nebula Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data negenes Estimating the Number of Essential Genes in a Genome neojags Neo-Normal Distributions Family for Markov Chain Monte Carlo (MCMC) Models in 'JAGS' netClust Model-Based Clustering of Network Data netUtils A Collection of Tools for Network Analysis netdiffuseR Analysis of Diffusion and Contagion Processes on Networks netgsa Network-Based Gene Set Analysis netify Tools for Network Data Workflows netrankr Analyzing Partial Rankings in Networks nett Network Analysis and Community Detection network Classes for Relational Data networkABC Network Reverse Engineering with Approximate Bayesian Computation networkDynamic Dynamic Extensions for Network Objects networkR Network Analysis and Visualization neuRosim Simulate fMRI Data neuralnetwork Fast Compact Multilayer Perceptrons neuroim Data Structures and Handling for Neuroimaging Data neuroim2 Data Structures for Brain Imaging Data nevada Network-Valued Data Analysis nfer Event Stream Abstraction using Interval Logic nftbart Nonparametric Failure Time Bayesian Additive Regression Trees ngme2 Linear Latent Non-Gaussian Models with Flexible Distributions ngram Fast n-Gram 'Tokenization' ngspatial Fitting the Centered Autologistic and Sparse Spatial Generalized Linear Mixed Models for Areal Data nhlscraper Scraper for National Hockey League Data nhm Non-Homogeneous Markov and Hidden Markov Multistate Models nhppp Simulating Nonhomogeneous Poisson Point Processes niaidMI Markov Model Multiple Imputation for NIAID OS niarules Numerical Association Rule Mining using Population-Based Nature-Inspired Algorithms nice Get or Set UNIX Niceness nieve Miscellaneous Utilities for Extreme Value Analysis nilsier Design-Based Estimators for NILS nimble MCMC, Particle Filtering, and Programmable Hierarchical Modeling nleqslv Solve Systems of Nonlinear Equations nlmeVPC Visual Model Checking for Nonlinear Mixed Effect Model nlmixr2est Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines nlmixr2extra Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions nlmixr2save Save 'nlmixr2' Fits in a Format Readable Outside 'nlmixr2' nlmm Generalized Laplace Mixed-Effects Models nloptr R Interface to NLopt nltm Non-Linear Transformation Models nmathopencl 'OpenCL'-Ported R 'Mathlib' for GPU-Accelerated Packages nmixgof Goodness of Fit Checks for Binomial N-Mixture Models nmslibR Non Metric Space (Approximate) Library nn2poly Neural Network Weights Transformation into Polynomial Coefficients nngeo k-Nearest Neighbor Join for Spatial Data nnlib2Rcpp A Tool for Creating Custom Neural Networks in C++ and using Them in R nnls The Lawson-Hanson Algorithm for Non-Negative Least Squares (NNLS) nnmf Nonnegative Matrix Factorization nnsolve Fast Non-Negative Least Squares nntmvn Draw Samples of Truncated Multivariate Normal Distributions nodeSub Simulate DNA Alignments Using Node Substitutions nomclust Hierarchical Cluster Analysis of Nominal Data noncompliance Causal Inference in the Presence of Treatment Noncompliance Under the Binary Instrumental Variable Model nonlinearTseries Nonlinear Time Series Analysis nonmem2rx Converts 'NONMEM' Models to 'rxode2' nonneg.cg Non-Negative Conjugate-Gradient Minimizer nonprobsvy Inference Based on Non-Probability Samples nopaco Non-Parametric Concordance Coefficient norm Analysis of Multivariate Normal Datasets with Missing Values nortestARMA Neyman Smooth Tests of Normality for the Errors of ARMA Models not Narrowest-Over-Threshold Change-Point Detection np Nonparametric Kernel Smoothing Methods for Mixed Data Types npROCRegression Kernel-Based Nonparametric ROC Regression Modelling npRmpi Parallel Nonparametric Kernel Smoothing Methods for Mixed Data Types Using 'MPI' npbr Nonparametric Boundary Regression npcp Some Nonparametric CUSUM Tests for Change-Point Detection in Possibly Multivariate Observations npcure Nonparametric Estimation in Mixture Cure Models npiv Nonparametric Instrumental Variables Estimation and Inference npregfast Nonparametric Estimation of Regression Models with Factor-by-Curve Interactions nprobust Kernel Density and Local Polynomial Regression Methods npsf Nonparametric and Stochastic Efficiency and Productivity Analysis npsp Nonparametric Spatial Statistics nse Numerical Standard Errors Computation in R nuggets Extensible Framework for Data Pattern Exploration nullcat Null Models for Categorical and Continuous Community Matrices numOSL Numeric Routines for Optically Stimulated Luminescence Dating numbat Haplotype-Aware CNV Analysis from scRNA-Seq numberofalleles Compute the Probability Distribution of the Number of Alleles in a DNA Mixture nvmix Multivariate Normal Variance Mixtures nwsrfsr NWS Hydrology Models: SAC-SMA, SNOW17, UH, CONSUSE, CHANLOSS o2geosocial Reconstruction of Transmission Chains from Surveillance Data o2plsda Multiomics Data Integration oaqc Computation of the Orbit-Aware Quad Census obliqueRSF Oblique Random Forests for Right-Censored Time-to-Event Data oc Optimal Classification Roll Call Analysis Software oce Analysis of Oceanographic Data ocf Ordered Correlation Forest odbc Connect to ODBC Compatible Databases (using the DBI Interface) odeGUTS Solve ODE for GUTS-RED-SD and GUTS-RED-IT Using Compiled Code oeli Some Utilities for Developing Data Science Software oem Orthogonalizing EM: Penalized Regression for Big Tall Data offlineChange Detect Multiple Change Points from Time Series ohenery Modeling of Ordinal Random Variables via Softmax Regression ohoegdm Ordinal Higher-Order Exploratory General Diagnostic Model for Polytomous Data olctools Open Location Code Handling in R oligo Preprocessing tools for oligonucleotide arrays ondisc Algorithms and Data Structures for Large Single-Cell Expression Matrices oneclust Maximum Homogeneity Clustering for Univariate Data onehot Fast Onehot Encoding for Data.frames onemap Construction of Genetic Maps in Experimental Crosses onion Octonions and Quaternions onlineCOV Online Change Point Detection in High-Dimensional Covariance Structure onlinePCA Online Principal Component Analysis onlineforecast Forecast Modelling for Online Applications onnxr Bindings to 'ONNX' Runtime ontologySimilarity Calculating Ontological Similarities opa An Implementation of Ordinal Pattern Analysis opdisDownsampling Optimal Distribution Preserving Down-Sampling of Bio-Medical Data openCR Open Population Capture-Recapture openair Tools for the Analysis of Air Pollution Data opencesp Generation and Evaluation of Synthetic Tabular Datasets opencltools 'OpenCL' Tools for R Package Developers opencv Bindings to 'OpenCV' Computer Vision Library opensimplex2 Generate Multi-Dimensional Open Simplex Noise openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL openxlsx Read, Write and Edit xlsx Files openxlsx2 Read, Write and Edit 'xlsx' Files oppr Optimal Project Prioritization optbin Optimal Binning of Data optiSel Optimum Contribution Selection and Population Genetics optimization Flexible Optimization of Complex Loss Functions with State and Parameter Space Constraints optmatch Functions for Optimal Matching opusminer OPUS Miner Algorithm for Filtered Top-k Association Discovery orbitr A Tidy Physics Engine for Building and Visualizing Orbital Simulations orbweaver Fast and Efficient Graph Data Structures orca Computation of Graphlet Orbit Counts in Sparse Graphs ordinal Regression Models for Ordinal Data ordinalClust Ordinal Data Clustering, Co-Clustering and Classification ordinalForest Ordinal Forests: Prediction and Variable Ranking with Ordinal Target Variables ordinalgmifs Ordinal Regression for High-Dimensional Data ordinalpattern Tests Based on Ordinal Patterns ore An R Interface to the Onigmo Regular Expression Library orf Ordered Random Forests orsk Converting Odds Ratio to Relative Risk in Cohort Studies with Partial Data Information orthoDr Semi-Parametric Dimension Reduction Models Using Orthogonality Constrained Optimization oscar Optimal Subset Cardinality Regression (OSCAR) Models Using the L0-Pseudonorm oskeyring Raw System Credential Store Access from R osktnorm A Moment-Targeting Normality Transformation Based on Tukey g-h Distribution osmdata Import 'OpenStreetMap' Data as Simple Features or Spatial Objects osmnxr Download, Model and Analyze 'OpenStreetMap' Street Networks osqp Quadratic Programming Solver using the 'OSQP' Library otelsdk R SDK and Exporters for OpenTelemetry ouch Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses outbreaker2 Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data outliertree Explainable Outlier Detection Through Decision Tree Conditioning outrigger Outrigger Regression overlap Estimates of Coefficient of Overlapping for Animal Activity Patterns pARI Permutation-Based All-Resolutions Inference pECV Entrywise Splitting Cross-Validation for Factor Models pEPA Tests of Equal Predictive Accuracy for Panels of Forecasts pGPx Pseudo-Realizations for Gaussian Process Excursions pMEM Predictive Moran's Eigenvector Maps pPCA Partial Principal Component Analysis of Partitioned Large Sparse Matrices pROC Display and Analyze ROC Curves pRSR Test of Periodicity using Response Surface Regression packcircles Circle Packing pacotest Testing for Partial Copulas and the Simplifying Assumption in Vine Copulas padr Quickly Get Datetime Data Ready for Analysis pagoda2 Single Cell Analysis and Differential Expression pairscale Pairwise Rescaling of Numeric Matrices pak Another Approach to Package Installation palm Fitting Point Process Models via the Palm Likelihood palsr Projected Actor Locations for Spatial Interaction Modeling pan Multiple Imputation for Multivariate Panel or Clustered Data pander An R 'Pandoc' Writer panelPomp Inference for Panel Partially Observed Markov Processes parTimeROC Parametric Time-Dependent Receiver Operating Characteristic parallelDist Parallel Distance Matrix Computation using Multiple Threads parallelly Enhancing the 'parallel' Package parallelpam Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data parglm Parallel GLM parma Portfolio Allocation and Risk Management Applications parmigene Parallel Mutual Information Estimation for Gene Network Reconstruction parseLatex Parse 'LaTeX' Code parsec Partial Orders in Socio-Economics parsedate Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats parsermd Formal Parser and Related Tools for R Markdown Documents particles A Graph Based Particle Simulator Based on D3-Force partition Agglomerative Partitioning Framework for Dimension Reduction partitions Additive Partitions of Integers party A Laboratory for Recursive Partytioning partykit A Toolkit for Recursive Partytioning parzer Parse Messy Geographic Coordinates pastboon Simulation of Parameterized Stochastic Boolean Networks patchDVI Package to Patch '.dvi' or '.synctex' Files patentr Access USPTO Bulk Data in Tidy Rectangular Format pathfindR Enrichment Analysis Utilizing Active Subnetworks pathling A Library for using 'Pathling' patternplot Versatile Pie Charts, Ring Charts, Bar Charts and Box Plots using Patterns, Colors and Images paws.common Paws Low-Level Amazon Web Services API pbatR Pedigree/Family-Based Genetic Association Tests Analysis and Power pbdMPI R Interface to MPI for HPC Clusters (Programming with Big Data Project) pbdSLAP Programming with Big Data -- Scalable Linear Algebra Packages pbdZMQ Programming with Big Data -- Interface to 'ZeroMQ' pbivnorm Vectorized Bivariate Normal CDF pbmcapply Tracking the Progress of Mc*pply with Progress Bar pbv Probabilities for Bivariate Normal Distribution pc Pattern Causality Analysis pcLasso Principal Components Lasso pcaL1 L1-Norm PCA Methods pcaMethods A collection of PCA methods pcaPP Robust PCA by Projection Pursuit pcadapt Fast Principal Component Analysis for Outlier Detection pcalg Methods for Graphical Models and Causal Inference pcaone Fast and Accurate Randomized Singular Value Decomposition Algorithms with 'PCAone' pccc Pediatric Complex Chronic Conditions pdInfoBuilder Platform Design Information Package Builder pdSpecEst An Analysis Toolbox for Hermitian Positive Definite Matrices pda Privacy-Preserving Distributed Algorithms pdc Permutation Distribution Clustering pdfCluster Cluster Analysis via Nonparametric Density Estimation pdftools Text Extraction, Rendering and Converting of PDF Documents pdist Partitioned Distance Function pdp Partial Dependence Plots pec Prediction Error Curves for Risk Prediction Models in Survival Analysis pecora Permutation Conditional Random Tests pedbp Pediatric Blood Pressure pedigree Pedigree Functions pedigreeTools Versatile Functions for Working with Pedigrees pedigreemm Pedigree-Based Mixed-Effects Models pedometrics Miscellaneous Pedometric Tools pegas Population and Evolutionary Genetics Analysis System pegs Pseudo-Expectation Gauss-Seidel pemultinom L1-Penalized Multinomial Regression with Statistical Inference penAFT Fit the Semiparametric Accelerated Failure Time Model with Elastic Net and Sparse Group Lasso Penalties penMSM Estimating Regularized Multi-state Models Using L1 Penalties penalized L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model penaltyLearning Penalty Learning penppml Penalized Poisson Pseudo Maximum Likelihood Regression pense Penalized Elastic Net S/MM-Estimator of Regression peperr Parallelised Estimation of Prediction Error peppm Piecewise Exponential Distribution with Random Time Grids permPATH Permutation Based Gene Expression Pathway Analysis perms Fast Permutation Computation permuco Permutation Tests for Regression, (Repeated Measures) ANOVA/ANCOVA and Comparison of Signals persistence Optimal Graph Partition using the Persistence personalized2part Two-Part Estimation of Treatment Rules for Semi-Continuous Data pexm Loading a JAGS Module for the Piecewise Exponential Distribution pg Polya Gamma Distribution Sampler pgKDEsphere Parametrically Guided Kernel Density Estimator for Spherical Data pgam Poisson-Gamma Additive Models pgdraw Generate Random Samples from the Polya-Gamma Distribution pgee.mixed Penalized Generalized Estimating Equations for Bivariate Mixed Outcomes pgenlibr 'PLINK' 2 Binary (.pgen) Reader pgmm Parsimonious Gaussian Mixture Models ph2bayes Bayesian Single-Arm Phase II Designs phacking Sensitivity Analysis for p-Hacking in Meta-Analyses phangorn Phylogenetic Reconstruction and Analysis phenex Auxiliary Functions for Phenological Data Analysis phenmod Auxiliary Functions for Phenological Data Processing, Modelling and Result Handling pheno Auxiliary Functions for Phenological Data Analysis phenofit Extract Remote Sensing Vegetation Phenology philentropy Similarity and Distance Quantification Between Probability Functions phinterval Set Operations on Time Intervals phonics Phonetic Spelling Algorithms phutil Persistence Homology Utilities phyclust Phylogenetic Clustering (Phyloclustering) phylobase Base Package for Phylogenetic Structures and Comparative Data phylocomr Interface to 'Phylocom' phylolm Phylogenetic Linear Regression phylopairs Comparative Analyses of Lineage-Pair Traits phylosem Phylogenetic Structural Equation Model phylosignal Exploring the Phylogenetic Signal in Continuous Traits phylotypr Classifying DNA Sequences to Taxonomic Groupings phylter Detect and Remove Outliers in Phylogenomics Datasets phyr Model Based Phylogenetic Analysis picante Integrating Phylogenies and Ecology picasso Sparse Learning with Convex and Concave Penalties picohdr Read, Write and Manipulate High Dynamic Range Images picreg Variable Selection using the Pivotal Information Criterion piglet Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes pikchr R Wrapper for 'pikchr' (PIC) Diagram Language pimeta Prediction Intervals for Random-Effects Meta-Analysis pingr Check if a Remote Computer is Up pintervals Model Agnostic Prediction Intervals pipeflow Fast Interactive Data Analysis Pipelines piqp R Interface to Proximal Interior Point Quadratic Programming Solver piton Parsing Expression Grammars in Rcpp pkgcache Cache 'CRAN'-Like Metadata and R Packages pkgdepends Package Dependency Resolution and Downloads pkgmatch Find R Packages Matching Either Descriptions or Other R Packages pkgstats Metrics of R Packages plac A Pairwise Likelihood Augmented Cox Estimator for Left-Truncated Data plantmix Genetic Study of Plant Mixtures plfm Probabilistic Latent Feature Analysis plgp Particle Learning of Gaussian Processes plier Implements the Affymetrix PLIER algorithm pliman Tools for Plant Image Analysis plmmr Penalized Linear Mixed Models for Correlated Data pln Polytomous Logit-Normit (Graded Logistic) Model Estimation plotHMM Plot Hidden Markov Models plotSEMM Graphing Nonlinear Relations Among Latent Variables from Structural Equation Mixture Models plotcli Command Line Interface Plotting plpoisson Prediction Limits for Poisson Distribution plsRglm Partial Least Squares Regression for Generalized Linear Models plssem Complex Partial Least Squares Structural Equation Modeling plugdensity Plug-in Kernel Density Estimation ply Bitboard Chess Engine plyr Tools for Splitting, Applying and Combining Data pmartR Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data pmclust Parallel Model-Based Clustering using Expectation-Gathering-Maximization Algorithm for Finite Mixture Gaussian Model png Read and write PNG images poLCA Polytomous Variable Latent Class Analysis poLCAParallel Polytomous Variable Latent Class Analysis Parallel poibin The Poisson Binomial Distribution poilog Poisson Lognormal and Bivariate Poisson Lognormal Distribution poisDoubleSamp Confidence Intervals with Poisson Double Sampling poisbinom A Faster Implementation of the Poisson-Binomial Distribution poismf Factorization of Sparse Counts Matrices Through Poisson Likelihood poissoned Poisson Disk Sampling in 2D and 3D poissonsuperlearner Poisson Super Learner policytree Policy Learning via Doubly Robust Empirical Welfare Maximization over Trees polspline Polynomial Spline Routines polyCub Cubature over Polygonal Domains polyRAD Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids polyapost Simulating from the Polya Posterior polyclip Polygon Clipping polykde Polyspherical Kernel Density Estimation polylabelr Find the Pole of Inaccessibility (Visual Center) of a Polygon polyqtlR QTL Analysis in Autopolyploid Bi-Parental F1 Populations polysat Tools for Polyploid Microsatellite Analysis polywog Bootstrapped Basis Regression with Oracle Model Selection pomdp Infrastructure for Partially Observable Markov Decision Processes (POMDP) pomdpSolve Interface to 'pomdp-solve' for Partially Observable Markov Decision Processes pomp Statistical Inference for Partially Observed Markov Processes pompp Presence-Only for Marked Point Process pooh Partial Orders and Relations poolfstat Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data pop.lion Models for Simulating Lion Populations pop.wolf Models for Simulating Wolf Populations popPCR Classify Digital PCR Droplets by Fitting Fluorescence Populations poppr Genetic Analysis of Populations with Mixed Reproduction popsom7 A Fast, User-Friendly Implementation of Self-Organizing Maps (SOMs) population Models for Simulating Populations poputils Demographic Analysis and Data Manipulation porridge Ridge-Type Penalized Estimation of a Potpourri of Models port4me Get the Same, Personal, Free 'TCP' Port over and over portvine Vine Based (Un)Conditional Portfolio Risk Measure Estimation poseticDataAnalysis Posetic Data Analysis postlink Post-Linkage Data Analysis potts Markov Chain Monte Carlo for Potts Models pow.int Binary Exponentiation ppcc Probability Plot Correlation Coefficient Test ppgmmga Projection Pursuit Based on Gaussian Mixtures and Evolutionary Algorithms ppmSuite A Collection of Models that Employ Product Partition Distributions as a Prior on Partitions pprof Modeling, Standardization and Testing for Provider Profiling pqrBayes Bayesian Penalized Quantile Regression pqrfe Penalized Quantile Regression with Fixed Effects praznik Tools for Information-Based Feature Selection and Scoring prcbench Testing Workbench for Precision-Recall Curves precrec Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves predictmeans Predicted Means for Linear and Semiparametric Models predtools Prediction Model Tools prefmod Utilities to Fit Paired Comparison Models for Preferences preprocessCore A collection of pre-processing functions presmoothedTP Presmoothed Landmark Aalen-Johansen Estimator of Transition Probabilities for Complex Multi-State Models prider Multiplexed Primer Design by Linear Set Coverage Approximation primerTree Visually Assessing the Specificity and Informativeness of Primer Pairs primes Fast Functions for Prime Numbers princurve Fit a Principal Curve in Arbitrary Dimension prioriactions Multi-Action Conservation Planning prioritizr Systematic Conservation Prioritization in R probe Sparse High-Dimensional Linear Regression with PROBE probout Unsupervised Multivariate Outlier Probabilities for Large Datasets processmapR Construct Process Maps Using Event Data processx Execute and Control System Processes proclhmm Latent Hidden Markov Models for Response Process Data procmaps Portable Address Space Mapping prodlim Product-Limit Estimation for Censored Event History Analysis profoc Probabilistic Forecast Combination Using CRPS Learning profvis Interactive Visualizations for Profiling R Code proj4 A simple interface to the PROJ.4 cartographic projections library projpred Projection Predictive Feature Selection propagate Propagation of Uncertainty prophet Automatic Forecasting Procedure prospectr Miscellaneous Functions for Processing and Sample Selection of Spectroscopic Data protViz Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics protoclust Hierarchical Clustering with Prototypes protolite Highly Optimized Protocol Buffer Serializers prototest Inference on Prototypes from Clusters of Features proximetricsR Spectral Preprocessing and Chemometric Calibration of NIR Sensors proxy Distance and Similarity Measures proxyC Computes Proximity in Large Sparse Matrices prqlr R Bindings for the 'prqlc' Rust Library ps List, Query, Manipulate System Processes psBayesborrow Bayesian Information Borrowing with Propensity Score Matching psSubpathway Flexible Identification of Phenotype-Specific Subpathways psbcGroup Penalized Parametric and Semiparametric Bayesian Survival Models with Shrinkage and Grouping Priors psbcSpeedUp Penalized Semiparametric Bayesian Cox Models pscl Political Science Computational Laboratory psd Adaptive, Sine-Multitaper Power Spectral Density and Cross Spectrum Estimation pseudoCure A Pseudo-Observations Approach for Analyzing Survival Data with a Cure Fraction pseudorank Pseudo-Ranks psgp Projected Spatial Gaussian Process Methods pslr Public Suffix List Engine psp Parameter Space Partitioning MCMC for Global Model Evaluation pspearman Spearman's Rank Correlation Test pspline Penalized Smoothing Splines psqn Partially Separable Quasi-Newton psvd Eigendecomposition, Singular-Values and the Power Method psychonetrics Structural Equation Modeling and Confirmatory Network Analysis psychotools Psychometric Modeling Infrastructure psychrolib Psychrometric Properties of Moist and Dry Air ptinpoly Point-in-Polyhedron Test (2D and 3D) ptw Parametric Time Warping publipha Bayesian Meta-Analysis with Publications Bias and P-Hacking pullword R Interface to Pullword Service pumBayes Bayesian Estimation of Probit Unfolding Models for Binary Preference Data puniform Meta-Analysis Methods Correcting for Publication Bias punycoder Unicode and Punycode Domain Name Processing pureseqtmr Predict Transmembrane Protein Topology purgeR Inbreeding-Purging Estimation in Pedigreed Populations purrr Functional Programming Tools purrrlyr Tools at the Intersection of 'purrr' and 'dplyr' pvEBayes Empirical Bayes Methods for Pharmacovigilance pvar Calculation and Application of p-Variation pwlmm PWIGLS for Two-Level Multivariate and Multilevel Linear Models pye Penalized Youden Index Estimator pyinit Pena-Yohai Initial Estimator for Robust S-Regression qGaussian The q-Gaussian Distribution qMRI Methods for Quantitative Magnetic Resonance Imaging ('qMRI') qVarSel Select Variables for Optimal Clustering qad Quantification of Asymmetric Dependence qap Heuristics for the Quadratic Assignment Problem (QAP) qbld Quantile Regression for Binary Longitudinal Data qbrms Quick Bayesian Regression Models Using 'INLA' with 'brms' Syntax qch Query Composite Hypotheses qcluster Clustering via Quadratic Scoring qfa Quantile-Frequency Analysis (QFA) of Time Series and Spline Quantile Regression (SQR) qfratio Moments and Distributions of Ratios of Quadratic Forms Using Recursion qgam Smooth Additive Quantile Regression Models qgg Statistical Tools for Quantitative Genetic Analyses qgraph Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation qif Quadratic Inference Function qlcal R Bindings to the Calendaring Functionality of 'QuantLib' qmd Quantification of Multivariate Dependence qmvs Queueing Model of Visual Search qoi Read and Write QOI Images qpcR Modelling and Analysis of Real-Time PCR Data qpdf Split, Combine and Compress PDF Files qpgraph Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data qqconf Creates Simultaneous Testing Bands for QQ-Plots qrencoder Quick Response Code (QR Code) / Matrix Barcode Creator qrjoint Joint Estimation in Linear Quantile Regression qrmtools Tools for Quantitative Risk Management qrng (Randomized) Quasi-Random Number Generators qs2 Efficient Serialization of R Objects qshap Fast Calculation of Feature Contributions in Boosting Trees qsplines Quaternions Splines qtl Tools for Analyzing QTL Experiments qtl2 Quantitative Trait Locus Mapping in Experimental Crosses qtl2convert Convert Data among QTL Mapping Packages qtl2ggplot Data Visualization for QTL Experiments qtl2pleio Testing Pleiotropy in Multiparental Populations quadprog Functions to Solve Quadratic Programming Problems quadrupen Sparse and Group Sparse Linear Models qualV Qualitative Validation Methods qualpalr Automatic Generation of Qualitative Color Palettes quanteda Quantitative Analysis of Textual Data quanteda.textmodels Scaling Models and Classifiers for Textual Data quanteda.textplots Plots for the Quantitative Analysis of Textual Data quanteda.textstats Textual Statistics for the Quantitative Analysis of Textual Data quantities Quantity Calculus for R Vectors quantreg Quantile Regression quantregForest Quantile Regression Forests quantregRanger Quantile Regression Forests for 'ranger' quantspec Quantile-Based Spectral Analysis of Time Series queuecomputer Computationally Efficient Queue Simulation quickPWCR Quickly Construct and Rate Large Binary Pairwised Comparisons quickblock Quick Threshold Blocking quickmatch Quick Generalized Full Matching quitefastmst Euclidean and Mutual Reachability Minimum Spanning Trees quollr Visualising How Nonlinear Dimension Reduction Warps Your Data qwraps2 Quick Wraps 2 r2pmml Convert R Models to 'PMML' r2sundials Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem r3PG Simulating Forest Growth using the 3-PG Model rAverage Parameter Estimation for the Averaging Model of Information Integration Theory rBDAT Implementation of BDAT Tree Taper Fortran Functions rBeta2009 The Beta Random Number and Dirichlet Random Vector Generating Functions rCausalMGM Scalable Causal Discovery and Model Selection on Mixed Datasets with 'rCausalMGM' rDEA Robust Data Envelopment Analysis (DEA) for R rEDM Empirical Dynamic Modeling ('EDM') rENA Epistemic Network Analysis rFerns Random Ferns Classifier rIACI Iberian Actuarial Climate Index Calculations rIsing High-Dimensional Ising Model Selection rJava Low-Level R to Java Interface rLFT Processing Linear Features rLTP R Interface to the 'LTP'-Cloud Service rLifting High-Performance Wavelet Lifting Transforms rMVP Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool rPref Database Preferences and Skyline Computation rSRD Sum of Ranking Differences Statistical Test rSpectral Spectral Modularity Clustering rTLS Tools to Process Point Clouds Derived from Terrestrial Laser Scanning rTRNG Advanced and Parallel Random Number Generation via 'TRNG' rTwig Realistic Quantitative Structure Models raceland Pattern-Based Zoneless Method for Analysis and Visualization of Racial Topography ragg Graphic Devices Based on AGG ragnar Retrieval-Augmented Generation (RAG) Workflows rags2ridges Ridge Estimation of Precision Matrices from High-Dimensional Data rainette The Reinert Method for Textual Data Clustering ramcmc Robust Adaptive Metropolis Algorithm ramsvm Reinforced Angle-Based Multicategory Support Vector Machines randnet Random Network Model Estimation, Selection and Parameter Tuning randomForest Breiman and Cutlers Random Forests for Classification and Regression randomForestRHF Random Hazard Forests randomForestSGT Random Forest Super Greedy Trees randomForestSRC Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC) randomLCA Random Effects Latent Class Analysis randomUniformForest Random Uniform Forests for Classification, Regression and Unsupervised Learning randomizr Easy-to-Use Tools for Common Forms of Random Assignment and Sampling randompack Fast Random Number Generation with Multiple Engines and Distributions randtoolbox Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests rangeBuilder Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons rangen Random Number Generators and Utilities ranger A Fast Implementation of Random Forests rankdist Distance Based Ranking Models ranktreeEnsemble Ensemble Models of Rank-Based Trees with Extracted Decision Rules rapidsplithalf A Fast Permutation-Based Split-Half Reliability Algorithm rappdirs Application Directories: Determine Where to Save Data, Caches, and Logs raptr Representative and Adequate Prioritization Toolkit in R rar Risk-Adjusted Regression rare Linear Model with Tree-Based Lasso Regularization for Rare Features raster Geographic Data Analysis and Modeling rasterKernelEstimates Kernel Based Estimates on in-Memory Raster Images ratematrix Bayesian Estimation of the Evolutionary Rate Matrix ravetools Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data raybevel Generates Polygon Straight Skeletons and 3D Bevels rayimage Image Processing for Simulated Cameras rayrender Build and Raytrace 3D Scenes rayshader Create Maps and Visualize Data in 2D and 3D rayvertex 3D Software Rasterizer rbacon Age-Depth Modelling using Bayesian Statistics rbedrock Analysis and Manipulation of Data from Minecraft Bedrock Edition rbibutils Read 'Bibtex' Files and Convert Between Bibliography Formats rbiom Integrated Analysis and Visualization of Microbiome Data rbm25 A Light Wrapper Around the 'BM25' 'Rust' Crate for Okapi BM25 Text Search rbscCI Blyth-Still-Casella Confidence Interval rcccd Class Cover Catch Digraph Classification rcdd Computational Geometry rcppmlpackexamples Example Use of 'mlpack' from C++ via R rcpptimer 'Rcpp' Tic-Toc Timer with 'OpenMP' Support rdist Calculate Pairwise Distances rdoxygen Create Doxygen Documentation for Source Code rdtools Efficient Manipulation of 'Rd' Files and Help Topics rdyncall Improved Foreign Function Interface and Dynamic Bindings to C Libraries re2 R Interface to Google RE2 (C++) Regular Expression Library reReg Recurrent Event Regression read.gt3x Parse 'ActiGraph' 'GT3X'/'GT3X+' 'Accelerometer' Data readNSx Read 'Blackrock-Microsystems' Files ('NEV', 'NSx') readODS Read and Write ODS Files readobj Fast Reader for 'Wavefront' OBJ 3D Scene Files readr Read Rectangular Text Data readsdmx Read SDMX-XML Data readsparse Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM' Formats readstata13 Import 'Stata' Data Files readtextgrid Read in a 'Praat' 'TextGrid' File readxl Read Excel Files ream Density, Distribution, and Sampling Functions for Evidence Accumulation Models rebmix Finite Mixture Modeling, Clustering & Classification recexcavAAR 3D Reconstruction of Archaeological Excavations reclin2 Record Linkage Toolkit recmap Compute the Rectangular Statistical Cartogram recometrics Evaluation Metrics for Implicit-Feedback Recommender Systems reconstructr Session Reconstruction and Analysis recor Rearrangement Correlation Coefficient recosystem Recommender System using Matrix Factorization rectpacker Rectangle Packing recurse Computes Revisitation Metrics for Trajectory Data reda Recurrent Event Data Analysis redatam Import 'REDATAM' Files redatamx R Interface to 'Redatam' Library redeem Relational Event and Durational Event Models redist Simulation Methods for Legislative Redistricting redistmetrics Redistricting Metrics redland RDF Library Bindings in R redux R Bindings to 'hiredis' reems Estimating Effective Migration Surfaces from Single Nucleotide Polymorphism Data refinr Cluster and Merge Similar Values Within a Character Vector registr Curve Registration for Exponential Family Functional Data reglogit Simulation-Based Regularized Logistic Regression regmed Regularized Mediation Analysis regmhmm 'regmhmm' Fits Hidden Markov Models with Regularization regnet Network-Based Regularization for Generalized Linear Models regsem Regularized Structural Equation Modeling rehh Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests relSim Relative Simulator relevent Relational Event Models relsurv Relative Survival rema Rare Event Meta Analysis remaCor Random Effects Meta-Analysis for Correlated Test Statistics remify Processing and Transforming Relational Event History Data remote Empirical Orthogonal Teleconnections in R remotePARTS Spatiotemporal Autoregression Analyses for Large Data Sets remstats Computes Statistics for Relational Event History Data remstimate Optimization Frameworks for Tie-Oriented and Actor-Oriented Relational Event Models remulate Simulate Dynamic Networks from Relational Event Models renv Project Environments repeated Non-Normal Repeated Measurements Models repfdr Replicability Analysis for Multiple Studies of High Dimension repolr Repeated Measures Proportional Odds Logistic Regression representr Create Representative Records After Entity Resolution repsim Measures of Representational Similarity Across Models reqres Powerful Classes for HTTP Requests and Responses resemble Similarity Retrieval and Local Learning for Spectral Chemometrics reservr Fit Distributions and Neural Networks to Censored and Truncated Data resevol Simulate Agricultural Production and Evolution of Pesticide Resistance reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package resourcecode Access to the 'RESOURCECODE' Hindcast Database restfulr R Interface to RESTful Web Services rethnicity Predicting Ethnic Group from Names reticulate Interface to 'Python' retistruct Retinal Reconstruction Program revdbayes Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis revealedPrefs Revealed Preferences and Microeconomic Rationality revss Robust Estimation in Very Small Samples rexpokit R Wrappers for EXPOKIT; Other Matrix Functions rflexscan The Flexible Spatial Scan Statistic rformat Base R Code Formatter rgenoud R Version of GENetic Optimization Using Derivatives rgeoda R Library for Spatial Data Analysis rgeomorphon A Lightweight Implementation of the 'Geomorphon' Algorithm rgl 3D Visualization Using OpenGL rgl2gltf Read and Write '.gltf' and '.glb' Files rgm Advanced Inference with Random Graphical Models rgraph6 Representing Graphs as 'graph6', 'digraph6' or 'sparse6' Strings rhdf5filters HDF5 Compression Filters rheroicons A Zero Dependency 'SVG' Icon Library for 'Shiny' rhoR Rho for Inter Rater Reliability ribiosArg Argument Handling for Command-Line, Stand-Alone R Scripts ribiosIO Input/Output Utilities of the 'ribios' Suite ribiosMath Mathematical and Statistical Tools in 'ribios' ribiosUtils Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library richCluster Fast, Robust Clustering Algorithms for Gene Enrichment Data rid Multiple Change-Point Detection in Multivariate Time Series ridge Ridge Regression with Automatic Selection of the Penalty Parameter ridgeBART Bayesian Additive Regression Trees with Ridge Function Outputs ridgetorus PCA on the Torus via Density Ridges riemtan Riemannian Metrics for Symmetric Positive Definite Matrices rim Interface to 'Maxima', Enabling Symbolic Computation ring Circular / Ring Buffers rioja Analysis of Quaternary Science Data rip.opencv Interface to 'OpenCV' Image Processing Routines ripserr Calculate Persistent Homology with Ripser-Based Engines riskParityPortfolio Design of Risk Parity Portfolios riskRegression Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks rivnet Extract and Analyze Rivers from Elevation Data rivr Steady and Unsteady Open-Channel Flow Computation rjaf Regularized Joint Assignment Forest with Treatment Arm Clustering rjags Bayesian Graphical Models using MCMC rje Miscellaneous Useful Functions for Statistics rjson JSON for R rjsoncons Query, Pivot, Patch, and Validate 'JSON' and 'NDJSON' rkriging Kriging Modeling rkvo Read Key/Value Pair Observations rlang Functions for Base Types and Core R and 'Tidyverse' Features rle Common Functions for Run-Length Encoded Vectors rlecuyer R Interface to RNG with Multiple Streams rlemon R Access to LEMON Graph Algorithms rlfsm Simulations and Statistical Inference for Linear Fractional Stable Motions rlibkriging Kriging Models using the 'libKriging' Library rliger Linked Inference of Genomic Experimental Relationships rly Tools to Create Formal Language Parser rmarchingcubes Calculate 3D Contour Meshes Using the Marching Cubes Algorithm rmargint Robust Marginal Integration Procedures rmatio Read and Write 'Matlab' Files rmgarch Multivariate GARCH Models rminqa Derivative-Free Optimization in R using C++ rmonocypher Easy Encryption of R Objects using Strong Modern Cryptography rmp Rounded Mixture Package rms Regression Modeling Strategies rmsb Bayesian Regression Modeling Strategies rmsfuns Quickly View Data Frames in 'Excel', Build Folder Paths and Create Date Vectors rmumps Wrapper for MUMPS Library rmutil Utilities for Nonlinear Regression and Repeated Measurements Models rncl An Interface to the Nexus Class Library rnetcarto Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R) rngWELL Toolbox for WELL Random Number Generators rnndescent Nearest Neighbor Descent Method for Approximate Nearest Neighbors robCompositions Compositional Data Analysis robStepSplitReg Robust Stepwise Split Regularized Regression robcat Robust Categorical Data Analysis robcp Robust Change-Point Tests roben Robust Bayesian Variable Selection for Gene-Environment Interactions robfilter Robust Time Series Filters robmixglm Robust Generalized Linear Models (GLM) using Mixtures roboBayes Robust Online Bayesian Monitoring robregcc Robust Regression with Compositional Covariates robscale Accelerated Estimation of Robust Location and Scale robsel Robust Selection Algorithm robslopes Fast Algorithms for Robust Slopes robsurvey Robust Survey Statistics Estimation robusTest Calibrated Correlation and Two-Sample Tests robust Port of the S+ "Robust Library" robust.prioritizr Robust Systematic Conservation Prioritization robustETM Robust Methods using Exponential Tilt Model robustHD Robust Methods for High-Dimensional Data robustSFA Robust Estimation of Stochastic Frontier Models with MDPDE robustarima Robust ARIMA Modeling robustbase Basic Robust Statistics robustlmm Robust Linear Mixed Effects Models robustmatrix Robust Matrix-Variate Parameter Estimation robustrank Robust Rank-Based Tests robustreg Robust Regression Functions robustvarComp Robust Estimation of Variance Component Models rococo Robust Rank Correlation Coefficient and Test rofanova Robust Functional Analysis of Variance roll Rolling and Expanding Statistics rolleigen Rolling Eigenanalysis rollinglda Construct Consistent Time Series from Textual Data rolloptim Rolling Optimizations rollshap Rolling Shapley Values rolog Query 'SWI'-'Prolog' from R rootSolve Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations rootWishartHD Exact and Log-Scale Tail Probabilities for Roy's Largest Root roptim General Purpose Optimization in R using C++ rotasym Tests for Rotational Symmetry on the Hypersphere rotations Working with Rotation Data round Rounding to Decimal Digits roxigraph 'RDF' and 'SPARQL' for R using 'Oxigraph' roxygen2 In-Line Documentation for R rpact Confirmatory Adaptive Clinical Trial Design and Analysis rpart.LAD Least Absolute Deviation Regression Trees rpc Ridge Partial Correlation rpf Response Probability Functions rpic The 'pic' Graphics Language Rendered to SVG, PNG and PDF rpm Modeling of Revealed Preferences Matchings rpms Recursive Partitioning for Modeling Survey Data rpql Regularized PQL for Joint Selection in GLMMs rqPen Penalized Quantile Regression rr Statistical Methods for the Randomized Response Technique rrMixture Reduced-Rank Mixture Models rrandvec Generate Random Vectors Whose Components Sum Up to One rrapply Revisiting Base Rapply rrcov Scalable Robust Estimators with High Breakdown Point rrcovHD Robust Multivariate Methods for High Dimensional Data rrcovNA Scalable Robust Estimators with High Breakdown Point for Incomplete Data rres Realized Relatedness Estimation and Simulation rrnni Manipulate with RNNI Tree Space rrpack Reduced-Rank Regression rrstools Analyzing RoboCupRescue Simulation Data rrum Bayesian Estimation of the Reduced Reparameterized Unified Model with Gibbs Sampling rsae Robust Small Area Estimation rsamplr Sampling Algorithms and Spatially Balanced Sampling rsdepth Ray Shooting Depth (i.e. RS Depth) Functions for Bivariate Analysis rsgl An Implementation of the 'SGL' Graphics Language rshift Paleoecology Functions for Regime Shift Analysis rsides SIDES-Based Subgroup Search Algorithms rsixel Encoding and Decoding Sixel Images rsocsim SOCSIM rsofun The P-Model and BiomeE Modelling Framework rspa Adapt Numerical Records to Fit (in)Equality Restrictions rsparse Statistical Learning on Sparse Matrices rspdlite R and C++ Interfaces to 'spdlite' C++ Header Library for Logging rstan R Interface to Stan rstanarm Bayesian Applied Regression Modeling via Stan rstanbdp Bayesian Deming Regression for Method Comparison rstiefel Random Orthonormal Matrix Generation and Optimization on the Stiefel Manifold rstpm2 Smooth Survival Models, Including Generalized Survival Models rstream Streams of Random Numbers rsvddpd Robust Singular Value Decomposition using Density Power Divergence rsvg Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or Bitmap Arrays rswipl Embed 'SWI'-'Prolog' rsyslog Interface to the 'syslog' System Logger rtdists Response Time Distributions rtestim Estimate the Effective Reproductive Number with Trend Filtering rtiktoken A Byte-Pair-Encoding (BPE) Tokenizer for OpenAI's Large Language Models rtk Rarefaction Tool Kit rtmpt Fitting (Exponential/Diffusion) RT-MPT Models rtop Interpolation of Data with Variable Spatial Support rtrees Deriving Phylogenies from Synthesis Trees rtrend Trend Estimating Tools rucrdtw R Bindings for the UCR Suite rugarch Univariate GARCH Models runjags Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS runner Running Operations for Vectors rupturesRcpp Object-Oriented Interface for Offline Change-Point Detection rush Rapid Asynchronous and Distributed Computing rust Ratio-of-Uniforms Simulation with Transformation ruv Detect and Remove Unwanted Variation using Negative Controls rvMF Fast Generation of von Mises-Fisher Distributed Pseudo-Random Vectors rvalues R-Values for Ranking in High-Dimensional Settings rvg R Graphics Devices for 'Office' Vector Graphics Output rvinecopulib High Performance Algorithms for Vine Copula Modeling rwfec R Wireless, Forward Error Correction rwig Wasserstein Index Generation (WIG) Model rxode2 Facilities for Simulating from ODE-Based Models rxode2ll Log-Likelihood Functions for 'rxode2' rxylib Import XY-Data into R rzmq R Bindings for 'ZeroMQ' s2 Spherical Geometry Operators Using the S2 Geometry Library s2net The Generalized Semi-Supervised Elastic-Net sBIC Computing the Singular BIC for Multiple Models sacRebleu Metrics for Assessing the Quality of Generated Text saccadr Extract Saccades via an Ensemble of Methods Approach sads Maximum Likelihood Models for Species Abundance Distributions saeHB.TF.beta SAE using HB Twofold Subarea Model under Beta Distribution saeRobust Robust Small Area Estimation saeczi Small Area Estimation for Continuous Zero Inflated Data sakura Extension to R Serialization salso Search Algorithms and Loss Functions for Bayesian Clustering samc Spatial Absorbing Markov Chains samon Sensitivity Analysis for Missing Data sampling Survey Sampling samplingVarEst Sampling Variance Estimation samplr Compare Human Performance to Sampling Algorithms samr SAM: Significance Analysis of Microarrays sanba Fitting Shared Atoms Nested Models via MCMC or Variational Bayes sanic Solving Ax = b Nimbly in C++ sanitizers C/C++ Source Code to Trigger Address and Undefined Behaviour Sanitizers sarima Simulation and Prediction with Seasonal ARIMA Models sarsop Approximate POMDP Planning Software sass Syntactically Awesome Style Sheets ('Sass') satdad Sensitivity Analysis Tools for Dependence and Asymptotic Dependence satellite Handling and Manipulating Remote Sensing Data sbde Semiparametric Bayesian Density Estimation sbfc Selective Bayesian Forest Classifier sbim Simulation-Based Inference using a Metamodel for Log-Likelihood Estimator sbm Stochastic Blockmodels sbmSDP Semidefinite Programming for Fitting Block Models of Equal Block Sizes sboost Machine Learning with AdaBoost on Decision Stumps sbrl Scalable Bayesian Rule Lists Model scDHA Single-Cell Decomposition using Hierarchical Autoencoder scINSIGHT Interpretation of Heterogeneous Single-Cell Gene Expression Data scITD Single-Cell Interpretable Tensor Decomposition scModels Fitting Discrete Distribution Models to Count Data scalablebayesm Distributed Markov Chain Monte Carlo for Bayesian Inference in Marketing scam Shape Constrained Additive Models scanstatistics Space-Time Anomaly Detection using Scan Statistics scar Shape-Constrained Additive Regression: a Maximum Likelihood Approach scattermore Scatterplots with More Points scclust Size-Constrained Clustering sccore Core Utilities for Single-Cell RNA-Seq scellpam Applying Partitioning Around Medoids to Single Cell Data with High Number of Cells sceua Shuffled Complex Evolution Algorithm for Optimization schoolmath Functions and Datasets for Math Used in School scip Interface to the SCIP Optimization Suite scistreer Maximum-Likelihood Perfect Phylogeny Inference at Scale scoper Spectral Clustering-Based Method for Identifying B Cell Clones scoredec S-Core Graph Decomposition scorematchingad Score Matching Estimation by Automatic Differentiation scorepeak Peak Functions for Peak Detection in Univariate Time Series scoringRules Scoring Rules for Parametric and Simulated Distribution Forecasts scout Implements the Scout Method for Covariance-Regularized Regression scquantum Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing scran Methods for Single-Cell RNA-Seq Data Analysis scregclust Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data scrm Simulating the Evolution of Biological Sequences scrypt Key Derivation Functions for R Based on Scrypt scs Splitting Conic Solver sctransform Variance Stabilizing Transformations for Single Cell UMI Data scuba Diving Calculations and Decompression Models scuttle Legacy Utilities for Single-Cell RNA-Seq Analysis sd2R Stable Diffusion Image Generation sdcHierarchies Create and (Interactively) Modify Nested Hierarchies sdcMicro Statistical Disclosure Control Methods for Anonymization of Data and Risk Estimation sdcSpatial Statistical Disclosure Control for Spatial Data sdcTable Methods for Statistical Disclosure Control in Tabular Data sde Simulation and Inference for Stochastic Differential Equations sdetorus Statistical Tools for Toroidal Diffusions sdim An R Package for Supervised Dimension Reduction sdmTMB Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB' sdprisk Measures of Risk for the Compound Poisson Risk Process with Diffusion sdrt Estimating the Sufficient Dimension Reduction Subspaces in Time Series sdsfun Spatial Data Science Complementary Features sdwd Sparse Distance Weighted Discrimination seas Seasonal Analysis and Graphics, Especially for Climatology secr Spatially Explicit Capture-Recapture secrdesign Sampling Design for Spatially Explicit Capture-Recapture secretbase Cryptographic Hash Functions and Data Encoding secrfunc Helper Functions for Package 'secr' secsse Several Examined and Concealed States-Dependent Speciation and Extinction seededlda Seeded Sequential LDA for Topic Modeling segMGarch Multiple Change-Point Detection for High-Dimensional GARCH Processes segclust2d Bivariate Segmentation/Clustering Methods and Tools segmag Determine Event Boundaries in Event Segmentation Experiments segmenTier Similarity-Based Segmentation of Multidimensional Signals segmentr Segment Data With Maximum Likelihood segregation Entropy-Based Segregation Indices segtest Tests for Segregation Distortion in Polyploids seine Semiparametric Ecological Inference seismicRoll Fast Rolling Functions for Seismology using 'Rcpp' selection.index Analysis of Selection Index in Plant Breeding selectiveInference Tools for Post-Selection Inference sem Structural Equation Models semaphore Shared Memory Atomic Operations semidist Measure Dependence Between Categorical and Continuous Variables semver 'Semantic Versioning V2.0.0' Parser sensitivity Global Sensitivity Analysis of Model Outputs and Importance Measures sensitivityIxJ Exact Nonparametric Sensitivity Analysis for I by J Contingency Tables sensobol Computation of Variance-Based Sensitivity Indices sentencepiece Text Tokenization using Byte Pair Encoding and Unigram Modelling sentometrics An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction sentopics Tools for Joint Sentiment and Topic Analysis of Textual Data seq2R Simple Method to Detect Compositional Changes in Genomic Sequences seqHMM Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series seqinr Biological Sequences Retrieval and Analysis seqminer Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R seqtrie Radix Tree and Trie-Based String Distances sequoia Pedigree Inference from SNPs seriation Infrastructure for Ordering Objects Using Seriation serocalculator Estimating Infection Rates from Serological Data serofoi Bayesian Estimation of the Force of Infection from Serological Data seroreconstruct Reconstructing Antibody Dynamics to Estimate the Risk of Influenza Virus Infection serosv Model Infectious Disease Parameters from Serosurveys serrsBayes Bayesian Modelling of Raman Spectroscopy sets Sets, Generalized Sets, Customizable Sets and Intervals setwidth Automatically Set the Width Option on Terminal Emulators sf Simple Features for R sfa Stochastic Frontier Analysis sfcr Simulate Stock-Flow Consistent Models sfcurve 2x2, 3x3 and Nxn Space-Filling Curves sffdr Surrogate Functional False Discovery Rates for Genome-Wide Association Studies sfheaders Converts Between R Objects and Simple Feature Objects sgd Stochastic Gradient Descent for Scalable Estimation sgdGMF Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent sgeostat An Object-Oriented Framework for Geostatistical Modeling in S+ sglasso Lasso Method for RCON(V,E) Models sgolay Efficient Savitzky-Golay Filtering sgs Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control shapr Prediction Explanation with Dependence-Aware Shapley Values shard Deterministic, Zero-Copy Parallel Execution for R sharpData Data Sharpening sharpPen Penalized Data Sharpening for Local Polynomial Regression sharpeRratio Moment-Free Estimation of Sharpe Ratios shide Date/Time Classes Based on Jalali Calendar shiftR Fast Enrichment Analysis via Circular Permutations shinytest2 Testing for Shiny Applications shortuuid Generate and Translate Standard UUIDs showtext Using Fonts More Easily in R Graphs shp2graph Convert a 'SpatialLinesDataFrame' -Class Object to an 'igraph'-Class Object shrinkDSM Efficient Bayesian Inference for Dynamic Survival Models with Shrinkage shrinkTVP Efficient Bayesian Inference for Time-Varying Parameter Models with Shrinkage shrinkTVPVAR Efficient Bayesian Inference for TVP-VAR-SV Models with Shrinkage shrinkem Approximate Bayesian Regularization for Parsimonious Estimates shrinkr Modular Bayesian Hierarchical Shrinkage Models sievePH Sieve Analysis Methods for Proportional Hazards Models sigminer Extract, Analyze and Visualize Mutational Signatures for Genomic Variations signal Signal Processing signalHsmm Predict Presence of Signal Peptides signnet Methods to Analyse Signed Networks simFrame Simulation Framework simPop Simulation of Complex Synthetic Data Information simRestore Simulate the Effect of Management Policies on Restoration Efforts simStateSpace Simulate Data from State Space Models simcdm Simulate Cognitive Diagnostic Model ('CDM') Data simcross Simulate Experimental Crosses simctest Safe Implementation of Monte Carlo Tests simecol Simulation of Ecological (and Other) Dynamic Systems simer Data Simulation for Life Science and Breeding simest Constrained Single Index Model Estimation simevent Simulation and Analysis of Event History Data simfam Simulate and Model Family Pedigrees with Structured Founders simlandr Simulation-Based Landscape Construction for Dynamical Systems simmer Discrete-Event Simulation for R simmr A Stable Isotope Mixing Model simplexgof Bootstrap-Calibrated Goodness-of-Fit Test for Simplex Regression simstudy Simulation of Study Data simtrial Clinical Trial Simulation simts Time Series Analysis Tools singR Simultaneous Non-Gaussian Component Analysis sirt Supplementary Item Response Theory Models sisireg Sign-Simplicity-Regression-Solver sitmo Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files sits Satellite Image Time Series Analysis for Earth Observation Data Cubes sketching Sketching of Data via Random Subspace Embeddings sklarsomega Measuring Agreement Using Sklar's Omega Coefficient skpr Design of Experiments Suite: Generate and Evaluate Optimal Designs skylight A Simple Sky Illuminance Model skymodelr Generates and Samples Realistic Terrestrial Atmospheres slam Sparse Lightweight Arrays and Matrices slasso S-LASSO Estimator for the Function-on-Function Linear Regression slca Structural Modeling for Multiple Latent Class Variables slcm Sparse Latent Class Model for Cognitive Diagnosis sld Estimation and Use of the Quantile-Based Skew Logistic Distribution sleev Semiparametric Likelihood Estimation with Errors in Variables slfm Fitting a Bayesian Sparse Latent Factor Model in Gene Expression Analysis slideimp Numeric Matrices K-NN and PCA Imputation slider Sliding Window Functions sm Smoothing Methods for Nonparametric Regression and Density Estimation smaa Stochastic Multi-Criteria Acceptability Analysis smacof Multidimensional Scaling smam Statistical Modeling of Animal Movements smarter A Collection of Modified R Functions to Make Basic Coding More Convenient smartsnp Fast Multivariate Analyses of Big Genomic Data smashr Smoothing by Adaptive Shrinkage smer Sparse Marginal Epistasis Test smerc Statistical Methods for Regional Counts smfishHmrf Hidden Markov Random Field for Spatial Transcriptomic Data smfsb Stochastic Modelling for Systems Biology smile Spatial Misalignment: Interpolation, Linkage, and Estimation smmR Simulation, Estimation and Reliability of Semi-Markov Models smoof Single and Multi-Objective Optimization Test Functions smooth Forecasting Using State Space Models smoothSurv Survival Regression with Smoothed Error Distribution smoothemplik Smoothed Empirical Likelihood smoots Nonparametric Estimation of the Trend and Its Derivatives in TS smriti Automated Routing Engine for Longitudinal Missing Data smurf Sparse Multi-Type Regularized Feature Modeling sna Tools for Social Network Analysis snic Superpixel Segmentation with the Simple Non-Iterative Clustering Algorithm snowboot Bootstrap Methods for Network Inference snpStats SnpMatrix and XSnpMatrix classes and methods snplist Tools to Create Gene Sets snpsettest A Set-Based Association Test using GWAS Summary Statistics snreg Regression with Skew-Normally Distributed Error Term sobol Quasi-Monte Carlo Sobol Sequence Generator socceR Evaluating Sport Tournament Predictions social Social Autocorrelation socratadata Explore Socrata Data with Ease sodium A Modern and Easy-to-Use Crypto Library softImpute Matrix Completion via Iterative Soft-Thresholded SVD som Self-Organizing Map sommer Solving Mixed Model Equations in R sorcering Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling Framework sourcetools Tools for Reading, Tokenizing and Parsing R Code sox Structured Learning in Time-Dependent Cox Models sp Classes and Methods for Spatial Data spAbundance Univariate and Multivariate Spatial Modeling of Species Abundance spBPS Bayesian Predictive Stacking for Scalable Geospatial Transfer Learning spBayes Univariate and Multivariate Spatial-Temporal Modeling spBayesSurv Bayesian Modeling and Analysis of Spatially Correlated Survival Data spCF Coarse-to-Fine Spatial Modeling spCP Spatially Varying Change Points spDBL Dynamic Bayesian Learning for Spatiotemporal Mechanistic Models spEDM Spatial Empirical Dynamic Modeling spFFBS Spatiotemporal Propagation for Multivariate Bayesian Dynamic Learning spGARCH Spatial ARCH and GARCH Models (spGARCH) spMC Continuous-Lag Spatial Markov Chains spNNGP Spatial Regression Models for Large Datasets using Nearest Neighbor Gaussian Processes spNetwork Spatial Analysis on Network spOccupancy Single-Species, Multi-Species, and Integrated Spatial Occupancy Models spStack Bayesian Geostatistics Using Predictive Stacking spTDyn Spatially Varying and Spatio-Temporal Dynamic Linear Models spTimer Spatio-Temporal Bayesian Modelling spaMM Mixed-Effect Models, with or without Spatial Random Effects spacc Fast Spatial Species Accumulation Curves spacefillr Space-Filling Random and Quasi-Random Sequences spam SPArse Matrix spam64 64-Bit Extension of the SPArse Matrix R Package 'spam' spant MR Spectroscopy Analysis Tools sparcl Perform Sparse Hierarchical Clustering and Sparse K-Means Clustering sparseDFM Estimate Dynamic Factor Models with Sparse Loadings sparseLM Interface to the 'sparseLM' Levenberg-Marquardt Library sparseLTSEigen RcppEigen back end for sparse least trimmed squares regression sparseMatrixStats Summary Statistics for Rows and Columns of Sparse Matrices sparseSEM Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework sparseSVM Solution Paths of Sparse High-Dimensional Support Vector Machine with Lasso or Elastic-Net Regularization sparseVCBART Sparse Varying Coefficient BART with Global-Local Priors" sparsediff R Interface to the 'SparseDiffEngine' Sparse Differentiation Backend sparsegl Sparse Group Lasso sparseinv Computation of the Sparse Inverse Subset sparselu Sparse LU Decomposition via SuiteSparse sparsenet Fit Sparse Linear Regression Models via Nonconvex Optimization sparsesvd Sparse Truncated Singular Value Decomposition (from 'SVDLIBC') sparsevb Spike-and-Slab Variational Bayes for Linear and Logistic Regression sparsevctrs Sparse Vectors for Use in Data Frames sparsio I/O Operations with Sparse Matrices sparta Sparse Tables sparvaride Variance Identification in Sparse Factor Analysis spass Study Planning and Adaptation of Sample Size spatPomp Inference for Spatiotemporal Partially Observed Markov Processes spate Spatio-Temporal Modeling of Large Data Using a Spectral SPDE Approach spatgraphs Graph Edge Computations for Spatial Point Patterns spaths Shortest Paths Between Points in Grids spatialGE Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression spatialising Ising Model for Spatial Data spatialreg Spatial Regression Analysis spatialsample Spatial Resampling Infrastructure spatialwarnings Spatial Early Warning Signals of Ecosystem Degradation spatialwidget Formats Spatial Data for Use in Htmlwidgets spatstat.Knet Extension to 'spatstat' for Large Datasets on a Linear Network spatstat.explore Exploratory Data Analysis for the 'spatstat' Family spatstat.geom Geometrical Functionality of the 'spatstat' Family spatstat.linnet Linear Networks Functionality of the 'spatstat' Family spatstat.model Parametric Statistical Modelling and Inference for the 'spatstat' Family spatstat.random Random Generation Functionality for the 'spatstat' Family spatstat.sparse Sparse Three-Dimensional Arrays and Linear Algebra Utilities spatstat.univar One-Dimensional Probability Distribution Support for the 'spatstat' Family spatstat.utils Utility Functions for 'spatstat' spbal Spatially Balanced Sampling Algorithms spboost Gradient Boosting for Nonlinear Spatial Autoregressive Models spc Statistical Process Control -- Calculation of ARL and Other Control Chart Performance Measures spca Least Squares Sparse Principal Components Analysis spcr Sparse Principal Component Regression spdep Spatial Dependence: Weighting Schemes, Statistics spduration Split-Population Duration (Cure) Regression speakeasyR Fast and Robust Multi-Scale Graph Clustering specs Single-Equation Penalized Error-Correction Selector (SPECS) sped Multi-Gene Descent Probabilities speedytax Rapidly Import Classifier Results into 'phyloseq' spexvb Parameter Expanded Variational Bayes for High-Dimensional Linear Regression spfa Semi-Parametric Factor Analysis spgs Statistical Patterns in Genomic Sequences spgwr Geographically Weighted Regression sphunif Uniformity Tests on the Circle, Sphere, and Hypersphere spiderbar Parse and Test Robots Exclusion Protocol Files and Rules spikeSlabGAM Bayesian Variable Selection and Model Choice for Generalized Additive Mixed Models spikeslab Prediction and Variable Selection Using Spike and Slab Regression spima Simulated Pseudo-Individual Data Meta-Analysis with ABC-SMC spinBayes Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection splancs Spatial and Space-Time Point Pattern Analysis splikit Analysing RNA Splicing in Single-Cell RNA Sequencing Data splines2 Regression Spline Functions and Classes splithalf Calculate Task Split Half Reliability Estimates splmm Simultaneous Penalized Linear Mixed Effects Models splus2R Supplemental S-PLUS Functionality in R splusTimeDate Times and Dates from 'S-PLUS' splusTimeSeries Time Series from 'S-PLUS' spnn Scale Invariant Probabilistic Neural Networks spopt Spatial Optimization for Regionalization, Facility Location, and Market Analysis sport Sequential Pairwise Online Rating Techniques spotr Estimate Spatial Population Indices from Ecological Abundance Data spray Sparse Arrays and Multivariate Polynomials spreadr Simulating Spreading Activation in a Network springer Sparse Group Variable Selection for Gene-Environment Interactions in the Longitudinal Study squat Statistics for Quaternion Temporal Data srm Structural Equation Modeling for the Social Relations Model srr 'rOpenSci' Software Review 'Roclets' ssMRCD Robust Estimators for Multi-Group and Spatial Data ssdtools Species Sensitivity Distributions ssgraph Bayesian Graph Structure Learning using Spike-and-Slab Priors ssh Secure Shell (SSH) Client for R sshicm Information Consistency-Based Measures for Spatial Stratified Heterogeneity sshist Optimal Density Estimation via Shimazaki-Shinomoto Method ssmooth Smooth Raster Time Series sspse Estimating Hidden Population Size using Respondent Driven Sampling Data sstvars Toolkit for Reduced Form and Structural Smooth Transition Vector Autoregressive Models stable Probability Functions and Generalized Regression Models for Stable Distributions staggered Efficient Estimation Under Staggered Treatment Timing stan4bart Bayesian Additive Regression Trees with Stan-Sampled Parametric Extensions starma Modelling Space Time AutoRegressive Moving Average (STARMA) Processes starsExtra Miscellaneous Functions for Working with 'stars' Rasters starvz R-Based Visualization Techniques for Task-Based Applications statcomp Statistical Complexity and Information Measures for Time Series Analysis statespacer State Space Modelling in 'R' statgenGWAS Genome Wide Association Studies statgenIBD Calculation of IBD Probabilities statgenQTLxT Multi-Trait and Multi-Trial Genome Wide Association Studies statip Statistical Functions for Probability Distributions and Regression statmod Statistical Modeling statnet.common Common R Scripts and Utilities Used by the Statnet Project Software stcos Space-Time Change of Support stcpR6 Sequential Test and Change-Point Detection Algorithms Based on E-Values / E-Detectors stdbscan Spatio-Temporal DBSCAN Clustering stdvectors C++ Standard Library Vectors in R steadyICA ICA and Tests of Independence via Multivariate Distance Covariance steepness Testing Steepness of Dominance Hierarchies stelfi Hawkes and Log-Gaussian Cox Point Processes Using Template Model Builder stepPlr L2 Penalized Logistic Regression with Stepwise Variable Selection stepR Multiscale Change-Point Inference stepSplitReg Stepwise Split Regularized Regression stepp Subpopulation Treatment Effect Pattern Plot (STEPP) stfit Spatio-Temporal Functional Imputation Tool stima Simultaneous Threshold Interaction Modeling Algorithm stlplus Enhanced Seasonal Decomposition of Time Series by Loess stm Estimation of the Structural Topic Model stochQN Stochastic Limited Memory Quasi-Newton Optimizers stochcorr Stochastic Correlation Modelling via Circular Diffusion stochtree Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference stochvol Efficient Bayesian Inference for Stochastic Volatility (SV) Models stochvolTMB Likelihood Estimation of Stochastic Volatility Models stockR Identifying Stocks in Genetic Data storr Simple Key Value Stores stors Step Optimised Rejection Sampling stosim Stochastic Simulator for Reliability Modeling of Repairable Systems stpp Space-Time Point Pattern Simulation, Visualisation and Analysis stpphawkes Missing Data for Marked Hawkes Process strat An Implementation of the Stratification Index stratEst Strategy Estimation stratification Univariate Stratification of Survey Populations stratifyR Optimal Stratification of Univariate Populations strawr Fast Implementation of Reading/Dump for .hic Files stream Infrastructure for Data Stream Mining streambugs Parametric Ordinary Differential Equations Model of Growth, Death, and Respiration of Macroinvertebrate and Algae Taxa strex Extra String Manipulation Functions stringdist Approximate String Matching, Fuzzy Text Search, and String Distance Functions stringfish Alt String Implementation stringi Fast and Portable Character String Processing Facilities stringmagic Character String Operations and Interpolation, Magic Edition striprtf Extract Text from RTF File strollur Store and Transfer Amplicon Sequence Data strucchange Testing, Monitoring, and Dating Structural Changes strucchangeRcpp Testing, Monitoring, and Dating Structural Changes: C++ Version structenforcement Struct-Like Data Type Checking and Enforcement sts Estimation of the Structural Topic and Sentiment-Discourse Model for Text Analysis subplex Unconstrained Optimization using the Subplex Algorithm subrank Computes Copula using Ranks and Subsampling subsampling Optimal Subsampling Methods for Statistical Models subselect Selecting Variable Subsets sumSome Permutation True Discovery Guarantee by Sum-Based Tests sumer Sumerian Cuneiform Text Analysis supclust Supervised Clustering of Predictor Variables Such as Genes super Interpreted String Literals supercells Superpixels of Spatial Data sureLDA A Novel Multi-Disease Automated Phenotyping Method for the EHR surtvep Cox Non-Proportional Hazards Model with Time-Varying Coefficients survAUC Estimators of Prediction Accuracy for Time-to-Event Data survC1 C-Statistics for Risk Prediction Models with Censored Survival Data survIDINRI IDI and NRI for Comparing Competing Risk Prediction Models with Censored Survival Data survPen Multidimensional Penalized Splines for (Excess) Hazard Models, Relative Mortality Ratio Models and Marginal Intensity Models survPresmooth Presmoothed Estimation in Survival Analysis survSNP Power Calculations for SNP Studies with Censored Outcomes survdistr Survival Distribution Container with Flexible Interpolation Methods surveillance Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena survextrap Bayesian Flexible Parametric Survival Modelling and Extrapolation survey Analysis of Complex Survey Samples surveybootstrap Bootstrap with Survey Data surveygraph Network Representations of Attitudes surveyplanning Survey Planning Tools surveysd Survey Standard Error Estimation for Cumulated Estimates and their Differences in Complex Panel Designs surveyvoi Survey Value of Information survidm Inference and Prediction in an Illness-Death Model survivalREC Nonparametric Estimation of the Distribution of Gap Times for Recurrent Events survivalROC Time-Dependent ROC Curve Estimation from Censored Survival Data survivalmodels Models for Survival Analysis survkl Estimate Survival Data with Data Integration survstan Fitting Survival Regression Models via 'Stan' sva Surrogate Variable Analysis svars Data-Driven Identification of SVAR Models svd Interfaces to Various State-of-Art SVD and Eigensolvers svgViewR 3D Animated Interactive Visualizations Using SVG and WebGL svglite An 'SVG' Graphics Device svines Stationary Vine Copula Models svycoxme Mixed-Effects Cox Models for Complex Samples svytest Survey Weight Diagnostic Tests swaglm Fast Sparse Wrapper Algorithm for Generalized Linear Models and Testing Procedures for Network of Highly Predictive Variables swatches Read, Inspect, and Manipulate Color Swatch Files swdpwr Power Calculation for Stepped Wedge Cluster Randomized Trials sweater Speedy Word Embedding Association Test and Extras Using R swephR High Precision Swiss Ephemeris switchBox Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm switchSelection Endogenous Switching and Sample Selection Regression Models swjm Stagewise Variable Selection for Joint Models of Semi-Competing Risks sylcount Syllable Counting and Readability Measurements symMCD Symmetrized MCD symengine Interface to the 'SymEngine' Library symmetry Testing for Symmetry of Data and Model Residuals synMicrodata Synthetic Microdata Generator synchronicity Boost Mutex Functionality in R sys Powerful and Reliable Tools for Running System Commands in R sysfonts Loading Fonts into R systemfonts System Native Font Finding systemicrisk Systemic Risk and Network Reconstruction tEDM Temporal Empirical Dynamic Modeling tabularMLC Tabular Maximum Likelihood Classifier tagcloud Tag Clouds tagtools Work with Data from High-Resolution Biologging Tags tailDepFun Minimum Distance Estimation of Tail Dependence Models tailplots Estimators and Plots for Gamma and Pareto Tail Detection talib Interface to 'TA-Lib' for Technical Analysis and Candlestick Patterns tall Text Analysis for All tame Timing, Anatomical, Therapeutic and Chemical Based Medication Clustering tantivyr Fast Full-Text Search for R with 'Tantivy' tardis Text Analysis with Rules and Dictionaries for Inferring Sentiment targeted Targeted Inference tau Text Analysis Utilities taxonomizr Functions to Work with NCBI Accessions and Taxonomy tbl2xts Convert Tibbles or Data Frames to Xts Easily tci Target Controlled Infusion (TCI) tclust Robust Trimmed Clustering tcv Determining the Number of Factors in Poisson Factor Models via Thinning Cross-Validation tdROC Nonparametric Estimation of Time-Dependent ROC, Brier Score, and Survival Difference from Right Censored Time-to-Event Data with or without Competing Risks tdata Prepare Your Time-Series Data for Further Analysis tdigest Wicked Fast, Accurate Quantiles Using t-Digests tdthap TDT Tests for Extended Haplotypes teems Trade and Environment Equilibrium Modeling System teigen Model-Based Clustering and Classification with the Multivariate t Distribution telegramR Interact with the 'Telegram' 'MTProto' API tensorA Advanced Tensor Arithmetic with Named Indices tensorBSS Blind Source Separation Methods for Tensor-Valued Observations tensorEVD A Fast Algorithm to Factorize High-Dimensional Tensor Product Matrices tensorMiss Handle Missing Tensor Data with C++ Integration tensorsparse Multiway Clustering via Tensor Block Models tergm Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models tergmLite Fast Simulation of Simple Temporal Exponential Random Graph Models tergo Style Your Code Fast terminaldigits Tests of Uniformity and Independence for Terminal Digits terminalgraphics Graphical Output in Terminals terra Spatial Data Analysis terrainmeshr Triangulate and Simplify 3D Terrain Meshes tesseract Open Source OCR Engine testforDEP Dependence Tests for Two Variables testthat Unit Testing for R tetrascatt Acoustic Scattering for Complex Shapes by Using the DWBA texanshootR Reproducible Audit Trails for Indefensible Research texmex Statistical Modelling of Extreme Values text.alignment Text Alignment with Smith-Waterman text2vec Modern Text Mining Framework for R textTinyR Text Processing for Small or Big Data Files textmineR Functions for Text Mining and Topic Modeling textrecipes Extra 'Recipes' for Text Processing textreg n-Gram Text Regression, aka Concise Comparative Summarization textreuse Detect Text Reuse and Document Similarity textshaping Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping tfCox Fits Piecewise Polynomial with Data-Adaptive Knots in Cox Model tfarima Transfer Function and ARIMA Models tfevents Write Events for 'TensorBoard' tgcd Thermoluminescence Glow Curve Deconvolution tglkmeans Efficient Implementation of K-Means++ Algorithm tgp Bayesian Treed Gaussian Process Models tgstat Amos Tanay's Group High Performance Statistical Utilities thgenetics Genetic Rare Variants Tests thinr Binary Image Thinning Algorithms this.path Get Executing Script's Path thisutils Collection of Utility Functions for Data Analysis and Computing thor Interface to 'LMDB' thunder Computation and Visualisation of Atmospheric Convective Parameters tibble Simple Data Frames tibbletime Time Aware Tibbles tibblify Rectangle Nested Lists tidyfast Fast Tidying of Data tidygraph A Tidy API for Graph Manipulation tidylda Latent Dirichlet Allocation Using 'tidyverse' Conventions tidynorm Tools for Tidy Vowel Normalization tidypopgen Tidy Population Genetics tidyr Tidy Messy Data tidyselect Select from a Set of Strings tidysq Tidy Processing and Analysis of Biological Sequences tidyxl Read Untidy Excel Files tiff Read and Write TIFF Images tigers Integration of Geography, Environment, and Remote Sensing tikzDevice R Graphics Output in LaTeX Format tiledb Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays timeDF Subset and Flag Data Frames with Times by the Use of Periods timechange Efficient Manipulation of Date-Times timeplyr Fast Tidy Tools for Date and Date-Time Manipulation timereg Flexible Regression Models for Survival Data timetools Seasonal/Sequential (Instants/Durations, Even or not) Time Series timsac Time Series Analysis and Control Package tind A Common Representation of Time Indices of Different Types tinyVAST Multivariate Spatio-Temporal Models using Structural Equations tinycodet Functions to Help in your Coding Etiquette tinyimg Optimize and Compress Images tipitaka Data and Tools for Analyzing the Pali Canon tipitaka.critical Lemmatized Critical Edition of the Pali Canon tis Time Indexes and Time Indexed Series tkrplot TK Rplot tlars The T-LARS Algorithm: Early-Terminated Forward Variable Selection tlrmvnmvt Low-Rank Methods for MVN and MVT Probabilities tm Text Mining Package tma Transmodal Analysis (TMA) tmbstan MCMC Sampling from 'TMB' Model Object using 'Stan' tmt Estimation of the Rasch Model for Multistage Tests tmvnsim Truncated Multivariate Normal Simulation tmvtnorm Truncated Multivariate Normal and Student t Distribution tmvtnsim Truncated Multivariate Normal and t Distribution Simulation tok Fast Text Tokenization tokenizers Fast, Consistent Tokenization of Natural Language Text tokenizers.bpe Byte Pair Encoding Text Tokenization tomledit Parse, Read, and Edit 'TOML' toonlite Read, Write, Validate, Stream, and Convert TOON Data topicmodels Topic Models topologyR Topological Connectivity Analysis for Numeric Data toporanga Topological Sort-Based Hierarchy Inference torch Tensors and Neural Networks with 'GPU' Acceleration torchvisionlib Additional Operators for Image Models touch Tools of Utilization and Cost in Healthcare tpfp Counts the Number of True Positives and False Positives tpr Temporal Process Regression tracerer Tracer from R trackdem Particle Tracking and Demography trajeR Group Based Modeling Trajectory tramME Transformation Models with Mixed Effects tranSurv Transformation-Based Regression under Dependent Truncation transfR Transfer of Hydrograph from Gauged to Ungauged Catchments transformr Polygon and Path Transformations transmdl Semiparametric Transformation Models transport Computation of Optimal Transport Plans and Wasserstein Distances trapezoid The Trapezoidal Distribution trc Truncated Rank Correlation treats Trees and Traits Simulations tree Classification and Regression Trees tree.interpreter Random Forest Prediction Decomposition and Feature Importance Measure treeSS Tree-Spatial Scan Statistic for Cluster Detection treeclim Numerical Calibration of Proxy-Climate Relationships treeshap Compute SHAP Values for Your Tree-Based Models Using the 'TreeSHAP' Algorithm treesitter Bindings to 'Tree-Sitter' treesitter.c 'R' Bindings to the 'C' Grammar for Tree-Sitter treesitter.r 'R' Grammar for 'Tree-Sitter' treespace Statistical Exploration of Landscapes of Phylogenetic Trees treestats Phylogenetic Tree Statistics treestructure Detect Population Structure Within Phylogenetic Trees trend Non-Parametric Trend Tests and Change-Point Detection trialr Clinical Trial Designs in 'rstan' triebeard 'Radix' Trees in 'Rcpp' tripack Triangulation of Irregularly Spaced Data triplediff Triple-Difference Estimators triptych Diagnostic Graphics to Evaluate Forecast Performance trtswitch Treatment Switching truncProxy Proximal Weighting Estimation for Dependent Left Truncation truncnorm Truncated Normal Distribution trunmnt Moments of Truncated Multivariate Normal Distribution trustOptim Trust Region Optimization for Nonlinear Functions with Sparse Hessians tsBSS Blind Source Separation and Supervised Dimension Reduction for Time Series tsDyn Nonlinear Time Series Models with Regime Switching tsPI Improved Prediction Intervals for ARIMA Processes and Structural Time Series tsdistributions Location Scale Standardized Distributions tseries Time Series Analysis and Computational Finance tseriesChaos Analysis of Nonlinear Time Series tseriesEntropy Entropy Based Analysis and Tests for Time Series tseriesTARMA Analysis of Nonlinear Time Series Through Threshold Autoregressive Moving Average Models (TARMA) Models tsfgrnn Time Series Forecasting Using GRNN tsfknn Time Series Forecasting Using Nearest Neighbors tsgarch Univariate GARCH Models tsissm Linear Innovations State Space Unobserved Components Model tsitter Tree-Sitter Parsing Tools tsmarch Multivariate ARCH Models tsmp Time Series with Matrix Profile tsnet Fitting, Comparing, and Visualizing Networks Based on Time Series Data tspmeta Instance Feature Calculation and Evolutionary Instance Generation for the Traveling Salesman Problem tsvio Simple Utilities for Tab-Separated-Value (TSV) Files tsxtreme Bayesian Modelling of Extremal Dependence in Time Series ttbary Barycenter Methods for Spatial Point Patterns tth TeX-to-HTML/MathML Translators TtH/TtM tulpaMesh Constrained Delaunay Triangulation Meshes for Spatial 'SPDE' Models tuneR Analysis of Music and Speech tvGarchKF Time-Varying Garch Models Through a State-Space Representation tvR Total Variation Regularization tvdenoising Univariate Total Variation Denoising twang Toolkit for Weighting and Analysis of Nonequivalent Groups twdtw Time-Weighted Dynamic Time Warping tweeDEseq RNA-seq data analysis using the Poisson-Tweedie family of distributions tweedie Evaluation of Tweedie Exponential Family Models tweedieDistr Tweedie Distribution tweenr Interpolate Data for Smooth Animations twingp A Fast Global-Local Gaussian Process Approximation twinning Data Twinning twinsvm Twin Support Vector Machines twosamples Fast Permutation Based Two Sample Tests typetracer Trace Function Parameter Types tzdb Time Zone Database Information ubms Bayesian Models for Data from Unmarked Animals using 'Stan' ucminf General-Purpose Unconstrained Non-Linear Optimization ucminfcpp 'C++' Reimplementation of the 'ucminf' Unconstrained Nonlinear Optimizer udpipe Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit udunits2 Udunits-2 Bindings for R ugomquantreg Quantile Regression Modeling for Unit-Gompertz Responses ulid Generate Universally Unique 'Lexicographically' 'Sortable' Identifiers umap Uniform Manifold Approximation and Projection ump Uniformly Most Powerful Tests ungroup Penalized Composite Link Model for Efficient Estimation of Smooth Distributions from Coarsely Binned Data unifed The Unifed Distribution unifiedml Unified Interface for Machine Learning Models unigd Universal Graphics Device unitquantreg Parametric Quantile Regression Models for Bounded Data units Measurement Units for R Vectors unityForest Improving Interaction Modelling and Interpretability in Random Forests unix POSIX System Utilities unmarked Models for Data from Unmarked Animals unnest Unnest Hierarchical Data Structures unrtf Extract Text from Rich Text Format (RTF) Documents unsum Reconstruct Raw Data from Summary Statistics unsystation Stationarity Test Based on Unsystematic Sub-Sampling updog Flexible Genotyping for Polyploids urca Unit Root and Cointegration Tests for Time Series Data urlparse Fast Simple URL Parser urltools Vectorised Tools for URL Handling and Parsing ursa Non-Interactive Spatial Tools for Raster Processing and Visualization utf8 Unicode Text Processing uuid Tools for Generating and Handling of UUIDs uuidx Modern UUIDs for R with a Rust Backend uwot The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction vMF Sampling from the von Mises-Fisher Distribution validate Data Validation Infrastructure valorate Velocity and Accuracy of the LOg-RAnk TEst valr Genome Interval Arithmetic vapour Access to the 'Geospatial Data Abstraction Library' ('GDAL') varPro Model-Independent Variable Selection via the Rule-Based Variable Priority varband Variable Banding of Large Precision Matrices varbvs Large-Scale Bayesian Variable Selection Using Variational Methods vasicekreg Regression Modeling Using Vasicek Distribution vaster Tools for Raster Grid Logic vcfR Manipulate and Visualize VCF Data vcfppR Rapid Manipulation of the Variant Call Format (VCF) vcpen Penalized Variance Components Analysis vcrpart Tree-Based Varying Coefficient Regression for Generalized Linear and Ordinal Mixed Models vctrs Vector Helpers vdiffr Visual Regression Testing and Graphical Diffing vecrep Compact Vector Replication vectorbitops Vector Bitwise Operations vectra Columnar Query Engine for Larger-than-RAM Data vegan Community Ecology Package vein Vehicular Emissions Inventories vennplot Venn Diagrams in 2D and 3D vetr Trust, but Verify vglmer Variational Inference for Hierarchical Generalized Linear Models viewscape Viewscape Analysis vimixr Collapsed Variational Inference for Dirichlet Process (DP) Mixture Model vinereg D-Vine Quantile Regression visPedigree Tidying, Analysis, and Fast Visualization of Animal and Plant Pedigrees viscomplexr Phase Portraits of Functions in the Complex Number Plane vistla Detecting Influence Paths with Information Theory vita Variable Importance Testing Approaches vntrs Variable Neighborhood Trust Region Search vol2birdR Vertical Profiles of Biological Signals in Weather Radar Data volesti Volume Approximation and Sampling of Convex Polytopes voronoifortune Voronoi Tessellation by Fortune Algorithm vroom Read and Write Rectangular Text Data Quickly vrpr Vehicle Routing Problem Solver Built on 'PyVRP' vsgoftest Goodness-of-Fit Tests Based on Kullback-Leibler Divergence vsn Variance stabilization and calibration for microarray data vws Vertical Weighted Strips wARMASVp Winsorized ARMA Estimation for Higher-Order Stochastic Volatility Models wCorr Weighted Correlations walker Bayesian Generalized Linear Models with Time-Varying Coefficients warbleR Streamline Bioacoustic Analysis warp Group Dates waspr Wasserstein Barycenters of Subset Posteriors watcher Watch the File System for Changes watson Fitting and Simulating Mixtures of Watson Distributions wav Read and Write WAV Files waveband Computes Credible Intervals for Bayesian Wavelet Shrinkage wavelets Functions for Computing Wavelet Filters, Wavelet Transforms and Multiresolution Analyses waveslim Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing wavethresh Wavelets Statistics and Transforms waysign Multi-Purpose and High-Performance Routing wbacon Weighted BACON Algorithms wbs Wild Binary Segmentation for Multiple Change-Point Detection wbsd Wild Bootstrap Size Diagnostics wbsts Multiple Change-Point Detection for Nonstationary Time Series wcc Windowed Cross Correlation wdm Weighted Dependence Measures wdnet Weighted and Directed Networks webfakes Fake Web Apps for HTTP Testing webp A New Format for Lossless and Lossy Image Compression webreadr Tools for Reading Formatted Access Log Files websocket 'WebSocket' Client Library webutils Utility Functions for Developing Web Applications weibulltools Statistical Methods for Life Data Analysis weightedCL Efficient and Feasible Inference for High-Dimensional Normal Copula Regression Models weightedScores Weighted Scores Method for Regression Models with Dependent Data weights Weighting and Weighted Statistics wfe Weighted Linear Fixed Effects Regression Models for Causal Inference whoa Evaluation of Genotyping Error in Genotype-by-Sequencing Data widals Weighting by Inverse Distance with Adaptive Least Squares winputall Variable Input Allocation Among Crops wk Lightweight Well-Known Geometry Parsing wnominate Roll Call Analysis Software womblR Spatiotemporal Boundary Detection Model for Areal Unit Data word2vec Distributed Representations of Words wordcloud Word Clouds wordspace Distributional Semantic Models in R wordvector Word and Document Vector Models wrassp Interface to the 'ASSP' Library writexl Export Data Frames to Excel 'xlsx' Format wrswoR Weighted Random Sampling without Replacement wru Who are You? Bayesian Prediction of Racial Category Using Surname, First Name, Middle Name, and Geolocation wsbackfit Weighted Smooth Backfitting for Structured Models wskm Weighted k-Means Clustering wsrf Weighted Subspace Random Forest for Classification wstats Weighted Descriptive Statistics wtest The W-Test for Genetic Interactions Testing wv Wavelet Variance x13binary Provide the 'x13ashtml' Seasonal Adjustment Binary xactonomial Inference for Functions of Multinomial Parameters xcms LC-MS and GC-MS Data Analysis xdcclarge Estimating a (c)DCC-GARCH Model in Large Dimensions xdvir Render 'LaTeX' in Plots xfun Supporting Functions for Packages Maintained by 'Yihui Xie' xgboost Extreme Gradient Boosting xiacf Nonlinear Dependence and Lead-Lag Analysis via Chatterjee's Xi xml2 Parse XML xmlwriter Fast and Elegant XML Generation xoi Tools for Analyzing Crossover Interference xplorerr Tools for Interactive Data Exploration xptr Manipulating External Pointers xrnet Hierarchical Regularized Regression xslt Extensible Style-Sheet Language Transformations xts eXtensible Time Series xutils Utility Functions of Fangzhou Xie xxhashlite Extremely Fast Hashing of R Objects, Raw Data and Files using 'xxHash' Algorithms yaConsensus Consensus Clustering of Omic Data yaImpute Nearest Neighbor Observation Imputation and Evaluation Tools yaml Methods to Convert R Data to YAML and Back yaml12 Fast 'YAML' 1.2 Parser and Formatter yardstick Tidy Characterizations of Model Performance ycevo Nonparametric Estimation of the Yield Curve Evolution ymd Parse 'YMD' Format Number or String to Date yuima The YUIMA Project Package for SDEs yyjsonr Fast 'JSON', 'NDJSON' and 'GeoJSON' Parser and Generator zarr Native and Extensible R Driver for 'Zarr' zcurve An Implementation of Z-Curves zebu Local Association Measures zenplots Zigzag Expanded Navigation Plots zfa Zoom-Focus Algorithm zigg Lightweight Interfaces to the 'Ziggurat' Pseudo Random Number Generator zip Cross-Platform 'zip' Compression zlib Compression and Decompression zonohedra Compute and Plot Zonohedra from Vector Generators zoo S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) zoomerjoin Superlatively Fast Fuzzy Joins ztpln Zero-Truncated Poisson Lognormal Distribution Packages in library '/data/localhost/ripley/R/test-dev': AATtools Reliability and Scoring Routines for the Approach-Avoidance Task ABACUS Apps Based Activities for Communicating and Understanding Statistics ABC.RAP Array Based CpG Region Analysis Pipeline ABCDscores Summary Scores of the Adolescent Brain Cognitive Development (ABCD) Study ABCanalysis Computed ABC Analysis ABCoptim Implementation of Artificial Bee Colony (ABC) Optimization ABHgenotypeR Easy Visualization of ABH Genotypes ABM Agent Based Model Simulation Framework ABPS The Abnormal Blood Profile Score to Detect Blood Doping ABRSQOL Quality-of-Life Solver for "Measuring Quality of Life under Spatial Frictions" ABSurvTDC Survival Analysis using Time Dependent Covariate for Animal Breeding ACDm Tools for Autoregressive Conditional Duration Models ACE.CoCo Analysis of Correlated High-Dimensional Expression (ACE) Data ACEP Análisis Computacional de Eventos de Protesta ACEsearch 'ACE' Search Engine API ACEsimFit ACE Kin Pair Data Simulations and Model Fitting ACEt Estimating Dynamic Heritability and Twin Model Comparison ACNE Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization ACSWR A Companion Package for the Book "A Course in Statistics with R" ACTCD Asymptotic Classification Theory for Cognitive Diagnosis ACV Optimal Out-of-Sample Forecast Evaluation and Testing under Stationarity ACWR Acute Chronic Workload Ratio Calculation ADAPTS Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells ADCT Adaptive Design in Clinical Trials ADDT Analysis of Accelerated Destructive Degradation Test Data ADER Data Analysis in Ecology ADGofTest Anderson-Darling GoF test ADLP Accident and Development Period Adjusted Linear Pools for Actuarial Stochastic Reserving ADMM Algorithms using Alternating Direction Method of Multipliers ADP Adoption Probability, Triers and Users Rate of a New Product ADPF Use Least Squares Polynomial Regression and Statistical Testing to Improve Savitzky-Golay ADSIHT Adaptive Double Sparse Iterative Hard Thresholding ADTSA Time Series Analysis ADVICE Automatic Direct Variable Selection via Interrupted Coefficient Estimation AEDForecasting Change Point Analysis in ARIMA Forecasting AEP Statistical Modelling for Asymmetric Exponential Power Distribution AER Applied Econometrics with R AEenrich Adverse Event Enrichment Tests AFFECT Accelerated Functional Failure Time Model with Error-Contaminated Survival Times AFR Toolkit for Regression Analysis of Kazakhstan Banking Sector Data AGBQR Adaptive Generalized Bayesian Quantile Regression AGCA4extremes Anchored Geodesic Component Analysis for Extremes AGD Analysis of Growth Data AGHmatrix Relationship Matrices for Diploid and Autopolyploid Species AGPRIS AGricultural PRoductivity in Space AHMbook Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology' Vols 1 and 2 AHPGaussian New Multicriteria Method: AHPGaussian AHPWR Compute Analytic Hierarchy Process AHPhybrid AHP Hybrid Method AHPtools Consistency in the Analytic Hierarchy Process AHSurv Flexible Parametric Accelerated Hazards Models AIBias Longitudinal Bias Auditing for Sequential Decision Systems AICcmodavg Model Selection and Multimodel Inference Based on (Q)AIC(c) AID Box-Cox Power Transformation AIDA Analysis of Interval DAta AIFFtools Read AIFF Files and Convert to WAVE Format AIGRA Agentic Item Generation, Review, and Analysis AIGovernance Statistical Auditing and Governance Reporting for Employment AI Systems AIPW Augmented Inverse Probability Weighting AIUQ Ab Initio Uncertainty Quantification AIscreenR AI Screening Tools in R for Systematic Reviewing ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account ALDEx3 Linear Models for Sequence Count Data ALDqr Quantile Regression Using Asymmetric Laplace Distribution ALFAM2 Dynamic Model of Ammonia Emission from Field-Applied Manure ALLSPICER ALLelic Spectrum of Pleiotropy Informed Correlated Effects ALS Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) ALSCPC Accelerated line search algorithm for simultaneous orthogonal transformation of several positive definite symmetric matrices to nearly diagonal form. ALUES Agricultural Land Use Evaluation System ALassoSurvIC Adaptive Lasso for the Cox Regression with Interval Censored and Possibly Left Truncated Data AMAPVox LiDAR Data Voxelisation AMCP A Model Comparison Perspective AMCTestmakeR Generate LaTeX Code for Auto-Multiple-Choice (AMC) AMDconfigurations Geometric Analysis of Configurations in High-Dimensional Spaces AMIM Compute the Adjusted Market Inefficiency Measure AMISforInfectiousDiseases Implement the AMIS Algorithm for Infectious Disease Models AMModels Adaptive Management Model Manager AMPLE Shiny Apps to Support Capacity Building on Harvest Control Rules AMR Antimicrobial Resistance Data Analysis ANN2 Artificial Neural Networks for Anomaly Detection ANOFA Analyses of Frequency Data ANOPA Analyses of Proportions using Anscombe Transform ANOVAIREVA Interactive Document for Working with Analysis of Variance ANOVAShiny Interactive Document for Working with Analysis of Variance ANOVAShiny2 Interactive Document for Working with Analysis of Variance ANSM5 Functions and Data for the Book "Applied Nonparametric Statistical Methods", 5th Edition AOUSDOHtools Analyzing AOU SDOH Survey Data AOV1R Inference in the Balanced One-Way ANOVA Model with Random Factor AOboot Bootstrapping in Different One-Way and Two-Way ANOVA APCI A New Age-Period-Cohort Model for Describing and Investigating Inter-Cohort Differences and Life Course Dynamics APCalign Resolving Plant Taxon Names Using the Australian Plant Census APCanalysis Analysis of Unreplicated Orthogonal Experiments using All Possible Comparisons APCinteraction Nonparametric Interaction Tests in Balanced Two-Way ANOVA Models APCtools Routines for Descriptive and Model-Based APC Analysis APFr Multiple Testing Approach using Average Power Function (APF) and Bayes FDR Robust Estimation APIS Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents APML0 Augmented and Penalized Minimization Method L0 APPEstimation Adjusted Prediction Model Performance Estimation APRScenario Structural Scenario Analysis for Bayesian Structural Vector Autoregression Models APS Analysing Prediction Stability of Non-Deterministic Prediction Models APTIcalc Air Pollution Tolerance Index (APTI) Calculator APackOfTheClones Visualization of Clonal Expansion for Single Cell Immune Profiles AQEval Air Quality Evaluation AQLSchemes Retrieving Acceptance Sampling Schemes AQuadtree Confidentiality of Spatial Point Data AQuality Water and Measurements Quality ARCHISSUR Active Recovery of a Constrained and Hidden Set by Stepwise Uncertainty Reduction Strategy ARCensReg Fitting Univariate Censored Linear Regression Model with Autoregressive Errors ARCokrig Autoregressive Cokriging Models for Multifidelity Codes ARDECO Annual Regional Database of the European Commission (ARDECO) ARDL ARDL, ECM and Bounds-Test for Cointegration ARGOS Automatic Regression for Governing Equations (ARGOS) ARHT Adaptable Regularized Hotelling's T^2 Test for High-Dimensional Data ARIMAANN Time Series Forecasting using ARIMA-ANN Hybrid Model ARIbrain All-Resolution Inference ARMALSTM Fitting of Hybrid ARMA-LSTM Models ARPALData Retrieving and Analyzing Air Quality and Weather Data from ARPA Lombardia ARPobservation Tools for Simulating Direct Behavioral Observation Recording Procedures Based on Alternating Renewal Processes ARTofR To Insert Title, Divider, and Block of Comments ARTool Aligned Rank Transform ARTtransfer Adaptive and Robust Pipeline for Transfer Learning ARUtools Management and Processing of Autonomous Recording Unit (ARU) Data ASGS.foyer Interface to the Australian Statistical Geography Standard ASML Algorithm Portfolio Selection with Machine Learning ASMbook Functions for the Book "Applied Statistical Modeling for Ecologists" ASRgenomics Complementary Genomic Functions ASSA Applied Singular Spectrum Analysis (ASSA) ASSISTant Adaptive Subgroup Selection in Group Sequential Trials AST Age-Spatial-Temporal Model ASV Stochastic Volatility Models with or without Leverage ATAforecasting Automatic Time Series Analysis and Forecasting using the Ata Method ATE.ERROR Estimating ATE with Misclassified Outcomes and Mismeasured Covariates ATNr Run Allometric Trophic Networks Models ATQ Alert Time Quality - Evaluating Timely Epidemic Metrics ATR Alternative Tree Representation ATbounds Bounding Treatment Effects by Limited Information Pooling AUC Threshold Independent Performance Measures for Probabilistic Classifiers AUKtest Calculate the AUK Estimator AUtests Approximate Unconditional and Permutation Tests AV1R 'AV1' Video Encoding for Biological Microscopy Data AVGAS A Variable Selection using Genetic Algorithms AWR 'AWS' Java 'SDK' for R AWR.Kinesis Amazon 'Kinesis' Consumer Application for Stream Processing AZIAD Analyzing Zero-Inflated and Zero-Altered Data AalenJohansen Conditional Aalen-Johansen Estimation AbSolution Interactive Feature-Based Analysis of AIRR-Seq Data Ac3net Inferring Directional Conservative Causal Core Gene Networks AcademicThemes Colour Plots with Palettes from Academic Institutions AccSamplingDesign Acceptance Sampling Plans Design AccelStab Accelerated Stability Kinetic Modelling AcceptReject Acceptance-Rejection Method for Generating Pseudo-Random Observations AcceptanceSampling Creation and Evaluation of Acceptance Sampling Plans Achilles Achilles Data Source Characterization ActCR Extract Circadian Rhythms Metrics from Actigraphy Data ActiveDriver Finding Cancer Driver Proteins with Enriched Mutations in Post-Translational Modification Sites ActiveDriverWGS A Driver Discovery Tool for Cancer Whole Genomes ActiveLearning4SPM Active Learning for Process Monitoring ActivePathways Integrative Pathway Enrichment Analysis of Multivariate Omics Data ActivityIndex Activity Index Calculation using Raw 'Accelerometry' Data ActuarialM Computation of Actuarial Measures Using Bell G Family AcuityView A Package for Displaying Visual Scenes as They May Appear to an Animal with Lower Acuity AdIsMF Adsorption Isotherm Model Fitting AdMit Adaptive Mixture of Student-t Distributions AdaSampling Adaptive Sampling for Positive Unlabeled and Label Noise Learning AdapDiscom Adaptive Sparse Regression for Block Missing Multimodal Data AdapSamp Adaptive Sampling Algorithms AdaptGauss Gaussian Mixture Models (GMM) AdaptiveBoxplot FDR(BH) Boxplot and FWER(Holm) Boxplot AddiVortes (Bayesian) Additive Voronoi Tessellations AdequacyModel Adequacy of Probabilistic Models and General Purpose Optimization AdhereR Adherence to Medications AdhereRViz Adherence to Medications AdmixPoly Global and Local Admixture Inference in Polyploids AdsorpR Adsorption Isotherm Models AdvBinomApps Upper Clopper-Pearson Confidence Limits for Burn-in Studies under Additional Available Information AdvDif4 Solving 1D Advection Bi-Flux Diffusion Equation AdvancedBasketballStats Advanced Basketball Statistics AdverseEvents 'shiny' Application for Adverse Event Analysis of 'OnCore' Data AeRobiology A Computational Tool for Aerobiological Data AeroEvapR Estimating Reservoir Evaporation via Aerodynamic Approach AeroSampleR Estimate Aerosol Particle Collection Through Sample Lines AgeBandDecomposition Age Band Decomposition Method for Tree Ring Standardization AgePopDenom Model Fine-Scale Age-Structured Population Data using Open-Source Data AgeTopicModels Inferring Age-Dependent Disease Topic from Diagnosis Data AggregateR Aggregate Numeric, Date and Categorical Variables AgreementInterval Agreement Interval of Two Measurement Methods AgriDiversiX Agricultural Crop Diversification Indices Analysis AgroR Experimental Statistics and Graphics for Agricultural Sciences AgroReg Regression Analysis Linear and Nonlinear for Agriculture AgroTech Data Analysis of Pesticide Application Technology AhoCorasickTrie Fast Searching for Multiple Keywords in Multiple Texts AiES Axon Integrity Evaluation System for Microscopy Images AirExposure Exposure Model to Air Pollutants Based on Mobility and Daily Activities AirMonitor Air Quality Data Analysis AirScreen Feature Screening via Adaptive Iterative Ridge (Air-HOLP and Air-OLS) AirportProblems Analysis of Cost Allocation for Airport Problems Ake Associated Kernel Estimations AlgDesign Algorithmic Experimental Design AlgeriAPIs Access Algerian Data via Public APIs AlignLV Multiple Group Item Response Theory Alignment Helpers for 'lavaan' and 'mirt' AllMetrics Calculating Multiple Performance Metrics of a Prediction Model AlleleRetain Allele Retention, Inbreeding, and Demography AlleleShift Predict and Visualize Population-Level Changes in Allele Frequencies in Response to Climate Change AllelicSeries Allelic Series Test Allspice RNA-Seq Profile Classifier AlphaPart Partition/Decomposition of Breeding Values by Paths of Information AlphaSimR Breeding Program Simulations AlteredPQR Detection of Altered Protein Quantitative Relationships Amelia A Program for Missing Data AmesHousing The Ames Iowa Housing Data AmigaFFH Commodore Amiga File Format Handler AmmoniaConcentration Un-Ionized Ammonia Concentration AmoudSurv Tractable Parametric Odds-Based Regression Models AmpGram Prediction of Antimicrobial Peptides AmpliconDuo Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts AmyloGram Prediction of Amyloid Proteins Anaconda Targeted Differential and Global Enrichment Analysis of Taxonomic Rank by Shared Asvs Analitica Exploratory Data Analysis, Group Comparison Tools, and Other Procedures AnalyzeFMRI Functions for Analysis of fMRI Datasets Stored in the ANALYZE or 'NIFTI' Format AnanseSeurat Construct ANANSE GRN-Analysis Seurat AncReg Ancestor Regression AnchorRegression Perform AnchorRegression Andromeda Asynchronous Disk-Based Representation of Massive Data AnglerCreelSurveySimulation Simulate a Bus Route Creel Survey of Anglers AnimalSequences Analyse Animal Sequential Behaviour and Communication AnnoProbe Annotate the Gene Symbols for Probes in Expression Array AnnotationBustR Extract Subsequences from GenBank Annotations AnnotationDbi Manipulation of SQLite-based annotations in Bioconductor AnnotationFilter Facilities for Filtering Bioconductor Annotation Resources AnnotationForge Tools for building SQLite-based annotation data packages AnnotationHub Client to access AnnotationHub resources AntAngioCOOL Anti-Angiogenic Peptide Prediction AntClassify Functional Guilds, Invasion Status, Endemism, and Rarity of Ants AnthropMMD An R Package for the Mean Measure of Divergence (MMD) Anthropometry Statistical Methods for Anthropometric Data AntibodyForests Delineating Inter- And Intra-Antibody Repertoire Evolution AntibodyTiters Antibody Titer Analysis of Vaccinated Patients AntsNet Unified Simulation of Isomorphisms Between Ant Colony Intelligence and Machine Learning AnxietySleep Sleep Quality and Anxiety in Confinement Aoptbdtvc A-Optimal Block Designs for Comparing Test Treatments with Controls ApacheLogProcessor Process the Apache Web Server Log Files AplosNCA Use 'Aplos NCA API' for Pharmacokinetic Analysis Apoderoides Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree AppliedPredictiveModeling Functions and Data Sets for 'Applied Predictive Modeling' ApplyPolygenicScore Utilities for the Application of a Polygenic Score to a VCF AquaAnalytix Water Quality Analysis AquaBEHER Estimation and Prediction of Wet Season Calendar and Soil Water Balance for Agriculture AquaEnv Integrated Development Toolbox for Aquatic Chemical Model Generation AquaticLifeHistory Life History Analysis Tools ArArRedux Rigorous Data Reduction and Error Propagation of Ar40 / Ar39 Data ArCo Artificial Counterfactual Package ArDec Time Series Autoregressive-Based Decomposition ArchaeoPhases Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling ArchaeoPhases.dataset Data Sets for 'ArchaeoPhases' Vignettes ArchipelagoEngine Spatial Weight Construction for Archipelagic Geographies ArctosR An Interface to the 'Arctos' Database ArgentinAPI Access Argentinian Data via APIs and Curated Datasets Argentum Access and Import WMS and WFS Data from Argentine Organizations AriGaMyANNSVR Hybrid ARIMA-GARCH and Two Specially Designed ML-Based Models Arothron Geometric Morphometric Methods and Virtual Anthropology Tools ArrayExpress Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet ArvindSt Five Novel Stochastic Regression Models with Arvind-Distributed Errors and Effects AsianOption Asian Option Pricing under Price Impact AsioHeaders 'Asio' C++ Header Files AssetPricing Optimal Pricing of Assets with Fixed Expiry Date AssocBin Measuring Association with Recursive Binning AssociationExplorer2 A User-Friendly 'shiny' Application for Exploring Associations and Visual Patterns AssumpSure 'shiny' Application for Statistical Test Assumption Checking and Guidance AsthmaNHANES Asthma Data Sets from NHANES AsyK Kernel Density Estimation AsymmetricSORDs Asymmetric Second Order Rotatable Designs (AsymmetricSORDs) AsynchLong Regression Analysis of Sparse Asynchronous Longitudinal Data AteMeVs Average Treatment Effects with Measurement Error and Variable Selection for Confounders Athlytics Sports Physiology Analysis from Local 'Strava' Data AtlasMaker Make Multiple 'leaflet' Maps in 'Shiny' AtmChile Download Air Quality and Meteorological Information of Chile AudioScatter Audiogram Scattergrams AurieLSHGaussian Creates a Neighbourhood Using Locality Sensitive Hashing for Gaussian Projections AustralianPoliticians Provides Datasets About Australian Politicians AutoAds Advertisement Metrics Calculation AutoDeskR An Interface to the 'AutoDesk' 'API' Platform AutoMLR Automated Multi-Outcome Machine Learning Combination Models AutoNN Automatic Neural Network Modeling for Time Series Forecasting AutoPlots Creating Echarts Visualizations as Easy as Possible AutoScore An Interpretable Machine Learning-Based Automatic Clinical Score Generator AutoStepwiseGLM Builds Stepwise GLMs via Train and Test Approach AutoStrataK Automatic Optimal Stratification for Survey Sampling AutoTransQF A Novel Automatic Shifted Log Transformation AutoWMM Perform the Weighted Multiplier Method on Trees Autoplotprotein Development of Visualization Tools for Protein Sequence AutoregressionMDE Minimum Distance Estimation in Autoregressive Model Autoseed Retrieve Disease-Related Genes from Public Sources AuxSurvey Survey Analysis with Auxiliary Discretized Variables AvInertia Calculate the Inertial Properties of a Flying Bird AzureAppInsights Include Azure Application Insights in Shiny Apps AzureAuth Authentication Services for Azure Active Directory AzureCognitive Interface to Azure Cognitive Services AzureContainers Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure' AzureCosmosR Interface to the 'Azure Cosmos DB' 'NoSQL' Database Service AzureGraph Simple Interface to 'Microsoft Graph' AzureKeyVault Key and Secret Management in 'Azure' AzureKusto Interface to 'Kusto'/'Azure Data Explorer' AzureQstor Interface to 'Azure Queue Storage' AzureRMR Interface to 'Azure Resource Manager' AzureStor Storage Management in 'Azure' AzureTableStor Interface to the Table Storage Service in 'Azure' AzureVM Virtual Machines in 'Azure' AzureVMmetadata Interface to Azure Virtual Machine Instance Metadata AzureVision Interface to Azure Computer Vision Services BACCO Bayesian Analysis of Computer Code Output (BACCO) BACprior Choice of Omega in the BAC Algorithm BAGofT A Binary Regression Adaptive Goodness-of-Fit Test (BAGofT) BALLI Expression RNA-Seq Data Analysis Based on Linear Mixed Model BAMBI Bivariate Angular Mixture Models BAMMtools Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees BANAM Bayesian Analysis of the Network Autocorrelation Model BAQM Babson Analytics and Quantitative Methods Tools BAR Bayesian Adaptive Randomization BAREB A Bayesian Repulsive Biclustering Model for 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Models using Birth-Death MCMC BEACH Biometric Exploratory Analysis Creation House BED Biological Entity Dictionary (BED) BEDASSLE Quantifies Effects of Geo/Eco Distance on Genetic Differentiation BEDMatrix Extract Genotypes from a PLINK .bed File BEKKs Multivariate Conditional Volatility Modelling and Forecasting BEMPdata Access the Bangladesh Environmental Mobility Panel Dataset BEND Bayesian Estimation of Nonlinear Data (BEND) BERTopic Topic Modeling with 'BERTopic' BESTree Branch-Exclusive Splits Trees BET Binary Expansion Testing BElikelihood Likelihood Method for Evaluating Bioequivalence BFF Bayes Factor Functions BFI Bayesian Federated Inference BFM Beta Factor Model BFS Get Data from the Swiss Federal Statistical Office BFpack Flexible Bayes Factor Testing of Scientific Expectations BGData A Suite of Packages for Analysis of Big Genomic Data BGFD Bell-G and Complementary Bell-G Family of Distributions BGGE Bayesian Genomic Linear Models Applied to GE Genome Selection BGGM Bayesian Gaussian Graphical Models BGLR Bayesian Generalized Linear Regression BGPhazard Markov Beta and Gamma Processes for Modeling Hazard Rates BGVAR Bayesian Global Vector Autoregressions BGmisc An R Package for Extended Behavior Genetics Analysis BH Boost C++ Header Files BHAI Estimate the Burden of Healthcare-Associated Infections BHMSMAfMRI Bayesian Hierarchical Multi-Subject Multiscale Analysis of Functional MRI (fMRI) Data BHSBVAR Structural Bayesian Vector Autoregression Models BI Blinding Assessment Indexes for Randomized, Controlled, Clinical Trials BICORN Integrative Inference of De Novo Cis-Regulatory Modules BIDistances Bioinformatic Distances BIEN Tools for Accessing the Botanical Information and Ecology Network Database BIFIEsurvey Tools for Survey Statistics in Educational Assessment BIGDAWG Case-Cotrol Analysis of Multi-Allelic Loci BIGL Biochemically Intuitive Generalized Loewe Model BIGpopA Pedigree Validation Genetic Composition of Diploids & Polyploids BIGr 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Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials BOJ Interface to Bank of Japan Statistics BOLDconnectR Retrieve, Transform and Analyze the Barcode of Life Data Systems Data BOP2FE Bayesian Optimal Phase II Design with Futility and Efficacy Stopping Boundaries BORG Bounded Outcome Risk Guard for Model Evaluation BORT Beyond Pareto: Bi-Objective and Multi-Objective Regression Trees’ BPM Bayesian Purity Model to Estimate Tumor Purity BPrinStratTTE Causal Effects in Principal Strata Defined by Antidrug Antibodies BRACE Bias Reduction Through Analysis of Competing Events (BRACE) BRACoD.R BRACoD: Bayesian Regression Analysis of Compositional Data BRCore A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers BREADR Estimates Degrees of Relatedness (Up to the Second Degree) for Extreme Low-Coverage Data BRETIGEA Brain Cell Type Specific Gene Expression Analysis BRINDA Computation of BRINDA Adjusted Micronutrient Biomarkers for Inflammation BRISC Fast Inference for Large Spatial Datasets using BRISC BRL Beta Record Linkage BRPL Methods for Bivariate Poverty Line Calculations BRRAT Bayesian Regression Robustness Assessment Test BRcal Boldness-Recalibration of Binary Events BSCB Bayesian Simultaneous Credible Bands for Polynomial Regression BSDA Basic Statistics and Data Analysis BSET A Bayesian Surrogate Evaluation Test BSGW Bayesian Survival Model with Lasso Shrinkage Using Generalized Weibull Regression BSL Bayesian Synthetic Likelihood BSPADATA Bayesian Proposal to Fit Spatial Econometric Models BSPBSS Bayesian Spatial Blind Source Separation BSS Brownian Semistationary Processes BSSasymp Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates BSSoverSpace Blind Source Separation for Multivariate Spatial Data using Eigen Analysis BSSprep Whitening Data as Preparation for Blind Source Separation BSTFA Bayesian Spatio-Temporal 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Bayesian Vector Autoregression BWGS BreedWheat Genomic Selection Pipeline BWStest Baumgartner Weiss Schindler Test of Equal Distributions BaM Functions and Datasets for "Bayesian Methods: A Social and Behavioral Sciences Approach" BaSTA Age-Specific Bayesian Survival Trajectory Analysis from Incomplete Census or Capture-Recapture/Recovery Data BaSkePro Bayesian Model to Archaeological Faunal Skeletal Profiles BacenAPI Data Collection from the Central Bank of Brazil BagWhiskerPlot Bag-and-Whisker Plot BalanceCheck Balance Check for Multiple Covariates in Matched Observational Studies BalancedSampling Balanced and Spatially Balanced Sampling Ball Statistical Inference and Sure Independence Screening via Ball Statistics BallMapper The Ball Mapper Algorithm BarBorGradient Function Minimum Approximator BarcodingR Species Identification using DNA Barcodes Barnard Barnard's Unconditional Test BaseSet Working with Sets the Tidy Way BaseTempSeed Estimation of Seed Germination Base Temperature 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Clinical Trial Design with and Without Historical Control Data BayesCVI Bayesian Cluster Validity Index BayesChange Bayesian Methods for Change Point Analysis BayesCombo Bayesian Evidence Combination BayesDIP Bayesian Decreasingly Informative Priors for Early Termination Phase II Trials BayesDecon Density Deconvolution Using Bayesian Semiparametric Methods BayesDesign Bayesian Single-Arm Design with Survival Endpoints BayesDissolution Bayesian Models for Dissolution Testing BayesERtools Bayesian Exposure-Response Analysis Tools BayesESS Determining Effective Sample Size BayesFBHborrow Bayesian Dynamic Borrowing with Flexible Baseline Hazard Function BayesFM Bayesian Inference for Factor Modeling BayesFR Fitting Functional Responses in 1- and 2-Prey Systems BayesFactor Computation of Bayes Factors for Common Designs BayesFluxR Implementation of Bayesian Neural Networks BayesForge Bayesian Inference using 'numpyro' and 'XLA' BayesGP Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models BayesGPfit Fast Bayesian Gaussian Process Regression Fitting BayesGWQS Bayesian Grouped Weighted Quantile Sum Regression BayesGmed Bayesian Causal Mediation Analysis using 'Stan' BayesGrowth Estimate Fish Growth Using MCMC Analysis BayesLCA Bayesian Latent Class Analysis BayesLN Bayesian Inference for Log-Normal Data BayesLogit PolyaGamma Sampling BayesMFSurv Bayesian Misclassified-Failure Survival Model BayesMallows Bayesian Preference Learning with the Mallows Rank Model BayesMallowsSMC2 Nested Sequential Monte Carlo for the Bayesian Mallows Model BayesMixSurv Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification BayesMoFo Bayesian Mortality Forecasting BayesMortalityPlus Bayesian Mortality Modelling BayesMultMeta Bayesian Multivariate Meta-Analysis BayesMultiMode Bayesian Mode Inference BayesNSGP Bayesian Analysis of Non-Stationary Gaussian Process Models BayesNetBP Bayesian Network Belief Propagation BayesPET Bayesian Prediction of Event Times for Blinded Randomized Controlled Trials BayesPIM Bayesian Prevalence-Incidence Mixture Model BayesPPD Bayesian Power Prior Design BayesPPDSurv Bayesian Power Prior Design for Survival Data BayesPPR Bayesian Projection Pursuit Regression BayesPieceHazSelect Variable Selection in a Hierarchical Bayesian Model for a Hazard Function BayesPocket Bayesian Causal Inference for Periodontal Diseases in Longitudinal Studies BayesPostEst Generate Postestimation Quantities for Bayesian MCMC Estimation BayesPower Sample Size and Power Calculation for Bayesian Testing with Bayes Factor BayesProject Fast Projection Direction for Multivariate Changepoint Detection BayesRS Bayes Factors for Hierarchical Linear Models with Continuous Predictors BayesRTMB Bayesian Inference Using 'RTMB' BayesRegDTR Bayesian Regression for Dynamic Treatment Regimes BayesRep Bayesian Analysis of Replication Studies BayesRepDesign Bayesian Design of Replication Studies BayesS5 Bayesian Variable Selection Using Simplified Shotgun Stochastic Search with Screening (S5) BayesSIM Integrated Interface of Bayesian Single Index Models using 'nimble' BayesSUR Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings BayesSampling Bayes Linear Estimators for Finite Population BayesSurveillance Bayesian Surveillance Methods for Healthcare Performance Monitoring BayesSurvival Bayesian Survival Analysis for Right Censored Data BayesSurvive Bayesian Survival Models for High-Dimensional Data BayesTSM Bayesian Progressive Three State Model with Censoring Due to Intervention BayesTools Tools for Bayesian Analyses BayesTree Bayesian Additive Regression Trees BayesTreePrior Bayesian Tree Prior Simulation BayesTwin Bayesian Analysis of Item-Level Twin Data BayesVarSel Bayes Factors, Model Choice and Variable Selection in Linear Models BayesVolcano Creating Volcano Plots from Bayesian Model Posteriors BayesX R Utilities Accompanying the Software Package BayesX BayesXsrc Distribution of the 'BayesX' C++ Sources BayesfMRI Spatial Bayesian Methods for Task Functional MRI Studies BayesianDEB Bayesian Dynamic Energy Budget Modelling BayesianDisaggregation Evidence-Based Bayesian Disaggregation of Aggregate Indices BayesianFitForecast Bayesian Parameter Estimation and Forecasting for Epidemiological Models BayesianInference Bayesian Inference BayesianLasso Bayesian Lasso Regression and Tools for the Lasso Distribution BayesianLaterality Predict Brain Asymmetry Based on Handedness and Dichotic Listening BayesianMCPMod Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod BayesianMediationA Bayesian Mediation Analysis BayesianNetwork Bayesian Network Modeling and Analysis BayesianPlatformDesignTimeTrend Simulate and Analyse Bayesian Platform Trial with Time Trend BayesianPower Sample Size and Power for Comparing Inequality Constrained Hypotheses BayesianQDM Bayesian Quantitative Decision-Making Framework for Binary and Continuous Endpoints BayesianReasoning Plot Positive and Negative Predictive Values for Medical Tests BayesianTools General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics Bayesiangammareg Double Generalized Gamma Regression Models Bayesiantreg Bayesian t Regression for Modeling Mean and Scale Parameters Bayesrel Bayesian Reliability Estimation Bchron Age-Depth Radiocarbon Modelling BeQut Bayesian Estimation for Quantile Regression Mixed Models BeSS Best Subset Selection in Linear, Logistic and CoxPH Models BeastJar JAR Dependency for MCMC Using 'BEAST' BeeBDC Occurrence Data Cleaning Benchmarking Benchmark and Frontier Analysis Using DEA and SFA BenfordTests Statistical Tests for Evaluating Conformity to Benford's Law Bergm Bayesian Exponential Random Graph Models BerkeleyForestsAnalytics Compute and Summarize Core Forest Metrics from Field Data Bernadette Bayesian Inference and Model Selection for Stochastic Epidemics Bessel Computations and Approximations for Bessel Functions Bestie Bayesian Estimation of Intervention Effects BetaBit Mini Games from Adventures of Beta and Bit BetaDanish The Beta-Danish Distribution for Lifetime Data Analysis BetaPASS Calculate Power and Sample Size with Beta Regression BetterReg Better Statistics for OLS and Binomial Logistic Regression BeviMed Bayesian Evaluation of Variant Involvement in Mendelian Disease BeyondBenford Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset Bhat General Likelihood Exploration BiCausality Binary Causality Inference Framework BiDAG Bayesian Inference for Directed Acyclic Graphs BiDimRegression Calculates the Bidimensional Regression Between Two 2D Configurations BiObjClass Classification of Algorithms BiTSLS Bidirectional Two-Stage Least Squares Estimation BiTrinA Binarization and Trinarization of One-Dimensional Data BiVariAn Bivariate Automatic Analysis BiasCorrector A GUI to Correct Measurement Bias in DNA Methylation Analyses BiasedUrn Biased Urn Model Distributions BibPlots Plot Functions for Use in Bibliometrics BifactorIndicesCalculator Bifactor Indices Calculator BigDataPE Secure and Intuitive Access to 'BigDataPE' 'API' Datasets BigDataStatMeth Scalable Statistical Computing with HDF5-Backed Matrices BigVAR Dimension Reduction Methods for Multivariate Time Series BimodalIndex The Bimodality Index BinGSD Calculate Boundaries and Conditional Power for Single Arm Group Sequential Test with Binary Endpoint BinMat Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs) BinNonNor Data Generation with Binary and Continuous Non-Normal Components BinNor Simultaneous Generation of Multivariate Binary and Normal Variates BinOrdNonNor Concurrent Generation of Binary, Ordinal and Continuous Data BinSegBstrap Piecewise Smooth Regression by Bootstrapped Binary Segmentation Binarize Binarization of One-Dimensional Data BinaryDosage Creates, Merges, and Reads Binary Dosage Files 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Bioassays and Probit Graphs BioStatR Initiation à La Statistique Avec R BioTIMEr Tools to Use and Explore the 'BioTIME' Database BioThermR Standardized Processing and Analysis of Thermal Imaging Data in Animal Studies BioTooltipR Add Bio Tooltips to HTML Reports BioTrajectory Image Processing Tools for Barnes Maze Experiments BioUtils Biological Data Analysis and Visualization BioVenn Create Area-Proportional Venn Diagrams from Biological Lists BioVizSeq Visualizing the Elements Within Bio-Sequences BioWorldR A Curated Collection of Biodiversity and Species Datasets and Utilities Biobase Biobase: Base functions for Bioconductor BiocBaseUtils Utility and internal functions for Bioconductor packages BiocCheck Bioconductor-specific package checks BiocFileCache Manage Files Across Sessions BiocGenerics S4 generic functions used in Bioconductor BiocIO Standard Input and Output for Bioconductor Packages BiocManager Access the Bioconductor Project Package Repository BiocNeighbors Nearest Neighbor Detection for Bioconductor Packages BiocParallel Bioconductor facilities for parallel evaluation BiocSingular Singular Value Decomposition for Bioconductor Packages BiocStyle Standard styles for vignettes and other Bioconductor documents BiocVersion Set the appropriate version of Bioconductor packages Biodem Biodemography Functions BiodiversityR Package for Community Ecology and Suitability Analysis Bioi Biological Image Analysis Bios2cor From Biological Sequences and Simulations to Correlation Analysis BiostatsUHNplus Nested Data Summary, Adverse Events and REDCap Biostrings Efficient manipulation of biological strings BipartiteModularityMaximization Partition Bipartite Network into Non-Overlapping Biclusters by Optimizing Bipartite Modularity BiplotML Logistic Biplot Estimation Using Machine Learning Algorithms BivGeo Basu-Dhar Bivariate Geometric Distribution BivLaplaceRL Bivariate Laplace Transforms, Stochastic Orders, and Entropy Measures in Reliability BivRec Bivariate 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Tests BootstrapQTL Bootstrap cis-QTL Method that Corrects for the Winner's Curse BootstrapTests Bootstrap-Based Hypothesis Testing using Different Resampling Schemes Boptbd Bayesian Optimal Block Designs Boruta Wrapper Algorithm for All Relevant Feature Selection BosonSampling Classical Boson Sampling BoundEdgeworth Bound on the Error of the First-Order Edgeworth Expansion BoundIRT Fit Bounded Continuous Item Response Theory Models to Data BoundaryStats Boundary Overlap Statistics BoutrosLab.plotting.general Functions to Create Publication-Quality Plots BradleyTerry2 Bradley-Terry Models BrainCon Inference the Partial Correlations Based on Time Series Data BrainNetTest Hypothesis Testing for Populations of Brain Networks BranchGLM Efficient Best Subset Selection for GLMs via Branch and Bound Algorithms Branching Simulation and Estimation for Branching Processes BrazilCrime Accesses Brazilian Public Security Data from SINESP Since 2015 BrazilDataAPI Access Brazilian Data via APIs and Curated Datasets BrazilMet Download and Processing of Automatic Weather Stations (AWS) Data of INMET-Brazil BreakPoints Identify Breakpoints in Series of Data Brobdingnag Very Large Numbers in R BrokenAdaptiveRidge Broken Adaptive Ridge Regression with Cyclops Brq Bayesian Analysis of Quantile Regression Models BsMD Bayes Screening and Model Discrimination BsplineQuantReg 'Constrained Quantile Regression with Cubic B-Splines' Buddle A Deep Learning for Statistical Classification and Regression Analysis with Random Effects BuildSys System for Building and Debugging C/C++ Dynamic Libraries BurStFin Burns Statistics Financial BurStMisc Burns Statistics Miscellaneous BusinessDuration Calculates Business Duration Between Two Dates ButtR Download and Extract Data from the 'OzButterflies' Database BuyseTest Generalized Pairwise Comparisons Bvalue B-Value and Empirical Equivalence Bound BwQuant Bandwidth Selectors for Local Linear Quantile Regression C19dNUTS Dataset of Regional COVID-19 Deaths per 100,000 Pop (NUTS) C443 See a Forest for the Trees C50 C5.0 Decision Trees and Rule-Based Models CA3variants Three-Way Correspondence Analysis Variants CADF Customer Analytics Data Formatting CADFtest A Package to Perform Covariate Augmented Dickey-Fuller Unit Root Tests CAESAR.Suite CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation CAFT Rank-Based Compositional Analysis using Log-Linear Models for Microbiome Data with Zero Cells CAGR Compound Annual Growth Rate CAISEr Comparison of Algorithms with Iterative Sample Size Estimation CALANGO Comparative Analysis with Annotation-Based Genomic Components CALF Coarse Approximation Linear Function CALIBERrfimpute Multiple Imputation Using MICE and Random Forest CANE Comprehensive Groups of Experiments Analysis for Numerous Environments CAOP.RAA.2024 Official Administrative Map of the Azores (CAOP 2024) CARBayes Spatial Generalised Linear Mixed Models for Areal Unit Data CARBayesST Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data CARBayesdata Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages CARM Covariate-Adjusted Adaptive Randomization via Mahalanobis-Distance CARME CAR-MM Modelling in Stan CARMS Continuous Time Markov Rate Modeling for Reliability Analysis CARRoT Predicting Categorical and Continuous Outcomes Using One in Ten Rule CASCORE Covariate Assisted Spectral Clustering on Ratios of Eigenvectors CASIdata Datasets from Computer Age Statistical Inference CASMI 'CASMI'-Based Functions CAST 'caret' Applications for Spatial-Temporal Models CATAcode Explore and Code Responses to Check-All-that-Apply Survey Items CATT The Cochran-Armitage Trend Test CATTexact Computation of the p-Value for the Exact Conditional Cochran-Armitage Trend Test CAinterprTools Graphical Aid in Correspondence Analysis Interpretation and Significance Testings CAvariants Correspondence Analysis Variants CB2 CRISPR Pooled Screen Analysis using Beta-Binomial Test CBAModel Stochastic 3D Structure Model for Binder-Conductive Additive Phase CBASSED50 Process CBASS-Derived PAM Data CBCgrps Compare Baseline Characteristics Between Groups CBPE Correlation-Based Penalized Estimators CBPS Covariate Balancing Propensity Score CBRT CBRT Data on Turkish Economy CBSr Fits Cubic Bezier Spline Functions to Intertemporal and Risky Choice Data CBT Confidence Bound Target Algorithm CBTF Caught by the Fuzz! - A Minimalistic Fuzz-Test Runner CBnetworkMA Contrast-Based Bayesian Network Meta Analysis CC Control Charts CCA Canonical Correlation Analysis CCAMLRGIS Antarctic Spatial Data Manipulation CCI Computational Test for Conditional Independence CCM Correlation Classification Method CCMMR Minimization of the Convex Clustering Loss Function CCMnet Congruence Class Models for Networks CCP Significance Tests for Canonical Correlation Analysis (CCA) CCSRfind Convert ICD-10 Codes to CCSR Codes CCWeights Perform Weighted Linear Regression for Calibration Curve CCd The Cauchy-Cacoullos (Discrete Cauchy) Distribution CDCPLACES Access the 'CDC PLACES' API CDF Centroid Decision Forest for High-Dimensional Classification CDFt Downscaling and Bias Correction via Non-Parametric CDF-Transform CDGHMM Hidden Markov Models for Multivariate Panel Data CDM Cognitive Diagnosis Modeling CDMConnector Connect to an OMOP Common Data Model CDSE 'Copernicus Data Space Ecosystem' API Wrapper CDSS Course-Dependent Skill Structures CDSim Simulating Climate Data for Research and Modelling CDSimX Simulating Climate Data for Research and Modelling CDVI Cuddy-Della Valle Index for Capturing the Instability in Time Series Data CDatanet Econometrics of Network Data CDsampling Constrained Sampling in Paid Research Studies CEACT Cost-Effectiveness Analysis Toolkit for Clinical Trials CEC Cross-Entropy Clustering CEDA CRISPR Screen and Gene Expression Differential Analysis CEDMr Capability-Ecological Developmental Model (CEDM) Analysis CEEMDANML CEEMDAN Decomposition Based Hybrid Machine Learning Models CEGO Combinatorial Efficient Global Optimization CEOdata Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion Polls in Catalonia CERFIT Causal Effect Random Forest of Interaction Trees CEoptim Cross-Entropy R Package for Optimization CFAcoop Colony Formation Assay: Taking into Account Cellular Cooperation CFC Cause-Specific Framework for Competing-Risk Analysis CFF Simple Similarity for User-Based Collaborative Filtering Systems CFM Analyzing Censored Factor Models CFO CFO-Type Designs in Phase I/II Clinical Trials CFilt Collaborative Filtering Models for Recommendation Systems CFtime Using CF-Compliant Calendars with Climate Projection Data CGE Computing General Equilibrium CGGP Composite Grid Gaussian Processes CGManalyzer Continuous Glucose Monitoring Data Analyzer CGMissingDataR Impute Missing Glucose Values in CGM Data CGNM Cluster Gauss-Newton Method CGP Composite Gaussian Process Models CGR Compound Growth Rate for Capturing the Growth Rate Over the Period CHAPGWAS CHAP-GWAS: Leveraging Chromosomal Haplotypes to Improve Genome-Wide Association Studies CHEMIST Causal Inference with High-Dimensional Error-Prone Covariates and Misclassified Treatments CHMM Coupled Hidden Markov Models CHNCapitalStock Compute Chinese Capital Stocks CHNOSZ Thermodynamic Calculations and Diagrams for Geochemistry CHOIRBM Plots the CHOIR Body Map CIAAWconsensus Isotope Ratio Meta-Analysis CIARA Cluster Independent Algorithm for Rare Cell Types Identification CICA Clusterwise Independent Component Analysis CICI Causal Inference with Continuous (Multiple Time Point) Interventions CIEE Estimating and Testing Direct Effects in Directed Acyclic Graphs using Estimating Equations CIM Compositional Impact of Migration CIMEHR Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data CIMTx Causal Inference for Multiple Treatments with a Binary Outcome CINE Classification International Normalized of Education CINID Curculionidae INstar IDentification CINNA Deciphering Central Informative Nodes in Network Analysis CINmetrics Calculate Chromosomal Instability Metrics CIPerm Computationally-Efficient Confidence Intervals for Mean Shift from Permutation Methods CIS.DGLM Covariates, Interaction, and Selection for DGLM CITAN CITation ANalysis Toolpack CITMIC Estimation of Cell Infiltration Based on Cell Crosstalk CIfinder Estimate the Confidence Intervals for Predictive Values CIplot Functions to Plot Confidence Interval CIpostSelect Confidence Interval Post-Selection of Variable CJAMP Copula-Based Joint Analysis of Multiple Phenotypes CJIVE Canonical Joint and Individual Variation Explained (CJIVE) CKAT Composite Kernel Association Test for Pharmacogenetics Studies CKLRT Composite Kernel Machine Regression Based on Likelihood Ratio Test CKNNRLD Clustering-Based K-Nearest Neighbor Regression for Longitudinal Data CLA Critical Line Algorithm in Pure R CLAST Exact Confidence Limits after a Sequential Trial CLIC The LIC for Distributed Cosine Regression Analysis CLME Constrained Inference for Linear Mixed Effects Models CLONETv2 Clonality Estimates in Tumor CLRtools Diagnostic Tools for Logistic and Conditional Logistic Regression CLSIEP15 Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations CLUSTShiny Interactive Document for Working with Cluster Analysis CLVTools Tools for Customer Lifetime Value Estimation CLimd Generating Rainfall Rasters from IMD NetCDF Data CMAPSS Commercial Modular Aero-Propulsion System Simulation Data Set CMF Collective Matrix Factorization CMFsurrogate Calibrated Model Fusion Approach to Combine Surrogate Markers CMGFM Covariate-Augumented Generalized Factor Model CMHNPA Cochran-Mantel-Haenszel and Nonparametric ANOVA CMHSU Mental Health Status, Substance Use Status and their Concurrent Status in North American Healthcare Administrative Databases CMIP6VisR Visualization and Analysis of Coupled Model Intercomparison Project, Phase-6 (CMIP6) Hydroclimatic Data CMLS Constrained Multivariate Least Squares CMMs Compositional Mediation Model CMShiny Interactive Document for Working with Confusion Matrix CMTFtoolbox Create (Advanced) Coupled Matrix and Tensor Factorization Models CMapViz Representation Tool For Output Of Connectivity Map (CMap) Analysis CMatching Matching Algorithms for Causal Inference with Clustered Data CMplot Circle Manhattan Plot CNAIM Common Network Asset Indices Methodology (CNAIM) CNID Get Basic Information from Chinese ID Number CNLTreg Complex-Valued Wavelet Lifting for Signal Denoising CNLTtsa Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis CNPS Nonparametric Statistics CNSigs Analysis of Copy Number Signatures CNVScope A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization CNVreg CNV-Profile Regression for Copy Number Variants Association Analysis with Penalized Regression CNprep Pre-Process DNA Copy Number (CN) Data for Detection of CN Events COAP High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model COINT Unit Root Tests with Structural Breaks and Fully-Modified Estimators COINr Composite Indicator Construction and Analysis COLP Causal Discovery for Categorical Data with Label Permutation COMBAT A Combined Association Test for Genes using Summary Statistics COMBO Correcting Misclassified Binary Outcomes in Association Studies COMIX Coarsened Mixtures of Hierarchical Skew Kernels COMMA Correcting Misclassified Mediation Analysis COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression CONCUR Copy Number Profile Curve-Based Association Test COR The COR for Optimal Subset Selection in Distributed Estimation CORE Cores of Recurrent Events CORPlot Cumulative Odds Ratio Plot COST Copula-Based Semiparametric Models for Spatio-Temporal Data COUNT Functions, Data and Code for Count Data COVID19 R Interface to COVID-19 Data Hub COVIDIBGE Downloading, Reading and Analyzing PNAD COVID19 Microdata COveR Clustering with Overlaps CP Conditional Power Calculations CPBayes Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations CPC Implementation of Cluster-Polarization Coefficient CPCAT The Closure Principle Computational Approach Test CPE Concordance Probability Estimates in Survival Analysis CPGLIB Competing Proximal Gradients Library CPMCGLM Correction of the P-Value after Multiple Coding in Generalized Linear Models CPNCoverageAnalysis Conceptual Properties Norming Studies as Parameter Estimation CPP Composition of Probabilistic Preferences (CPP) CPoptim Convex Partition Optimisation CPsurv Nonparametric Change Point Estimation for Survival Data CR2 Compute Cluster Robust Standard Errors with Degrees of Freedom Adjustments CRABS Congruent Rate Analyses in Birth-Death Scenarios CRANsearcher RStudio Addin for Searching Packages in CRAN Database Based on Keywords CRBHSF Cyber-Resilient Bayesian Healthcare Surveillance Framework CRE Interpretable Discovery and Inference of Heterogeneous Treatment Effects CREAM Clustering of Genomic Regions Analysis Method CREDS Calibrated Ratio Estimator under Double Sampling Design CRMetrics Cell Ranger Output Filtering and Metrics Visualization CRTConjoint Conditional Randomization Testing (CRT) Approach for Conjoint Analysis CRTSize Sample Size Estimation Functions for Cluster Randomized Trials CRTgeeDR Doubly Robust Inverse Probability Weighted Augmented GEE Estimator CRTspat Workflow for Cluster Randomised Trials with Spillover CRediTas Generate CRediT Author Statements CSCNet Fitting and Tuning Regularized Cause-Specific Cox Models with Elastic-Net Penalty CSDownscale Statistical Downscaling of Climate Predictions CSESA CRISPR-Based Salmonella Enterica Serotype Analyzer CSHShydRology Canadian Hydrological Analyses CSIndicators Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions CSMES Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain Cost Conditions CSTE Covariate Specific Treatment Effect (CSTE) Curve CSTools Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales CSclone Bayesian Nonparametric Modeling in R CSeQTL Cell Type-Specific Expression Quantitative Trait Loci Mapping CSeqpat Frequent Contiguous Sequential Pattern Mining of Text CSwR Companion to the Book "Computational Statistics with R" CTD A Method for 'Connecting The Dots' in Weighted Graphs CTE Constant Temperature Equivalent CTNote CTN Outcomes, Treatments, and Endpoints CTRing Density Profiles of Wood from CT Scan Images CTShiny Interactive Document for Working with Classification Tree Analysis CTShiny2 Interactive Document for Working with Classification Tree Analysis CTT Classical Test Theory Functions CTTShiny Classical Test Theory via Shiny CTTvis Visualize Item Metrics of the Classical Test Theory Framework CTxCC Multivariate Normal Mean Monitoring Through Critical-to-X Control Chart CUB A Class of Mixture Models for Ordinal Data CUFF Charles's Utility Function using Formula CUMP Analyze Multivariate Phenotypes by Combining Univariate Results CUSUMdesign Compute Decision Interval and Average Run Length for CUSUM Charts CUtools Clinical Utility Tools to Analyze a Predictive Model CVD Color Vision Deficiencies CVST Fast Cross-Validation via Sequential Testing CVThresh Level-Dependent Cross-Validation Thresholding CVXR Disciplined Convex Optimization CVglasso Lasso Penalized Precision Matrix Estimation CVrisk Compute Risk Scores for Cardiovascular Diseases CWT Continuous Wavelet Transformation for Spectroscopy CaDENCE Conditional Density Estimation Network Construction and Evaluation CaMeA Causal Meta-Analysis for Aggregated Data CaPO4Sim A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis Cairo R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output CalSim The Calibration Simplex CalcThemAll.PRM Calculate Pesticide Risk Metric (PRM) Values from Multiple Pesticides...Calc Them All CalibratR Mapping ML Scores to Calibrated Predictions CalibrateSSB Weighting and Estimation for Panel Data with Non-Response CalibrationCurves Calibration Performance CamelRatiosIndex Multivariate-Weighted Indexing of CAMEL Ratios for Bank Performance CamelUp 'CamelUp' Board Game as a Teaching Aid for Introductory Statistics CancerEvolutionVisualization Publication Quality Phylogenetic Tree Plots CancerGram Prediction of Anticancer Peptides Canek Batch Correction of Single Cell Transcriptome Data CanonicalFamilyExtra Extra Canonical Link Family Objects for Generalized Linear Models Capsule Comprehensive Reproducibility Framework for R and Bioinformatics Analysis CardiacDP Automated Cardiac Data Processing via ACF, GA & Tracking Index CardioCurveR Nonlinear Modeling of R-R Interval Dynamics CardioDataSets A Comprehensive Collection of Cardiovascular and Heart Disease Datasets CareDensity Calculate the Care Density or Fragmented Care Density Given a Patient-Sharing Network CarletonStats Functions for Statistics Classes at Carleton College Carlson Carlson Elliptic Integrals and Incomplete Elliptic Integrals Cascade Selection, Reverse-Engineering and Prediction in Cascade Networks CascadeData Experimental Data of Cascade Experiments in Genomics CaseBasedReasoning Case Based Reasoning CaseCohortCoxSurvival Case-Cohort Cox Survival Inference CatDataAnalysis Datasets for Categorical Data Analysis by Agresti CatDyn Fishery Stock Assessment by Catch Dynamics Models CatEncoders Encoders for Categorical Variables CatPredi Optimal Categorisation of Continuous Variables in Prediction Models CatReg Solution Paths for Linear and Logistic Regression Models with Categorical Predictors, with SCOPE Penalty CatastRo Interface to the Spanish 'Catastro' Web Services Category Category Analysis CausCor Calculate Correlations and Estimate Causality CausalGPS Matching on Generalized Propensity Scores with Continuous Exposures CausalImpact Inferring Causal Effects using Bayesian Structural Time-Series Models CausalMBSTS MBSTS Models for Causal Inference and Forecasting CausalMetaR Causally Interpretable Meta-Analysis CausalMixGPD Bayesian Nonparametric Conditional Density Modeling in Causal Inference and Clustering with a Heavy-Tail Extension CausalModels Causal Inference Modeling for Estimation of Causal Effects CausalQueries Make, Update, and Query Binary Causal Models CausalSpline Nonlinear Causal Dose-Response Estimation via Splines CautiousLearning Control Charts with Guaranteed In-Control Performance and Cautious Parameters Learning CbKST Competence-Based Knowledge Space Theory CePa Centrality-Based Pathway Enrichment CeRNASeek Identification and Analysis of ceRNA Regulation CellDEEP Cell DiffErential Expression by Pooling ('CellDEEP') CellWindX Marker Gene Analysis and Visualization for Single-Cell Data CenBAR Broken Adaptive Ridge AFT Model with Censored Data CensMFM Finite Mixture of Multivariate Censored/Missing Data CensRegSMSN Censored Linear Regression Models under Heavy‑tailed Distributions CensSpatial Censored Spatial Models Census2016 Data from the Australian Census 2016 CepReg A Cepstral Model for Covariate-Dependent Time Series CepalStatR Access to the 'CEPALSTAT API' CerioliOutlierDetection Outlier Detection Using the Iterated RMCD Method of Cerioli (2010) Certara.DarwinReporter Data Visualization Utilities for 'pyDarwin' Machine Learning Pharmacometric Model Development Certara.ModelResults Generate Diagnostics for Pharmacometric Models Using 'shiny' Certara.NLME8 Utilities for Certara's Nonlinear Mixed-Effects Modeling Engine Certara.R Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara Certara.RDarwin Interface for 'pyDarwin' Machine Learning Pharmacometric Model Development Certara.RsNLME Pharmacometric Modeling Certara.RsNLME.ModelBuilder Pharmacometric Model Building Using 'shiny' Certara.RsNLME.ModelExecutor Execute Pharmacometric Models Using 'shiny' Certara.VPCResults Generate Visual Predictive Checks (VPC) Using 'shiny' Certara.Xpose.NLME Enhances 'xpose' Diagnostics for Pharmacometric Models from 'Certara.RsNLME' and Phoenix NLME ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and Visualization ChainLadder Statistical Methods and Models for Claims Reserving in General Insurance ChangePointTaylor Identify Changes in Mean ChangepointTesting Change Point Estimation for Clustered Signals ChannelAttribution Markov Model for Online Multi-Channel Attribution ChannelAttributionApp Shiny Web Application for the Multichannel Attribution Problem Chaos01 0-1 Test for Chaos ChaosGame Chaos Game CharAnalysis Peak Detection and Fire History from Sediment-Charcoal Records Characterization Implement Descriptive Studies Using the Common Data Model ChauBoxplot Chauvenet-Type Boxplot CheckDigit Calculate and Verify Check Digits ChemmineR Cheminformatics Toolkit for R ChemoSpec Exploratory Chemometrics for Spectroscopy ChemoSpec2D Exploratory Chemometrics for 2D Spectroscopy ChemoSpecUtils Functions Supporting Packages ChemoSpec and ChemoSpec2D ChernoffDist Chernoff's Distribution ChessGmooG FIDE Chess Players Ratings for 2015 and 2020 ChestVolume Estimate the Chest Volume with Markers Data ChileDataAPI Access Chilean Data via APIs and Curated Datasets ChillModels Processing Chill and Heat Models for Temperate Fruit Trees ChinAPIs Access Chinese Data via Public APIs and Curated Datasets ChineseNames Chinese Name Database 1930-2008 ChoiceModelR Choice Modeling in R CholWishart Cholesky Decomposition of the Wishart Distribution CimpleG A Method to Identify Single CpG Sites for Classification and Deconvolution CircMLE Maximum Likelihood Analysis of Circular Data CircNNTSR Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models CircNNTSRSymmetric Circular Data using Symmetric NNTS Models CircNNTSRaxial Axial Data using NNTS Models CircNNTSRmult Multivariate Circular Data using MNNTS Models CircOutlier Detection of Outliers in Circular-Circular Regression CircStats Circular Statistics, from "Topics in Circular Statistics" (2001) CircaCP Sleep and Circadian Metrics Estimation from Actigraphy Data CirceR Construct Cohort Inclusion and Restriction Criteria Expressions CirclesIntersections Algorithm for Computation of the Intersection Areas of N Circles CircularBoxplots Grouped Boxplots for Circular Data CircularDDM Circular Drift-Diffusion Model CircularRegression Circular Regression Models CircularSilhouette Fast Silhouette on Circular or Linear Data Clusters CiteSource Data-Driven Search Strategy Development and Evidence Synthesis Reporting Ckmeans.1d.dp Optimal, Fast, and Reproducible Univariate Clustering Claddis Measuring Morphological Diversity and Evolutionary Tempo ClaimsProblems Analysis of Conflicting Claims ClamR Time Series Modeling for Climate Change Proxies ClassComparison Classes and Methods for "Class Comparison" Problems on Microarrays ClassDiscovery Classes and Methods for "Class Discovery" with Microarrays or Proteomics ClassificationEnsembles Automatically Builds 12 Classification Models (6 Individual and 6 Ensembles of Models) from Classification Data ClassifyITS Fungal Assignment Pipeline CleanBSequences Curing of Biological Sequences Cleanet Automated Doublet Detection and Classification for Cytometry Data CleaningValidation Cleaning Validation Functions for Pharmaceutical Cleaning Process ClickClust Model-Based Clustering of Categorical Sequences ClickHouseHTTP A Simple HTTP Database Interface to 'ClickHouse' CliftLRD Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent for Irregularly Sampled Time Series ClimClass Climate Classification According to Several Indices ClimInd Climate Indices ClimMobTools API Client for the 'ClimMob' Platform ClimProjDiags Set of Tools to Compute Various Climate Indices ClimaRep Estimating Climate Analogue Areas ClinSigMeasures Clinical Significance Measures ClinTrialPredict Predicting and Simulating Clinical Trial with Time-to-Event Endpoint ClinicalTrialSummary Summary Measures for Clinical Trials with Survival Outcomes ClinicalUtilityRecal Recalibration Methods for Improved Clinical Utility of Risk Scores CliquePercolation Clique Percolation for Networks CloneSeeker Seeking and Finding Clones in Copy Number and Sequencing Data CluMP Clustering of Micro Panel Data ClueR Cluster Evaluation ClusBoot Bootstrap a Clustering Solution to Establish the Stability of the Clusters ClusPred Simultaneous Semi-Parametric Estimation of Clustering and Regression ClusROC ROC Analysis in Three-Class Classification Problems for Clustered Data ClusTCR2 Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2' ClusTorus Prediction and Clustering on the Torus by Conformal Prediction ClussCluster Simultaneous Detection of Clusters and Cluster-Specific Genes in High-Throughput Transcriptome Data ClustAssess Tools for Assessing Clustering ClustBlock Clustering of Datasets ClustGeo Hierarchical Clustering with Spatial Constraints ClustImpute K-Means Clustering with Build-in Missing Data Imputation ClustMC Cluster-Based Multiple Comparisons ClustOfVar Clustering of Variables ClustVarLV Clustering of Variables Around Latent Variables ClusterBootstrap Analyze Clustered Data using the Cluster Bootstrap ClusterR Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering ClusterRandSSAdj Small Sample Adjustment of Cluster Randomized Trial ClusterRankTest Rank Tests for Clustered Data ClusterStability Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions ClusterVAR Fitting Latent Class Vector-Autoregressive (VAR) Models ClusteredMutations Location and Visualization of Clustered Somatic Mutations Clustering Techniques for Evaluating Clustering CoClust A Copula-Based Clustering Algorithm CoDaImpact Interpreting CoDa Regression Models CoDaLoMic Compositional Models to Longitudinal Microbiome Data CoDiNA Co-Expression Differential Network Analysis CoFM Copula Factor Models CoImp Parametric and Nonparametric Copula-Based Imputation Methods CoMiRe Convex Mixture Regression CoNI Correlation Guided Network Integration (CoNI) CoRpower Power Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials CoSMoS Complete Stochastic Modelling Solution CoTiMA Continuous Time Meta-Analysis ('CoTiMA') CoalescentPhylo Phylogenetics via Root Distances Method Under the Coalescent CoastlineFD Calculation of the Fractal Dimension of a Coastline CodataGS Genomic Prediction Using SNP Codata CodeDepends Analysis of R Code for Reproducible Research and Code Comprehension CodelistGenerator Identify Relevant Clinical Codes and Evaluate Their Use CohortCharacteristics Summarise and Visualise Characteristics of Patients in the OMOP CDM CohortConstructor Build and Manipulate Study Cohorts Using a Common Data Model CohortContrast Enrichment Analysis of Clinically Relevant Concepts in Common Data Model Cohort Data CohortGenerator Cohort Generation for the OMOP Common Data Model CohortMethod Comparative Cohort Method with Large Scale Propensity and Outcome Models CohortPlat Simulation of Cohort Platform Trials for Combination Treatments CohortSurvival Estimate Survival from Common Data Model Cohorts CohortSymmetry Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model CoinMinD Simultaneous Confidence Intervals for Multinomial Proportions Coinprofile Coincident Profile ColOpenData Download Colombian Demographic, Climate and Geospatial Data CollocInfer Collocation Inference for Dynamic Systems ColombiAPI Access Colombian Data via APIs and Curated Datasets ColorNameR Give Colors a Name Colossus "Risk Model Regression and Analysis with Complex Non-Linear Models" ComBatFamQC Comprehensive Batch Effect Diagnostics and Harmonization ComICS Computational Methods for Immune Cell-Type Subsets ComRiskModel Fitting of Complementary Risk Models CombinS Construction Methods for Series of PBIB Designs via Combinatory Method S CombinePortfolio Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies CommEcol Community Ecology Analyses CommKern Network-Based Communities and Kernel Machine Methods CommonDataModel OMOP CDM DDL and Documentation Generator CommonJavaJars Useful Libraries for Building a Java Based GUI under R CommonMean.Copula Common Mean Vector under Copula Models Comp2ROC Compare Two ROC Curves that Intersect CompAREdesign Statistical Functions for the Design of Studies with Composite Endpoints CompClassMetrics Classification Measures when Subclasses are Involved CompDist Multisection Composite Distributions CompExpDes Designs for Computer Experimentations CompGR Complete Annual Growth Rate Generator CompMix A Comprehensive Toolkit for Environmental Mixtures Analysis CompModels Pseudo Computer Models for Optimization CompPareto Discrete Composite Distributions with Pareto Tails CompQuadForm Distribution Function of Quadratic Forms in Normal Variables CompR Paired Comparison Data Analysis CompareCausalNetworks Interface to Diverse Estimation Methods of Causal Networks CompareMultipleModels Finding the Best Model Using Eight Metrics Values CompareTests Correct for Verification Bias in Diagnostic Accuracy & Agreement ComparisonSurv Comparison of Survival Curves Between Two Groups Compind Composite Indicators Functions ComplexHeatmap Make Complex Heatmaps ComplexUpset Create Complex UpSet Plots Using 'ggplot2' Components CompositeReliability Determine the Composite Reliability of a Naturalistic, Unbalanced Dataset Compositional Compositional Data Analysis CompositionalClust Clustering with Compositional Data CompositionalHDDA High Dimensional Discriminant Analysis with Compositional Data CompositionalML Machine Learning with Compositional Data CompositionalNAimp Missing Value Imputation with Compositional Data CompositionalRF Multivariate Random Forest with Compositional Responses CompositionalSR Spatial Regression Models with Compositional Data CompoundDb Creating and Using (Chemical) Compound Annotation Databases CompoundEvents Statistical Modeling of Compound Events ComradesM The Comrades Marathon 1921 to 2019 ConFluxPro Soil Gas Analysis and Flux Modeling ConNEcT Contingency Measure-Based Networks for Binary Time Series ConSciR Tools for Conservation Science ConSpline Partial Linear Least-Squares Regression using Constrained Splines ConconiAnaerobicThresholdTest Conconi Estimate of Anaerobic Threshold from a TCX File ConcordanceTest An Alternative to the Kruskal-Wallis Based on the Kendall Tau Distance CondCopulas Estimation and Inference for Conditional Copula Models CondMVT Conditional Multivariate t Distribution, Expectation Maximization Algorithm, and Its Stochastic Variants CondiS Censored Data Imputation for Direct Modeling ConfMatrix Confusion Matrix ConfidenceEllipse Computation of 2D and 3D Elliptical Joint Confidence Regions ConfigParser Package to Parse an INI File, Including Variable Interpolation ConformalSmallest Efficient Tuning-Free Conformal Prediction ConfusionTableR Confusion Matrix Toolset CongressData A Functional Tool for 'CongressData' CongreveLamsdell2016 Distance Metrics for Trees Generated by Congreve and Lamsdell Conigrave Flexible Tools for Multiple Imputation ConjointChecks Implementation of a Method to Check the Cancellation Axioms of Additive Conjoint Measurement ConnMatTools Tools for Working with Connectivity Data ConnectednessApproach Connectedness Approach Connection Measures of Independence and Connection Without Linear Models ConsRank Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach ConsRankClass Classification and Clustering of Preference Rankings ConsReg Fits Regression & ARMA Models Subject to Constraints to the Coefficient ConsensusClusterPlus ConsensusClusterPlus ConsensusClustering Consensus Clustering ConsensusOPLS Consensus OPLS for Multi-Block Data Fusion ContRespPP Predictive Probability for a Continuous Response with an ANOVA Structure ContaminatedMixt Clustering and Classification with the Contaminated Normal ContourFunctions Create Contour Plots from Data or a Function ConvergenceClubs Finding Convergence Clubs ConvergenceConcepts Seeing Convergence Concepts in Action ConversationAlign Process Text and Compute Linguistic Alignment in Conversation Transcripts ConvertPar Estimating IRT Parameters via Machine Learning Algorithms Convolutioner Convolution of Data CooRTweet Coordinated Networks Detection on Social Media CooccurrenceAffinity Affinity in Co-Occurrence Data CoopGame Important Concepts of Cooperative Game Theory CoordinateCleaner Automated Cleaning of Occurrence Records from Biological Collections CopCTS Copula-Based Semiparametric Analysis for Time Series Data with Detection Limits CopernicusClimate Search Download and Handle Data from Copernicus Climate Data Service CopernicusDEM Copernicus Digital Elevation Models CopernicusDataspace Search Download and Handle Data from the Copernicus Data Space Ecosystem CopernicusMarine Search Download and Handle Data from Copernicus Marine Service Information Copula.Markov Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series Copula.Markov.survival Copula Markov Model with Dependent Censoring Copula.surv Analysis of Bivariate Survival Data Based on Copulas CopulaCenR Copula-Based Regression Models for Multivariate Censored Data CopulaGAMM Copula-Based Mixed Regression Models CopulaInference Estimation and Goodness-of-Fit of Copula-Based Models with Arbitrary Distributions CopulaREMADA Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies CopulaSCR Analysis of Semi-Competing Risks Data Using Copula-Based Models CorMID Correct Mass Isotopologue Distribution Vectors CoreMicrobiomeR Identification of Core Microbiome CorrBin Nonparametrics with Clustered Binary and Multinomial Data CorrMixed Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models CorrToolBox Modeling Correlational Magnitude Transformations in Discretization Contexts CorrectOverloadedPeaks Correct Overloaded Peaks from GC-APCI-MS Data CorrectedFDR Correcting False Discovery Rates Correlplot A Collection of Functions for Graphing Correlation Matrices CortSineScore Compute Cortisol Sine Score (CSS) for Diurnal Cortisol Analysis Counterfactual Estimation and Inference Methods for Counterfactual Analysis Counternull Randomization-Based Inference Countr Flexible Univariate Count Models Based on Renewal Processes CountsEPPM Mean and Variance Modeling of Count Data CovCorTest Statistical Tests for Covariance and Correlation Matrices and their Structures CovEsts Nonparametric Estimators for Covariance Functions CovSel Model-Free Covariate Selection CovTools Statistical Tools for Covariance Analysis CovidMutations Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019) CoxAIPW Doubly Robust Inference for Cox Marginal Structural Model with Informative Censoring CoxBcv Bias-Corrected Sandwich Variance Estimators for Marginal Cox Analysis of Cluster Randomized Trials CoxBoost Cox Models by Likelihood Based Boosting for a Single Survival Endpoint or Competing Risks CoxICPen Variable Selection for Cox's Model with Interval-Censored Data CoxLikelihood Robust Likelihood Ratio Test and Confidence Intervals for the Cox Model CoxMK A Model-X Knockoff Method for Genome-Wide Survival Association Analysis CoxPlus Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects Coxmos Cox MultiBlock Survival CpGFilter CpG Filtering Method Based on Intra-Class Correlation Coefficients CpGassoc Association Between Methylation and a Phenotype of Interest CpmERCCutoff Calculation of Log2 Counts per Million Cutoff from ERCC Controls CptNonPar Nonparametric Change Point Detection for Multivariate Time Series CreditRisk Evaluation of Credit Risk with Structural and Reduced Form Models Cronbach Cronbach's Alpha CropBreeding Stability Analysis in Crop Breeding CropScapeR Access Cropland Data Layer Data via the 'CropScape' Web Service CropWaterBalance Climate Water Balance for Irrigation Purposes CrossCarry Analysis of Data from a Crossover Design with GEE CrossClustering A Partial Clustering Algorithm CrossExpression Cross-Expression Analysis of Spatial Transcriptomics Data CrossValidate Classes and Methods for Cross Validation of "Class Prediction" Algorithms Crossover Analysis and Search of Crossover Designs Crosstabs.Loglinear Cross Tabulation and Loglinear Analyses of Categorical Data CryptRndTest Statistical Tests for Cryptographic Randomness CsChange Testing for Change in C-Statistic Cubist Rule- And Instance-Based Regression Modeling CureDepCens Dependent Censoring Regression Models with Cure Fraction CurricularAnalytics Exploring and Analyzing Academic Curricula CurricularComplexity Toolkit for Analyzing Curricular Complexity CurricularComplexityData Data for Exploring Curricular Complexity CustomDerivative Pricing Various Types of Custom Derivatives CustomerScoringMetrics Evaluation Metrics for Customer Scoring Models Depending on Binary Classifiers CustosAscensor Costs Allocation for the Installation of an Elevator CutpointsOEHR Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model CvmortalityMult Cross-Validation for Multi-Population Mortality Models Cyclops Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis CytOpT Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation CytoProfile Cytokine Profiling Analysis Tool CytoSimplex Simplex Visualization of Cell Fate Similarity in Single-Cell Data CytobankAPI Cytobank API Wrapper for R D3GB Interactive Genome Browser D3mirt Descriptive 2D and 3D Descriptive Multidimensional Item Response Theory Modeling D3partitionR Interactive Charts of Nested and Hierarchical Data with 'D3.js' D4TAlink.light GDP - Workflow Management DA Discriminant Analysis for Evolutionary Inference DAAG Data Analysis and Graphics Data and Functions DAAGbio Data Sets and Functions, for Demonstrations with Expression Arrays and Gene Sequences DACF Data Analysis with Ceiling and/or Floor Data DAGassist Test Robustness with Directed Acyclic Graphs DAIME Effects of Changing Deposition Rates DAISIE Dynamical Assembly of Islands by Speciation, Immigration and Extinction DAISIEprep Extracts Phylogenetic Island Community Data from Phylogenetic Trees DAKS Data Analysis and Knowledge Spaces DALEX moDel Agnostic Language for Exploration and eXplanation DALEXtra Extension for 'DALEX' Package DALSM Nonparametric Double Additive Location-Scale Model (DALSM) DALY The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R DAMOCLES Dynamic Assembly Model of Colonization, Local Extinction and Speciation DANDELION Discovery of Candidate Disease Genes Using Trans-Regulatory Effects DAPAR Tools for the Differential Analysis of Proteins Abundance with R DAST Spatio-Temporal Disaggregation for Maps with Changing Areal Boundaries DATAstudio The Research Data Warehouse of Miguel de Carvalho DArand Differential Analysis with Random Reference Genes DBCVindex Calculates the Density-Based Clustering Validation (DBCV) Index DBHC Sequence Clustering with Discrete-Output HMMs DBI R Database Interface DBItest Testing DBI Backends DBModelSelect Distribution-Based Model Selection DBNMFrank Rank Selection for Non-Negative Matrix Factorization DBR Discrete Beta Regression DBTC Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis DBfit A Double Bootstrap Method for Analyzing Linear Models with Autoregressive Errors DBmaps A Metadata-Driven Framework for Streamlining Database Joins DCCA Detrended Fluctuation and Detrended Cross-Correlation Analysis DCEM Clustering Big Data using Expectation Maximization Star (EM*) Algorithm DCEmgmt DCE Data Reshaping and Processing DCEtool Efficient and Accessible Discrete Choice Experiments DCG Data Cloud Geometry (DCG): Using Random Walks to Find Community Structure in Social Network Analysis DCL Claims Reserving under the Double Chain Ladder Model DCLEAR Distance Based Cell Lineage Reconstruction DCchoice Analyzing Dichotomous Choice Contingent Valuation Data DChaos Chaotic Time Series Analysis DCluster Functions for the Detection of Spatial Clusters of Diseases DClusterm Model-Based Detection of Disease Clusters DDD Diversity-Dependent Diversification DDESONN A Deep Dynamic Experimental Self-Organizing Neural Network Framework DDHFm Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays) DDIwR DDI with R DDL Doubly Debiased Lasso (DDL) DDM Death Registration Coverage Estimation DDPM Data Sets for Discrete Probability Models DDPstar Density Regression via Dirichlet Process Mixtures of Normal Structured Additive Regression Models DDRTree Learning Principal Graphs with DDRTree DEBBI Differential Evolution-Based Bayesian Inference DECIDE DEComposition of Indirect and Direct Effects DECIPHER Tools for curating, analyzing, and manipulating biological sequences DEET Differential Expression Enrichment Tool DEEVD Density Estimation by Extreme Value Distributions DEHOGT Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data DELTD Kernel Density Estimation using Lifetime Distributions DEM The Distributed EM Algorithms in Multivariate Gaussian Mixture Models DENSaftertransform Estimating Density after Logarithmic or Power Transformation of Data DEPONS2R Read, Plot and Analyse Output from the DEPONS Model DER Income Polarization Index DES Discrete Event Simulation DESA Detecting Epidemics using School Absenteeism DESNP Differentially Expressed Single Nucleotide Polymorphism DESeq2 Differential gene expression analysis based on the negative binomial distribution DET Representation of DET Curve with Confidence Intervals DEXiR 'DEXi' Library DEmixR Fit Two-Component Normal and Lognormal Mixture Models DEoptim Global Optimization by Differential Evolution DEoptimR Differential Evolution Optimization in Pure R DEploid Deconvolute Mixed Genomes with Unknown Proportions DEploid.utils 'DEploid' Data Analysis and Results Interpretation DEplotting Visualization Tools for German Regional Data DFA Detrended Fluctuation Analysis DFA.CANCOR Linear Discriminant Function and Canonical Correlation Analysis DFBA Distribution-Free Bayesian Analysis DFD Extract Drugs from Differential Expression Data from LINCS Database DFIT Differential Functioning of Items and Tests DGEAR Differential Gene Expression Analysis with R DGEobj Differential Gene Expression (DGE) Analysis Results Data Object DGEobj.utils Differential Gene Expression (DGE) Analysis Utility Toolkit DGLMExtPois Double Generalized Linear Models Extending Poisson Regression DGP4LCF Dependent Gaussian Processes for Longitudinal Correlated Factors DHARMa Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models DHBins Hexmaps for NZ District Health Boards DHS.rates Calculates Demographic Indicators DHSr Create Large Scale Repeated Regression Summary Statistics Dataset and Visualization Seamlessly DICErClust Deep Significance Clustering for Clinical Risk Stratification DICOMread Reading and Saving DICOM Image Files DIDHAD Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Untreated Groups DIDmultiplegt Estimators DID with Multiple Groups and Periods DIDmultiplegtDYN Estimation in Staggered First Switch Designs, where Groups Experience their First Treatment Change at Different Points in Time DIETCOST Calculate the Cost and Environmental Impact of a Ideal Diet DIFM Dynamic ICAR Spatiotemporal Factor Models DIFboost Detection of Differential Item Functioning (DIF) in Rasch Models by Boosting Techniques DIFlasso A Penalty Approach to Differential Item Functioning in Rasch Models DIFplus Multilevel Mantel-Haenszel Statistics for Differential Item Functioning Detection DIFshiny Differential Item Functioning via Shiny Application DIFtree Item Focussed Trees for the Identification of Items in Differential Item Functioning DIGSS Determination of Intervals Using Georeferenced Survey Simulation DIME Differential Identification using Mixture Ensemble DIMORA Diffusion Models R Analysis DIRECT Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior DIRMR Distributed Imputation for Random Effects Models with Missing Responses DIVINE Curated Datasets and Tools for Epidemiological Data Analysis DIZtools Lightweight Utilities for 'DIZ' R Package Development DIZutils Utilities for 'DIZ' R Package Development DImodels Diversity-Interactions (DI) Models DImodelsMulti Fit Multivariate Diversity-Interactions Models with Repeated Measures DImodelsVis Visualising and Interpreting Statistical Models Fit to Compositional Data DIscBIO A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics DJL Distance Measure Based Judgment and Learning DLASSO Implementation of Adaptive or Non-Adaptive Differentiable Lasso and SCAD Penalties in Linear Models DLEGFM Distributed Loading Estimation for General Factor Model DLFM Distributed Laplace Factor Model DLL Decorrelated Local Linear Estimator DLMRMV Distributed Linear Regression Models with Response Missing Variables DLMtool Data-Limited Methods Toolkit DLPCA The Distributed Local PCA Algorithm DMCfun Diffusion Model of Conflict (DMC) in Reaction Time Tasks DMMF Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model DMRnet Delete or Merge Regressors Algorithms for Linear and Logistic Model Selection and High-Dimensional Data DMtest Differential Methylation Tests (DMtest) DNAcopy DNA Copy Number Data Analysis DNAmf Diffusion Non-Additive Model with Tunable Precision DNAmixturesLite Statistical Inference for Mixed Traces of DNA (Lite-Version) DNAmotif DNA Sequence Motifs DNAseqtest Generating and Testing DNA Sequences DNAtools Tools for Analysing Forensic Genetic DNA Data DNMF Discriminant Non-Negative Matrix Factorization DNNSIM Single-Index Neural Network for Skewed Heavy-Tailed Data DNetFinder Estimating Differential Networks under Semiparametric Gaussian Graphical Models DOEM The Distributed Online Expectation Maximization Algorithms to Solve Parameters of Poisson Mixture Models DOIcreator Append DOIs to References in Word Documents DOPE Drug Ontology Parsing Engine DOS Design of Observational Studies DOS2 Design of Observational Studies, Companion to the Second Edition DOSE Disease Ontology Semantic and Enrichment analysis DOSPortfolio Dynamic Optimal Shrinkage Portfolio DOVE Durability of Vaccine Efficacy DOYPAColors Don't Overthink Your Palette of Colors DOvalidation Kernel Hazard Estimation with Best One-Sided and Double One-Sided Cross-Validation DPCD Dirichlet Process Clustering with Dissimilarities DPComb Discrete p-Value Combination Tests DPI The Directed Prediction Index for Causal Direction Inference from Observational Data DPP Inference of Parameters of Normal Distributions from a Mixture of Normals DPQ Density, Probability, Quantile ('DPQ') Computations DPQBootstrap Dirichlet Quantile Bootstrap for Time Series DPQmpfr DPQ (Density, Probability, Quantile) Distribution Computations using MPFR DPTM Dynamic Panel Multiple Threshold Model with Fixed Effects DPpack Differentially Private Statistical Analysis and Machine Learning DQA Data Quality Assessment Tools DQAgui Graphical User Interface for Data Quality Assessment DQAstats Core Functions for Data Quality Assessment DR.SC Joint Dimension Reduction and Spatial Clustering DRDID Doubly Robust Difference-in-Differences Estimators DREGAR Regularized Estimation of Dynamic Linear Regression in the Presence of Autocorrelated Residuals (DREGAR) DRHotNet Differential Risk Hotspots in a Linear Network DRIP Discontinuous Regression and Image Processing DRPT Density Ratio Permutation Test DRR Dimensionality Reduction via Regression DRaWR Discriminative Random Walk with Restart DRclass Consider Ambiguity in Probabilistic Descriptions Using Density Ratio Classes DRomics Dose Response for Omics DRquality Quality Measurements for Dimensionality Reduction DRsurvCRT Doubly-Robust Estimation for Survival Outcomes in Cluster-Randomized Trials DRviaSPCN Drug Repurposing in Cancer via a Subpathway Crosstalk Network DSAIDE Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution) DSAIRM Dynamical Systems Approach to Immune Response Modeling DSAM Data Splitting Algorithms for Model Developments DSBayes Bayesian Subgroup Analysis in Clinical Trials DSDRM Distributed Sampling for Dynamic Regression Models DSFM Distributed Skew Factor Model Estimation Methods DSGEr Transcriptional Disruption Score for Gene Sets DSI 'DataSHIELD' Interface DSIR Data Science Infrastructure for Global Health DSL Distributed Storage and List DSLite 'DataSHIELD' Implementation on Local Datasets DSMolgenisArmadillo 'DataSHIELD' Client for 'MOLGENIS Armadillo' DSOpal 'DataSHIELD' Implementation for 'Opal' DSSAT A Comprehensive R Interface for the DSSAT Cropping Systems Model DSWE Data Science for Wind Energy DSjobtracker What Skills and Qualifications are Required for Data Science Related Jobs? DSpoty Get 'Spotify' API Multiple Information DT A Wrapper of the JavaScript Library 'DataTables' DT2 'DataTables' 2.x for R DTAT Dose Titration Algorithm Tuning DTAXG Diagnostic Test Assessment in the Absence of Gold Standard DTAplots Creates Plots Accompanying Bayesian Diagnostic Test Accuracy Meta-Analyses DTComPair Comparison of Binary Diagnostic Tests in a Paired Study Design DTDA Doubly Truncated Data Analysis DTDA.cif Doubly Truncated Data Analysis, Cumulative Incidence Functions DTDA.ni Doubly Truncated Data Analysis, Non Iterative DTEAssurance Assurance Methods for Clinical Trials with a Delayed Treatment Effect DTEBOP2 Bayesian Optimal Phase II Randomized Clinical Trial Design with Delayed Outcomes DTFM Distributed Online Covariance Matrix Tests for Truncated Factor Model DTMCPack Suite of Functions Related to Discrete-Time Discrete-State Markov Chains DTRKernSmooth Estimate and Make Inference About Optimal Treatment Regimes via Smoothed Methods DTRlearn2 Statistical Learning Methods for Optimizing Dynamic Treatment Regimes DTRreg DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv) DTS Discrete Tempered Stable Distributions DTSEA Drug Target Set Enrichment Analysis DTSR Distributed Trimmed Scores Regression for Handling Missing Data DTSg A Class for Working with Time Series Data Based on 'data.table' and 'R6' with Largely Optional Reference Semantics DTWBI Imputation of Time Series Based on Dynamic Time Warping DTWUMI Imputation of Multivariate Time Series Based on Dynamic Time Warping DTwrappers Simplified Data Analysis with Wrapper Functions for the 'Data.Table' Package DTwrappers2 Extensions of 'DTwrappers' DUToolkit Visualizing and Quantifying Decision Uncertainty DVHmetrics Analyze Dose-Volume Histograms and Check Constraints DWDLargeR Fast Algorithms for Large Scale Generalized Distance Weighted Discrimination DWLS Gene Expression Deconvolution Using Dampened Weighted Least Squares DWaveNARDL Dual Wavelet Based NARDL Model DWreg Parametric Regression for Discrete Response DYM Did You Mean? DamageDetective Detecting Damaged Cells in Single-Cell RNA Sequencing Data DamiaNN Neural Network Numerai DandEFA Dandelion Plot for R-Mode Exploratory Factor Analysis DanielBiostatistics10th Functions for Wayne W. Daniel's Biostatistics, Tenth Edition Dark The Analysis of Dark Adaptation Data DarkDiv Estimating Dark Diversity and Site-Specific Species Pools DasGuptR Das Gupta Standardisation and Decomposition Dasst Tools for Reading, Processing and Writing 'DSSAT' Files DataClean Data Cleaning DataCraftR Create Datasets Interactively Using 'shiny' DataDNA Data Frame Fingerprints and Lineage Figures DataEditR An Interactive Editor for Viewing, Entering, Filtering & Editing Data DataExplorer Automate Data Exploration and Treatment DataFusionGDM Machine Learning for Integrating Partially Overlapped Genetic Datasets DataGraph Export Data from 'R' to 'DataGraph' DataLoader Import Multiple File Types DataMetProcess Meteorological Data Processing DataPackageR Construct Reproducible Analytic Data Sets as R Packages DataQualityDashboard Execute and View Data Quality Checks on OMOP CDM Database DataSetsUni A Collection of Univariate Data Sets DataSetsVerse A Metapackage for Thematic and Domain-Specific Datasets DataSimilarity Quantifying Similarity of Datasets and Multivariate Two- And k-Sample Testing DataSpaceR Interface to 'the CAVD DataSpace' DataSum Modern Data Summaries and Diagnostic Reports for Statistical Analysis DataVisualizations Visualizations of High-Dimensional Data DataViz Data Visualisation Using an HTML Page and 'D3.js' DatabaseConnector Connecting to Various Database Platforms DatabaseConnectorJars JAR Dependencies for the 'DatabaseConnector' Package DatabionicSwarm Swarm Intelligence for Self-Organized Clustering DatastreamDSWS2R Provides a Link Between the 'LSEG Datastream' System and R DatastreamR Datastream API DateTimeRangePicker A Datetime Range Picker Widget for Usage in 'Shiny' Applications Davies The Davies Quantile Function Dcurvature Discrete Curvature with 'shiny' Explorer DeBoinR Box-Plots and Outlier Detection for Probability Density Functions DeCAFS Detecting Changes in Autocorrelated and Fluctuating Signals DeRezende.Ferreira Zero Coupon Yield Curve Modelling DeSciDe Tool for Unbiased Literature Searching and Gene List Curation DebiasInfer Efficient Inference on High-Dimensional Linear Model with Missing Outcomes DecisionDrift Detecting, Decomposing, and Stress-Testing Temporal Change in Repeated Decision Systems DeclareDesign Declare and Diagnose Research Designs DecomposeR Empirical Mode Decomposition for Cyclostratigraphy DecorateR Fit and Deploy DECORATE Trees DedooseR Monitoring and Analyzing Dedoose Qualitative Data Exports Deducer A Data Analysis GUI for R DeductiveR Deductive Rational Method DeepLearningCausal Causal Inference with Super Learner and Deep Neural Networks DegreeDayCalc Degree-Day Phenology Calculator ('shiny' Application) Delaporte Statistical Functions for the Delaporte Distribution DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets DelayedEffect.Design Sample Size and Power Calculations using the APPLE, SEPPLE, APPLE+ and SEPPLE+ Methods DelayedMatrixStats Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects Delta Measure of Agreement Between Two Raters DeltaMAN Delta Measurement of Agreement for Nominal Data DemoDecomp Decompose Demographic Functions DemographicTable Create Demographic Table DendSer Dendrogram Seriation: Ordering for Visualisation DendroSync A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies DensParcorr Dens-Based Method for Partial Correlation Estimation in Large Scale Brain Networks DepCens Dependent Censoring Regression Models DepLogo Dependency Logo DepMod Decision-Analytic Modelling for Depression Prevention and Treatment DepthProc Statistical Depth Functions for Multivariate Analysis Deriv Symbolic Differentiation DescTools Tools for Descriptive Statistics DescToolsAddIns Interactive Functions to be Used as Shortcuts in 'RStudio' DescribeDF Description of a Data Frame DescribeDisplay An Interface to the 'DescribeDisplay' 'GGobi' Plugin DescriptiveRepresentationCalculator Characterizing Observed and Expected Representation DescriptiveStats.OBeu Descriptive Statistics 'OpenBudgets.eu' DescriptiveWH Descriptive Statistics Design.parameters Parameters of the Experimental Designs DesignLibrary Library of Research Designs Desimml Distributed Estimation in Single-Index Models with Multiple Links ('Desimml') DetLifeInsurance Life Insurance Premium and Reserves Valuation DetMCD Implementation of the DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter) DevTreatRules Develop Treatment Rules with Observational Data Devore7 Data sets from Devore's "Prob and Stat for Eng (7th ed)" Dforest Decision Forest DiDforBigData A Big Data Implementation of Difference-in-Differences Estimation with Staggered Treatment DiNAMIC.Duo Finding Recurrent DNA Copy Number Alterations and Differences DiPALM Differential Pattern Analysis via Linear Modeling DiPhiSeq Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data DiPs Directional Penalties for Optimal Matching in Observational Studies DiSCos Distributional Synthetic Controls Estimation DiSSMod Fitting Sample Selection Models for Discrete Response Variables DiagrammeR Graph/Network Visualization DiagrammeRsvg Export DiagrammeR Graphviz Graphs as SVG DiallelAnalysisR Diallel Analysis with R DiceDesign Designs of Computer Experiments DiceEval Construction and Evaluation of Metamodels DiceKriging Kriging Methods for Computer Experiments DiceOptim Kriging-Based Optimization for Computer Experiments DiceView Methods for Visualization of Computer Experiments Design and Surrogate Dict R6 Based Key-Value Dictionary Implementation DidacticBoost A Simple Implementation and Demonstration of Gradient Boosting DiffCorr Analyzing and Visualizing Differential Correlation Networks in Biological Data DiffNet Identifying Significant Node Scores using Network Diffusion Algorithm DiffXTables Pattern Analysis Across Contingency Tables DigestiveDataSets A Curated Collection of Digestive System and Gastrointestinal Disease Datasets Dimodal Spacing Tests for Multi-Modality DirStats Nonparametric Methods for Directional Data Dire Linear Regressions with a Latent Outcome Variable DirectEffects Estimating Controlled Direct Effects for Explaining Causal Findings DirectStandardisation Adjusted Means and Proportions by Direct Standardisation DirectedClustering Directed Weighted Clustering Coefficient Directional A Collection of Functions for Directional Data Analysis DirichletMultinomial Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data DirichletRF "Dirichlet Random Forest" DirichletReg Dirichlet Regression DisImpact Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups DisaggregateTS High-Dimensional Temporal Disaggregation DisasterAlert Disaster Alert and Sentiment Analysis DiscreteDLM Bayesian Distributed Lag Model Fitting for Binary and Count Response Data DiscreteDatasets Example Data Sets for Use with Discrete Statistical Tests DiscreteDists Discrete Statistical Distributions DiscreteFDR FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteFWER FWER-Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteInverseWeibull Discrete Inverse Weibull Distribution DiscreteLaplace Discrete Laplace Distributions DiscreteQvalue Improved q-Values for Discrete Uniform and Homogeneous Tests DiscreteTests Vectorised Computation of P-Values and Their Supports for Several Discrete Statistical Tests DiscreteWeibull Discrete Weibull Distributions (Type 1 and 3) DisimForMixed Calculate Dissimilarity Matrix for Dataset with Mixed Attributes DistPlotter A Graphical User Interface for Plotting Common Univariate Distributions Distance Distance Sampling Detection Function and Abundance Estimation DistatisR DiSTATIS Three Way Metric Multidimensional Scaling Distributacalcul Probability Distribution Functions DistributionIV Distributional Instrumental Variable (DIV) Model DistributionOptimization Distribution Optimization DistributionTest Powerful Goodness-of-Fit Tests Based on the Likelihood Ratio DistributionUtils Distribution Utilities Ditwah Ditwah Storm Data and Tools for Storm Monitoring and Early Warning November 2025, Sri Lanka DivE Diversity Estimator DiversificationR Econometric Tools to Measure Portfolio Diversification DiversityStats Diversity Indices with Statistical Inference DoE.MIParray Creation of Arrays by Mixed Integer Programming DoE.base Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages DoE.wrapper Wrapper Package for Design of Experiments Functionality DockerParallel Using the Docker Container to Create R Workers on Local or Cloud Platform Docovt Distributed Online Covariance Matrix Tests Dogoftest Distributed Online Goodness-of-Fit Tests for Distributed Datasets Domean Distributed Online Mean Tests DominoDataR 'Domino Data R SDK' DonutMap Donut Maps with 'sf', 'ggplot2', and 'leaflet' DoseFinding Planning and Analyzing Dose Finding Experiments DoubleCone Test Against Parametric Regression Function DoubleExpSeq Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter DoubleML Double Machine Learning in R Dowd Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's Book Measuring Market Risk DownBallotR Access Federal, State, and Local Election Data Dpit Distribution Pitting DrBats Data Representation: Bayesian Approach That's Sparse DrData Interactive Statistical Analysis and Machine Learning Platform DrImpute Imputing Dropout Events in Single-Cell RNA-Sequencing Data DrillR R Driver for Apache Drill DrivePlotR Linked Plot Maps for Multivariate High-Resolution Spatio-Temporal Data DropletUtils Utilities for Handling Single-Cell Droplet Data DrugExposureDiagnostics Diagnostics for OMOP Common Data Model Drug Records DrugSim2DR Predict Drug Functional Similarity to Drug Repurposing DrugUtilisation Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model DstarM Analyze Two Choice Reaction Time Data with the D*M Method Dtableone Tabular Comparison of Paired Diagnostic Tests Durga Effect Size Estimation and Visualisation DyMEP Dynamic Multi Environment Phenology-Model DySS Dynamic Screening Systems DyadRatios Dyad Ratios Algorithm for Latent Variable Estimation DyadiCarma Dyadic Matrices and their Algebra using 'Rcpp' and 'RcppArmadillo' Dykstra Quadratic Programming using Cyclic Projections DynClust Denoising and Clustering for Dynamical Image Sequence (2D or 3D)+t DynCount Bayesian Dynamic Models for Poisson and Binomial Time Series DynDoc Dynamic document tools DynForest Random Forest with Multivariate Longitudinal Predictors DynNom Visualising Statistical Models using Dynamic Nomograms DynTxRegime Methods for Estimating Optimal Dynamic Treatment Regimes DynareR Bringing the Power of 'Dynare' to 'R', 'R Markdown', and 'Quarto' DysPIA Dysregulated Pathway Identification Analysis DysPIAData Background and Pathway Data Used in 'DysPIA' E2E Ensemble Learning Framework for Diagnostic and Prognostic Modeling EATME Exponentially Weighted Moving Average with Adjustments to Measurement Error EAVA Deterministic Verbal Autopsy Coding with Expert Algorithm Verbal Autopsy EBASE Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism EBCHS An Empirical Bayes Method for Chi-Squared Data EBEN Empirical Bayesian Elastic Net EBImage Image processing and analysis toolbox for R EBMAforecast Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs Sampling or EM-Algorithms EBcoBART Co-Data Learning for Bayesian Additive Regression Trees EBrank Empirical Bayes Ranking ECDFniche Empirical Cumulative Distribution Function Niche Modeling Tools ECG Center of Gravity Methods ECGofTestDx A Goodness-of-Fit Test for Elliptical Distributions with Diagnostic Capabilities ECMLE Approximating Evidence via Bounded Harmonic Means ECOSolveR Embedded Conic Solver in R ECOTOXr Download and Extract Data from US EPA's ECOTOX Database ECTSVR Cointegration Based Support Vector Regression Model ECTTDNN Cointegration Based Timedelay Neural Network Model ECharts2Shiny Embedding Interactive Charts Generated with ECharts Library into Shiny Applications ECoL Complexity Measures for Supervised Problems EDCimport Import Data from EDC Software EDISON Network Reconstruction and Changepoint Detection EDIutils An API Client for the Environmental Data Initiative Repository EDNE.EQ Implements the EDNE-Test for Equivalence EDOIF Empirical Distribution Ordering Inference Framework (EDOIF) EDOtrans Euclidean Distance-Optimized Data Transformation EE.Data Objects for Predicting Energy Expenditure EEAaq Handle Air Quality Data from the European Environment Agency Data Portal EEEA Explicit Exploration Strategy for Evolutionary Algorithms EEM Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data EEMDSVR Ensemble Empirical Mode Decomposition and Its Variant Based Support Vector Regression Model EEMDelm Ensemble Empirical Mode Decomposition and Its Variant Based ELM Model EEMDlstm EEMD Based LSTM Model for Time Series Forecasting EEML Ensemble Explainable Machine Learning Models EFA.MRFA Dimensionality Assessment Using Minimum Rank Factor Analysis EFA.dimensions Exploratory Factor Analysis Functions for Assessing Dimensionality EFAfactors Determining the Number of Factors in Exploratory Factor Analysis EFAtools Fast and Flexible Implementations of Exploratory Factor Analysis Tools EFAutilities Utility Functions for Exploratory Factor Analysis EFDR Wavelet-Based Enhanced FDR for Detecting Signals from Complete or Incomplete Spatially Aggregated Data EFM Elliptical Factor Models EFSATools EFSA Ensemble of Data Collections Tools EGAnet Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics EGM Intracardiac Electrograms EGRET Exploration and Graphics for RivEr Trends EGRETci Exploration and Graphics for RivEr Trends Confidence Intervals EGRNi Ensemble Gene Regulatory Network Inference EHR Electronic Health Record (EHR) Data Processing and Analysis Tool EHRmuse Multi-Cohort Selection Bias Correction using IPW and AIPW Methods EHRtemporalVariability Delineating Temporal Dataset Shifts in Electronic Health Records EIAapi Query Data from the 'EIA' API EIEntropy Ecological Inference Applying Entropy EIX Explain Interactions in 'XGBoost' EKMCMC MCMC Procedures for Estimating Enzyme Kinetics Constants EL Two-Sample Empirical Likelihood EL2Surv Empirical Likelihood (EL) for Comparing Two Survival Functions ELAplus Energy Landscape Analysis for Ecological Communities ELIC LIC for Distributed Elliptical Model ELISAtools ELISA Data Analysis with Batch Correction ELT Experience Life Tables ELYP Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model ELmethodVar Empirical Likelihood Inference of Variance Components in Linear Mixed-Effects Models EMAR Empirical Model Assessment EMAS Epigenome-Wide Mediation Analysis Study EMAtools Data Management Tools for Real-Time Monitoring/Ecological Momentary Assessment Data EMC2 Bayesian Hierarchical Analysis of Cognitive Models of Choice EMCluster EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution EMD Empirical Mode Decomposition and Hilbert Spectral Analysis EMDANNhybrid Empirical Mode Decomposition Based Artificial Neural Network Model EMDSVRhybrid Empirical Mode Decomposition Based Support Vector Regression Model EMGCR Fit a Mixture Cure Rate Model with Custom Link Function EMJMCMC Evolutionary Mode Jumping Markov Chain Monte Carlo Expert Toolbox EML Read and Write Ecological Metadata Language Files EMLI Computationally Efficient Maximum Likelihood Identification of Linear Dynamical Systems EMMAgeo End-Member Modelling of Grain-Size Data EMMIXSSL Semi-Supervised Gaussian Mixture Model with a Missing-Data Mechanism EMMIXgene A Mixture Model-Based Approach to the Clustering of Microarray Expression Data EMMIXmfa Mixture Models with Component-Wise Factor Analyzers EMMLi A Maximum Likelihood Approach to the Analysis of Modularity EMMREML Fitting Mixed Models with Known Covariance Structures EMOTIONS Ensemble Models for Lactation Curves EMP Expected Maximum Profit Classification Performance Measure EMSC Extended Multiplicative Signal Correction EMSNM EM Algorithm for Sigmoid Normal Model EMSS Some EM-Type Estimation Methods for the Heckman Selection Model EMSaov The Analysis of Variance with EMS EMT Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data EMbC Expectation-Maximization Binary Clustering EMgaussian Expectation-Maximization Algorithm for Multivariate Normal (Gaussian) with Missing Data EMpeaksR Conducting the Peak Fitting Based on the EM Algorithm ENMTools Analysis of Niche Evolution using Niche and Distribution Models ENMeval Automated Tuning and Evaluations of Ecological Niche Models EPLSIM Partial Linear Single Index Models for Environmental Mixture Analysis EPT Ensemble Patch Transform, Visualization and Decomposition EPX Ensemble of Phalanxes EQL Extended-Quasi-Likelihood-Function (EQL) EQRN Extreme Quantile Regression Neural Networks for Risk Forecasting EQUALCompareImages Comparison of Images for Researchers Without Coding Skills EQUALPrognosis Analysing Prognostic Studies EQUALSTATS Algorithm Driven Statistical Analysis for Researchers without Coding Skills EQUALencrypt Encryption and Decryption of Files and Data for Researchers Without Coding Skills EQUALrepeat Algorithm Driven Time Series Analysis for Researchers without Coding Skills EQUIVNONINF Testing for Equivalence and Noninferiority ER Effect + Residual Modelling ERDbuilder Entity Relationship Diagrams Builder ERP Significance Analysis of Event-Related Potentials Data ERPM Exponential Random Partition Models ERPeq Probabilistic Hazard Assessment ERSA Exploratory Regression 'Shiny' App ES Edge Selection ESG A Package for Asset Projection ETAS Modeling Earthquake Data Using 'ETAS' Model ETASbootstrap Bootstrap Confidence Interval Estimation for 'ETAS' Model Parameters ETC Equivalence to Control ETDQualitizer Automated Eye Tracking Data Quality Determination for Screen-Based Eye Trackers ETLUtils Utility Functions to Execute Standard Extract/Transform/Load Operations (using Package 'ff') on Large Data ETRep Analysis of Elliptical Tubes Under the Relative Curvature Condition EUfootball Football Match Data of European Leagues EVI Epidemic Volatility Index as an Early-Warning Tool EValue Sensitivity Analyses for Unmeasured Confounding and Other Biases in Observational Studies and Meta-Analyses EVchargcost Computes and Plot the Optimal Charging Strategy for Electric Vehicles EWGoF Goodness-of-Fit Tests for the Exponential and Two-Parameter Weibull Distributions EWOC.Comb Escalation with Overdose Control using 2 Drug Combinations EWS Early Warning System EWSmethods Forecasting Tipping Points at the Community Level EXPAR Fitting of Exponential Autoregressive (EXPAR) Model EXPARMA Fitting of Exponential Autoregressive Moving Average (EXPARMA) Model EXRQ Extreme Regression of Quantiles EZFragility Compute Neural Fragility for Ictal iEEG Time Series EZbakR Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data EZtune Tunes AdaBoost, Elastic Net, Support Vector Machines, and Gradient Boosting Machines Eagle Multiple Locus Association Mapping on a Genome-Wide Scale Ease Simulating Explicit Population Genetics Models EasyABC Efficient Approximate Bayesian Computation Sampling Schemes EasyDescribe A Convenient Way of Descriptive Statistics EasyMx Easy Model-Builder Functions for 'OpenMx' EasyStat Automated Statistical Analysis, Visualization and Multi-Format Narrative Reporting EbayesThresh Empirical Bayes Thresholding and Related Methods Ecdat Data Sets for Econometrics Ecfun Functions for 'Ecdat' EcoCleanR Enhancing Data Quality of Biogeographic Ranges with Application for Marine Invertebrates EcoDiet Estimating a Diet Matrix from Biotracer and Stomach Content Data EcoEnsemble A General Framework for Combining Ecosystem Models EcoMetrics Econometrics Model Building EcoNetGen Simulate and Sample from Ecological Interaction Networks EcoNiche Community Niche Position and Width Estimation Tools EcoTroph An Implementation of the EcoTroph Ecosystem Modelling Approach Ecohydmod Ecohydrological Modelling EconAndProdEfficiency Economic and Production Efficiency EconCausal Causal Analysis for Macroeconomic Time Series (ECM-MARS, BSTS, Bayesian GLM-AR(1)) EconGeo Computing Key Indicators of the Spatial Distribution of Economic Activities EcotoneFinder Characterising and Locating Ecotones and Communities Ecume Equality of 2 (or k) Continuous Univariate and Multivariate Distributions EdSurvey Analysis of NCES Education Survey and Assessment Data EffectLiteR Average and Conditional Effects EffectStars Visualization of Categorical Response Models EffectStars2 Effect Stars EffectTreat Prediction of Therapeutic Success EfficientMaxEigenpair Efficient Initials for Computing the Maximal Eigenpair EgoCor Simple Presentation of Estimated Exponential Semi-Variograms EleChemr Electrochemical Reactions Simulation ElectDecomp Decomposition of Seats-to-Votes Distortions ElicitationWizard LLM-Based Bayesian Prior Elicitation Wizard Elja Linear, Logistic and Generalized Linear Models Regressions for the EnvWAS/EWAS Approach ElliptCopulas Inference of Elliptical Distributions and Copulas EloChoice Preference Rating for Visual Stimuli Based on Elo Ratings EloOptimized Optimized Elo Rating Method for Obtaining Dominance Ranks EloRating Animal Dominance Hierarchies by Elo Rating EmbedSOM Fast Embedding Guided by Self-Organizing Map EmiR Evolutionary Minimizer for R EmissV Tools for Create Emissions for Air Quality Models EmpiricalBrownsMethod Uses Brown's method to combine p-values from dependent tests EmpiricalCalibration Routines for Performing Empirical Calibration of Observational Study Estimates EmpiricalDynamics Empirical Discovery of Differential Equations from Time Series Data EnTraineR Enhanced Teaching Assistant (AI) for Statistical Analysis EncompassTest Direct Multi-Step Forecast Based Comparison of Nested Models via an Encompassing Test EnergyOnlineCPM Distribution Free Multivariate Control Chart Based on Energy Test EngrEcon Engineering Economics Analysis for Engineering Projects Cost Analysis EngrExpt Data sets from "Introductory Statistics for Engineering Experimentation" EnhancedVolcano Publication-ready volcano plots with enhanced colouring and labeling EnrichIntersect Enrichment Analysis and Intersecting Sankey Diagram EnsCat Clustering of Categorical Data EntropicStatistics Functions Based on Entropic Statistics EntropyEstimation Estimation of Entropy and Related Quantities EnvCpt Detection of Structural Changes in Climate and Environment Time Series EnvNJ Whole Genome Phylogenies Using Sequence Environments EnvNicheR Niche Estimation EnvStats Package for Environmental Statistics, Including US EPA Guidance EnviroPRA2 Environmental Probabilistic Risk Assessment Tools Epi Statistical Analysis in Epidemiology EpiContactTrace Epidemiological Tool for Contact Tracing EpiCurve Plot an Epidemic Curve EpiDISH Epigenetic Dissection of Intra-Sample-Heterogeneity EpiDynamics Dynamic Models in Epidemiology EpiEstim Estimate Time Varying Reproduction Numbers from Epidemic Curves EpiForsk Code Sharing at the Department of Epidemiology Research at Statens Serum Institut EpiILM Spatial and Network Based Individual Level Models for Epidemics EpiInvert Variational Techniques in Epidemiology EpiLPS A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters EpiModel Mathematical Modeling of Infectious Disease Dynamics EpiNova Flexible Extended State-Space Epidemiological Models with Modern Inference EpiPvr Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays EpiReport Epidemiological Report EpiScopeK Comprehensive Epidemiological Analysis Toolkit EpiSemble Ensemble Based Machine Learning Approach for Predicting Methylation States EpiSignalDetection Signal Detection Analysis EpiSimR A 'Shiny' App to Simulate the Dynamics of Epidemic and Endemic Diseases Spread EpiStandard Directly Standardise Rates by Age EpiStats Tools for Epidemiologists EpiTest Test for Gene x Gene Interactions in Bi-Parental Populations EpidigiR Digital Epidemiological Analysis and Visualization Tools EpistemicGameTheory Constructing an Epistemic Model for the Games with Two Players Epoch IEEG (Intracranial Electroencephalography) Epoch Data Tools Equalden.HD Testing the Equality of a High Dimensional Set of Densities EquiSurv Modeling, Confidence Intervals and Equivalence of Survival Curves EquiTrends Equivalence Testing for Pre-Trends in Difference-in-Differences Designs EraBrewer Color Palettes from the Album Covers of Each Taylor Swift Era ErlangC Solve Erlang-C Model EstCRM Calibrating Parameters for the Samejima's Continuous IRT Model EstHTSeed Hydro Time Analysis of Seed Germination EstemPMM Polynomial Maximization Method for Non-Gaussian Regression EstimDiagnostics Diagnostic Tools and Unit Tests for Statistical Estimators EstimateBreed Estimation of Environmental Variables and Genetic Parameters EstimateGroupNetwork Perform the Joint Graphical Lasso and Selects Tuning Parameters EstimationTools Maximum Likelihood Estimation for Probability Functions from Data Sets EthSEQ Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data EuclideanSD An Euclidean View of Center and Spread Euclimatch Euclidean Climatch Algorithm Eunomia Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets EvCombR Evidence Combination in R Evacluster Evaluation Clustering Methods for Disease Subtypes Diagnosis EvalTest Tools for Evaluating Diagnostic Test Performance EvaluateCore Quality Evaluation of Core Collections EvaluationMeasures Collection of Model Evaluation Measure Functions Evapotranspiration Modelling Actual, Potential and Reference Crop Evapotranspiration EventPredInCure Event Prediction Including Cured Population EventWinRatios Event-Specific Win Ratios for Terminal and Non-Terminal Events EvidenceSynthesis Synthesizing Causal Evidence in a Distributed Research Network EviewsR A Seamless Integration of 'EViews' and R EvoPhylo Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics EvolutionaryGames Important Concepts of Evolutionary Game Theory Evomorph Evolutionary Morphometric Simulation EwR Econometrics with R ExGaussEstim Quantile Maximization Likelihood Estimation and Bayesian Ex-Gaussian Estimation ExNRuleEnsemble A k Nearest Neibour Ensemble Based on Extended Neighbourhood Rule ExPanDaR Explore Your Data Interactively ExPosition Exploratory Analysis with the Singular Value Decomposition Exact Unconditional Exact Test ExactCIdiff Inductive Confidence Intervals for the Difference Between Two Proportions ExactCIone Admissible Exact Intervals for One-Dimensional Discrete Distributions ExactCox Exact Test and Exact Confidence Interval for the Cox Model ExactMed Exact Mediation Analysis for Binary Outcomes ExactMultinom Multinomial Goodness-of-Fit Tests ExactVaRTest Exact Finite-Sample Value-at-Risk Back-Testing ExamPAData Data Sets for Predictive Analytics Exam ExceedanceTools Confidence/Credible Regions for Exceedance Sets and Contour Lines ExcelFunctionsR Imports Excel Functions to R ExcessMass Excess Mass Calculation and Plots ExclusionTable Creating Tables of Excluded Observations ExhaustiveSearch A Fast and Scalable Exhaustive Feature Selection Framework ExpAnalysis3d Pacote Para Analise De Experimentos Com Graficos De Superficie Resposta ExpBites Analyzing Human Exposure to Mosquito Biting ExpDE Modular Differential Evolution for Experimenting with Operators ExpDes Experimental Designs Package ExpGenetic Non-Additive Expression Analysis of Hybrid Offspring ExpRep Experiment Repetitions ExperimentHub Client to access ExperimentHub resources ExpertChoice Design of Discrete Choice and Conjoint Analysis ExplodeLayout Calculate Exploded Coordinates Based on Original Node Coordinates and Node Clustering Membership ExploreTheData A Set of Tools for Exploratory Data Analysis ExposR Models Topographic Exposure to Hurricane Winds ExpressionCellNet Network-Based Analysis of Gene Expression Perturbations ExtDist Extending the Range of Functions for Probability Distributions ExtMallows An Extended Mallows Model and Its Hierarchical Version for Ranked Data Aggregation ExtendedABSurvTDC Survival Analysis using Indicators under Time Dependent Covariates ExtendedLaplace The Extended Laplace Distribution ExtrPatt Spatial Dependencies and Indices for Extremes ExtractTrainData Extract Values from Raster ExtremalDep Extremal Dependence Models ExtremeBounds Extreme Bounds Analysis (EBA) ExtremeCI Realistic Confidence Intervals for Non-Stationary Extreme Value Statistics ExtremeConformal Extreme Conformal Prediction Intervals ExtremeRisks Extreme Risk Measures EzGP Easy-to-Interpret Gaussian Process Models for Computer Experiments FABInference FAB p-Values and Confidence Intervals FACTMLE Maximum Likelihood Factor Analysis FADA Variable Selection for Supervised Classification in High Dimension FADPclust Functional Data Clustering Using Adaptive Density Peak Detection FAIRmaterials Ontology Tools with Data FAIRification in Development FAMetA Fatty Acid Metabolic Analysis FAMoS A Flexible Algorithm for Model Selection FAO56 Evapotranspiration Based on FAO Penman-Monteith Equation FAOSTAT Download Data from the FAOSTAT Database FAPA Factor Analytic Profile Analysis of Ipsatized Data FARDEEP Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte from Expression Profiles using Least Trimmed Squares FARS Factor-Augmented Regression Scenarios FAS Factor-Augmented Sparse Regression Tuning-Free Testing FAST.R Analyze and Visualize FAST-Generated Data FAVA Quantify Compositional Variability Across Relative Abundance Vectors FAVAR Bayesian Analysis of a FAVAR Model FAdist Distributions that are Sometimes Used in Hydrology FAfA Factor Analysis for All FAmle Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions FAwR Functions and Datasets for "Forest Analytics with R" FBFsearch Algorithm for Searching the Space of Gaussian Directed Acyclic Graph Models Through Moment Fractional Bayes Factors FBMS Flexible Bayesian Model Selection and Model Averaging FBN FISH Based Normalization and Copy Number Inference of SNP Microarray Data FCO Flexible Cutoffs for Model Fit Evaluation in Covariance-Based Structural Models FCPS Fundamental Clustering Problems Suite FCUSUM Fourier CUSUM Cointegration Test FCVAR Estimation and Inference for the Fractionally Cointegrated VAR FD Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology FDOTT Optimal Transport Based Testing in Factorial Design FDRestimation Estimate, Plot, and Summarize False Discovery Rates FDRsamplesize2 Computing Power and Sample Size for the False Discovery Rate in Multiple Applications FDRsampsize Compute Sample Size that Meets Requirements for Average Power and FDR FDX False Discovery Exceedance Controlling Multiple Testing Procedures FDboost Boosting Functional Regression Models FEA Finite Element Modeling for R FENmlm Fixed Effects Nonlinear Maximum Likelihood Models FER Financial Engineering in R FESta Fishing Effort Standardisation FEprovideR Fixed Effects Logistic Model with High-Dimensional Parameters FFD Freedom from Disease FFTrees Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees FFdownload Download Data from Kenneth French's Website FGLMtrunc Truncated Functional Generalized Linear Models FGRepo Functional Genomics Repository for POST-GWAS Analysis FGalgorithm Flury and Gautschi algorithms FHDI Fractional Hot Deck and Fully Efficient Fractional Imputation FHtest Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class FI Provide Functions for Forest Inventory Calculations FIESTA Forest Inventory Estimation and Analysis FIESTAutils Utility Functions for Forest Inventory Estimation and Analysis FILEST Fine-Level Structure Simulator FIND Objective Comparison of Phase I Dose-Finding Designs FIRM Flexible Integration of Single-Cell RNA-Seq Data FITSio FITS (Flexible Image Transport System) Utilities FKF Fast Kalman Filter FKSUM Fast Kernel Sums FKmL Fréchet Distance-Based K-Means and Extensions for Longitudinal Data FLAG Flexible and Accurate Gaussian Graphical Models FLAME Interpretable Matching for Causal Inference FLASHMM Fast and Scalable Single Cell Differential Expression Analysis using Mixed-Effects Models FLOPART Functional Labeled Optimal Partitioning FLORAL Fit Log-Ratio Lasso Regression for Compositional Data FLR Fuzzy Logic Rule Classifier FLSSS Mining Rigs for Problems in the Subset Sum Family FLightR Reconstruct Animal Paths from Solar Geolocation Loggers Data FMAT The Fill-Mask Association Test FMAdist Frequentist Model Averaging Distribution FMC Factorial Experiments with Minimum Level Changes FMCensSkewReg Finite Mixture of Censored Regression Models with Skewed Distributions FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis FMM Rhythmic Patterns Modeling by FMM Models FMP Filtered Monotonic Polynomial IRT Models FMStable Finite Moment Stable Distributions FMradio Factor Modeling for Radiomics Data FMsmsnReg Regression Models with Finite Mixtures of Skew Heavy-Tailed Errors FNN Fast Nearest Neighbor Search Algorithms and Applications FOCI Feature Ordering by Conditional Independence FORD Feature Ordering by Integrated R Square Dependence FPCA3D Three Dimensional Functional Component Analysis FPCdpca The FPCdpca Criterion on Distributed Principal Component Analysis FPDclustering PD-Clustering and Related Methods FPLdata Read in Fantasy Premier League Data FRACTION Numeric Number into Fraction FRAPO Financial Risk Modelling and Portfolio Optimisation with R FRApp FRAP Data Analysis Using Nonlinear Mixed Effect Models with 'shiny' FRB Fast and Robust Bootstrap FRCC Fast Regularized Canonical Correlation Analysis FRCI Fuzzy & Randomized Confidence Intervals FREEtree Tree Method for High Dimensional Longitudinal Data FREQ FREQ: Estimate population size from capture frequencies FRESA.CAD Feature Selection Algorithms for Computer Aided Diagnosis FRI Relative Importance of Main and Interaction Effects FRK Fixed Rank Kriging FSA Simple Fisheries Stock Assessment Methods FSAdata Data to Support Fish Stock Assessment ('FSA') Package FSDAM Forward Stepwise Deep Autoencoder-Based Monotone NLDR FSK2R An Interface Between the 'FSKX' Standard and 'R' FSM Finite Selection Model FSSF Generate Fully-Sequential Space-Filling Designs Inside a Unit Hypercube FSTpackage Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotation Scores FSelector Selecting Attributes FSelectorRcpp 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support FSinR Feature Selection in R FTSgof White Noise and Goodness-of-Fit Tests for Functional Time Series FUNTA Functional Tangential Angle Pseudo-Depth FVDDPpkg Implement Fleming-Viot-Dependent Dirichlet Processes FWDselect Selecting Variables in Regression Models FWRGB Fresh Weight Determination from Visual Image of the Plant FaaSr 'FaaSr' Local Test Development Package FactChar Characterization and Diagnostic Tools for Factorial Block Designs FactEff Efficiencies of Block Designs for Factorial and Fractional Factorial Experiments FactoClass Combination of Factorial Methods and Cluster Analysis FactoInvestigate Automatic Description of Factorial Analysis FactoMineR Multivariate Exploratory Data Analysis and Data Mining FactorAssumptions Set of Assumptions for Factor and Principal Component Analysis FactorCopula Factor, Bi-Factor, Second-Order and Factor Tree Copula Models FactorCopulaModel Factor Copula Models FactorHet Estimate Heterogeneous Effects in Factorial Experiments Using Grouping and Sparsity Factoshiny Perform Factorial Analysis from 'FactoMineR' with a Shiny Application Fahrmeir Data from the Book "Multivariate Statistical Modelling Based on Generalized Linear Models", First Edition, by Ludwig Fahrmeir and Gerhard Tutz FakeDataR Privacy-Preserving Synthetic Data for 'LLM' Workflows FamEvent Family Age-at-Onset Data Simulation and Penetrance Estimation Familias Probabilities for Pedigrees Given DNA Data Families Kinship Ties in (Virtual) Multi-Generation Populations FastBandChol Fast Estimation of a Covariance Matrix by Banding the Cholesky Factor FastCUB Fast Estimation of CUB Models via Louis' Identity FastGP Efficiently Using Gaussian Processes with Rcpp and RcppEigen FastGaSP Fast and Exact Computation of Gaussian Stochastic Process FastHamming Fast Computation of Pairwise Hamming Distances FastImputation Learn from Training Data then Quickly Fill in Missing Data FastJM Semi-Parametric Joint Modeling of Longitudinal and Survival Data FastKM A Fast Multiple-Kernel Method Based on a Low-Rank Approximation FastKNN Fast k-Nearest Neighbors FastKRR Kernel Ridge Regression using 'RcppArmadillo' FastPCS FastPCS Robust Fit of Multivariate Location and Scatter FastRCS Fits the FastRCS Robust Multivariable Linear Regression Model FastRWeb Fast Interactive Framework for Web Scripting Using R FastRet Retention Time Prediction in Liquid Chromatography FastSegmentation Unsupervised Cell Segmentation by Fast Gaussian Processes FastStepGraph A Fast Algorithm for Sparse Precision Matrix Estimation FastSurvival Fast Kaplan-Meier, Log-Rank, and Hazard Ratio Estimation for Survival Analysis FastUtils Fast, Readable Utility Functions FatTailsR Kiener Distributions and Fat Tails in Finance and Neuroscience FateID Quantification of Fate Bias in Multipotent Progenitors FaultTree Fault Trees for Risk and Reliability Analysis FeaLect Scores Features for Feature Selection FeatureExtraction Generating Features for a Cohort FeatureImpCluster Feature Importance for Partitional Clustering FeatureTerminatoR Feature Selection Engine to Remove Features with Minimal Predictive Power FedData Download Geospatial Data Available from Several Federated Data Sources FedIRT Federated Item Response Theory Models FertNet Process Data from the Social Networks and Fertility Survey Fgmutils Forest Growth Model Utilities FiRE Finder of Rare Entities (FiRE) FiSh Fisher-Shannon Method FielDHub A Shiny App for Design of Experiments in Life Sciences FieldSimR Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials FilmsGmooG IMDb Film Ratings from the Summer of 2022 FinAna Financial Analysis and Regression Diagnostic Analysis FinCal Time Value of Money, Time Series Analysis and Computational Finance FinCovRegularization Covariance Matrix Estimation and Regularization for Finance FinNet Quickly Build and Manipulate Financial Networks FinTS Companion to Tsay (2005) Analysis of Financial Time Series FinanceGraphs Flexible Graphs for Analysis of Financial Data and Time Series FinancialMath Financial Mathematics for Actuaries FindIt Finding Heterogeneous Treatment Effects FinePop Fine-Scale Population Analysis FinePop2 Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis) FisPro Fuzzy Inference System Design and Optimization Fiscal Income Tax Calculations (UK) FishDiveR Classify Aquatic Animal Behaviours from Vertical Movement Data FishPhyloMaker Phylogenies for a List of Finned-Ray Fishes FishProxCompAnalyzer Proximate Composition Analysis of Fish and Feed Ingredients FisherEM The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data FitDynMix Estimation of Dynamic Mixtures FitUltD Fit Univariate Mixed and Usual Distributions FixSeqMTP Fixed Sequence Multiple Testing Procedures FixedPoint Algorithms for Finding Fixed Point Vectors of Functions FjordLight Available Light Within the Water Column and on the Seafloor of Arctic Fjords FlexDir Tools to Work with the Flexible Dirichlet Distribution FlexGAM Generalized Additive Models with Flexible Response Functions FlexParamCurve Tools to Fit Flexible Parametric Curves FlexRL A Flexible Model for Record Linkage FlexReg Regression Models for Bounded Continuous and Discrete Responses FlexScan Flexible Scan Statistics FlexVarJM Estimate Joint Models with Subject-Specific Variance FlickrAPI Access to Flickr API FloodFreqPlot Flood Probability Plotting and Graphical Frequency Analysis FlowRegEnvCost The Environmental Costs of Flow Regulation FlowScreen Daily Streamflow Trend and Change Point Screening FlowerMate Reciprocity Indices for Style-Polymorphic Plants Fluidigm Handling Fluidigm Data FluxPoint Change Point Detection for Non-Stationary and Cross-Correlated Time Series FluxSeparator Separation of Diffusive and Ebullitive Fluxes FlyingR Simulation of Bird Flight Range FnR Inbreeding and Numerator Relationship Coefficients FoCo2 Coherent Forecast Combination for Linearly Constrained Multiple Time Series FoRDM Forest Many-Objective Robust Decision Making ('FoRDM') FoReco Forecast Reconciliation FoRecoML Forecast Reconciliation with Machine Learning ForCausality A Curated Collection of 'Causal Inference' Datasets and Tools ForIT Functions to Estimate Tree Volume and Phytomass in the Italian Forest Inventory 2005 ForLion 'ForLion' Algorithm to Find D-Optimal Designs for Experiments ForagingOrg Organization Measures for Visual Foraging ForeCA Forecastable Component Analysis ForeComp Size-Power Tradeoff Visualization for Equal Predictive Ability of Two Forecasts ForecastCombinations Forecast Combinations ForecastingEnsembles Time Series Forecasting Using 23 Individual Models ForestDisc Forest Discretization ForestElementsR Data Structures and Functions for Working with Forest Data ForestFit Statistical Modelling for Plant Size Distributions ForestGapR Tropical Forest Canopy Gaps Analysis ForestTools Tools for Analyzing Remote Sensing Forest Data FormShare A Simple Connection Between the 'FormShare App' and 'R' for Advanced Analytics FormulR Comprehensive Tools for Drug Formulation Analysis and Visualization Formula Extended Model Formulas FossilSim Simulation and Plots for Fossil and Taxonomy Data FossilSimShiny Shiny Application for 'FossilSim' FourScores A Game for Human vs. Human or Human vs. AI FourWayHMM Parsimonious Hidden Markov Models for Four-Way Data FourgameteP FourGamete Test FrF2 Fractional Factorial Designs with 2-Level Factors FrF2.catlg128 Catalogues of Resolution IV 128 Run 2-Level Fractional Factorials Up to 33 Factors that Do Have 5-Letter Words FracFixR Compositional Statistical Framework for RNA Fractionation Analysis FracKrigingR Spatial Multivariate Data Modeling FractalParameterEstimation Simulation and Parameter Estimation of Randomized Sierpinski Carpets using the p-p-p-q-Model FragiliTidy Tidyverse-Compatible Fragility Index Calculations Fragman Fragment Analysis in R FrailtyCompRisk Competing Risks Models for Multi-Center Survival Data with Frailty Frames2 Estimation in Dual Frame Surveys FreqProf Frequency Profiles Computing and Plotting Fstability Calculate Feature Stability FuelDeep3D 3D Fuel Segmentation Using Terrestrial Laser Scanning and Deep Learning FunChisq Model-Free Functional Chi-Squared and Exact Tests FunSurv Modeling Time-to-Event Data with Functional Predictors FunWithNumbers Fun with Fractions and Number Sequences FuncDiv Compute Contributional Diversity Metrics FunctanSNP Functional Analysis (with Interactions) for Dense SNP Data FunctionalCalibration Aggregated Functional Data Calibration using Splines and Wavelets FunnelPlotR Funnel Plots for Comparing Institutional Performance FusionLearn Fusion Learning FuzzyAHP (Fuzzy) AHP Calculation FuzzyClass Fuzzy and Non-Fuzzy Classifiers FuzzyImputationTest Imputation Procedures and Quality Tests for Fuzzy Data FuzzyM Fuzzy Cognitive Maps Operations FuzzyNumbers Tools to Deal with Fuzzy Numbers FuzzyPovertyR Estimation of Fuzzy Poverty Measures FuzzyQ Fuzzy Quantification of Common and Rare Species FuzzyR Fuzzy Logic Toolkit for R FuzzyResampling Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers FuzzySTs Fuzzy Statistical Tools FuzzySimRes Simulation and Resampling Methods for Epistemic Fuzzy Data FuzzySpec Fuzzy Spectral Clustering with Variable-Weighted Adjacency Matrices FuzzyStatTra Statistical Methods for Trapezoidal Fuzzy Numbers G2Sd Grain-Size Statistics and Description of Sediment GA Genetic Algorithms GABB Facilitation of Data Preparation and Plotting Procedures for RDA and PCA Analyses GACE Generalized Adaptive Capped Estimator for Time Series Forecasting GACFF Genetic Similarity in User-Based Collaborative Filtering GAD Analysis of Variance from General Principles GADAG A Genetic Algorithm for Learning Directed Acyclic Graphs GAGAs Global Adaptive Generative Adjustment Algorithm for Generalized Linear Models GAGBLUP Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction GAIPE Graphical Extension with Accuracy in Parameter Estimation (GAIPE) GALAHAD Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with Softplus Reparameterization and Trust-Region Control GALLO Genomic Annotation in Livestock for Positional Candidate LOci GAMens Applies GAMbag, GAMrsm and GAMens Ensemble Classifiers for Binary Classification GANPA Gene Association Network-Based Pathway Analysis (GANPA) GANPAdata The GANPA Datasets Package GAPR Generalized Association Plots GARCH.X Estimation and Exogenous Covariate Selection for ARCH-m(X), Additive ARCH-m(x), and GARCH-X Models GARCHIto Class of GARCH-Ito Models GARCHSK Estimating a GARCHSK Model and GJRSK Model GARCOM Gene and Region Counting of Mutations ("GARCOM") GAReg Genetic Algorithms in Regression GAparsimony Searching Parsimony Models with Genetic Algorithms GB2 Generalized Beta Distribution of the Second Kind: Properties, Likelihood, Estimation GB2group Estimation of the Generalised Beta Distribution of the Second Kind from Grouped Data GB5mcPred Gradient Boosting Algorithm for Predicting Methylation States GBASS Generalized Bayesian Adaptive Smoothing Splines GBJ Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies GBOP2 Generalized Bayesian Optimal Phase II Design (G-BOP2) GCCfactor GCC Estimation of the Multilevel Factor Model GCD Global Charcoal Database GCEstim Regression Coefficients Estimation Using the Generalized Cross Entropy GCPBayes Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure GCPM Generalized Credit Portfolio Model GCSM Implements Generic Composite Similarity Measure GCalignR Simple Peak Alignment for Gas-Chromatography Data GCubeR Estimation of Forest Volume, Biomass, and Carbon GD Geographical Detectors for Assessing Spatial Factors GDAdata Datasets for the Book Graphical Data Analysis with R GDAtools Geometric Data Analysis GDILM.ME Spatial Modeling of Infectious Diseases with Co-Variate Error GDILM.SIR Inference for Infectious Disease Transmission in SIR Framework GDINA The Generalized DINA Model Framework GDPuc Easily Convert GDP Data GDSARM Gauss - Dantzig Selector: Aggregation over Random Models GE General Equilibrium Modeling GEC Generalized Exponentiated Composite Distributions GECal Generalized Entropy Calibration GEEaSPU Adaptive Association Tests for Multiple Phenotypes using Generalized Estimating Equations (GEE) GEEmediate Mediation Analysis for Generalized Linear Models Using the Difference Method GEInfo Gene-Environment Interaction Analysis Incorporating Prior Information GEInter Robust Gene-Environment Interaction Analysis GEMSS Generalization Error Minimization in SubSampling for Gaussian Processes GENEAclassify Segmentation and Classification of Accelerometer Data GENEAcore Pre-Processing of 'GENEActiv' Data GENEAread Package for Reading Binary Files GENLIB Genealogical Data Analysis GENMETA Implements Generalized Meta-Analysis Using Iterated Reweighted Least Squares Algorithm GEOmap Topographic and Geologic Mapping GEOmetadb A compilation of metadata from NCBI GEO GEOquery Get data from NCBI Gene Expression Omnibus (GEO) GESE Gene-Based Segregation Test GET Global Envelopes GETdesigns Generalized Extended Triangular Designs ('GETdesigns') GEVACO Joint Test of Gene and GxE Interactions via Varying Coefficients GEVcdn GEV Conditional Density Estimation Network GEint Misspecified Models for Gene-Environment Interaction GEmetrics Best Linear Unbiased Prediction of Genotype-by-Environment Metrics GFA Group Factor Analysis GFD Tests for General Factorial Designs GFDmcv General Hypothesis Testing Problems for Multivariate Coefficients of Variation GFDrmst Multiple RMST-Based Tests in General Factorial Designs GFDrmtl Multiple RMTL-Based Tests for Competing Risks Data in General Factorial Designs GFDsurv Tests for Survival Data in General Factorial Designs GFE Gross Flows Estimation under Complex Surveys GFFStrandLoc Strand-Wise Gene and Protein Extraction from GFF3 Files GFGM.copula Generalized Farlie-Gumbel-Morgenstern Copula GFM Generalized Factor Model GFisher Generalized Fisher's Combination Tests Under Dependence GGClassification Gabriel Graph Based Large-Margin Classifiers GGEBiplots GGE Biplots with 'ggplot2' GGIR Raw Accelerometer Data Analysis GGIRread Wearable Accelerometer Data File Readers GGMncv Gaussian Graphical Models with Nonconvex Regularization GGMridge Gaussian Graphical Models Using Ridge Penalty Followed by Thresholding and Reestimation GGRidge Graphical Group Ridge GGUM Generalized Graded Unfolding Model GGally Extension to 'ggplot2' GGenemy Audit 'ggplot2' Visualizations for Accessibility and Best Practices GGoutlieR Identify Individuals with Unusual Geo-Genetic Patterns GHCNr Download Weather Station Data from GHCNd GHRexplore Exploratory Analysis of Temporal and Spatio-Temporal Health Data GHRmodel Bayesian Hierarchical Modelling of Spatio-Temporal Health Data GIC A General Iterative Clustering Algorithm GIFT Access to the Global Inventory of Floras and Traits (GIFT) GIGrvg Random Variate Generator for the GIG Distribution GIMMEgVAR Group Iterative Multiple Model Estimation with 'graphicalVAR' GINAX Performs Genome-Wide Iterative Fine-Mapping for Non-Gaussian Data using GINA-X GISINTEGRATION GIS Integration GISSB Network Analysis on the Norwegian Road Network GISTools Further Capabilities in Geographic Information Science GInSARCorW GACOS InSAR Correction Workflow GIplot Gaussian Interval Plot (GIplot) GJRM Generalised Joint Regression Modelling GJRM.data Data Sets for Copula Additive Distributional Regression Using R GK2011 Gaines and Kuklinski (2011) Estimators for Hybrid Experiments GLAD Gain and Loss Analysis of DNA GLBFP General Linear Blend Frequency Polygon Density Estimation GLCMTextures GLCM Textures of Raster Layers GLDEX Fitting Single and Mixture of Generalised Lambda Distributions GLDreg Fit GLD Regression/Quantile/AFT Model to Data GLMBasedRaschEstimation GLM-Based Estimation for Rasch Model Parameters GLMMRR Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data GLMMadaptive Generalized Linear Mixed Models using Adaptive Gaussian Quadrature GLMMcosinor Fit a Cosinor Model Using a Generalized Mixed Modeling Framework GLMMselect Bayesian Model Selection for Generalized Linear Mixed Models GLMcat Generalized Linear Models for Categorical Responses GLMpack Data and Code to Accompany Generalized Linear Models, 2nd Edition GLMsData Generalized Linear Model Data Sets GLSME Generalized Least Squares with Measurement Error GLSUP Generalised Linear Step-Up Procedure for Multiple Hypothesis Testing GLmom Generalized L-Moments Estimation for Extreme Value Distributions GMAC Genomic Mediation Analysis with Adaptive Confounding Adjustment GMC Generalized Measure of Correlation (GMC) GMCM Fast Estimation of Gaussian Mixture Copula Models GMDH Short Term Forecasting via GMDH-Type Neural Network Algorithms GMDH2 Binary Classification via GMDH-Type Neural Network Algorithms GMDHreg Regression using GMDH Algorithms GMLTM Generalized Multicomponent Latent Trait Model for Diagnosis GMMAT Generalized Linear Mixed Model Association Tests GMMBoost Likelihood-Based Boosting for Generalized Mixed Models GMMinit Optimal Initial Value for Gaussian Mixture Model GMPro Graph Matching with Degree Profiles GMSE Generalised Management Strategy Evaluation Simulator GMSimpute Generalized Mass Spectrum Missing Peaks Abundance Imputation GMX Extended Graphical Model Checks for the Rasch Family of Models GNAR Methods for Fitting Network Time Series Models GNE Computation of Generalized Nash Equilibria GNRS Access the 'Geographic Name Resolution Service' GNSSseg Homogenization of GNSS Series GOCompare Comprehensive GO Terms Comparison Between Species GOFShiny Interactive Document for Working with Goodness of Fit Analysis GOFclustering Goodness-of-Fit Testing for Model-Based Clustering GORCure Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data GOSemSim GO-terms Semantic Similarity Measures GOplot Visualization of Functional Analysis Data GOstats Tools for manipulating GO and microarrays GPAbin Unifying Multiple Biplot Visualisations into a Single Display GPArotateDF Derivative Free Gradient Projection Factor Rotation GPArotation Gradient Projection Factor Rotation GPBayes Tools for Gaussian Process Modeling in Uncertainty Quantification GPCMlasso Differential Item Functioning in Generalized Partial Credit Models GPCsign Gaussian Process Classification as Described in Bachoc et al. (2020) GPEMR Growth Parameter Estimation Method GPFDA Gaussian Process for Functional Data Analysis GPGame Solving Complex Game Problems using Gaussian Processes GPL2025 Convert Chip ID of the GPL2015 into GeneBank Accession and ENTREZID GPLTR Generalized Partially Linear Tree-Based Regression Model GPP Gaussian Process Projection GPRMortality Gaussian Process Regression for Mortality Rates GPSCDF Generalized Propensity Score Cumulative Distribution Function GPSeqClus Sequential Clustering Algorithm for Location Data GPTCM Generalized Promotion Time Cure Model with Bayesian Shrinkage Priors GPTreeO Dividing Local Gaussian Processes for Online Learning Regression GPUmatrix Basic Linear Algebra with GPU GPareto Gaussian Processes for Pareto Front Estimation and Optimization GPfit Gaussian Processes Modeling GPflexViz Graphical Visualizations Related to Genomic Prediction GPoM Generalized Polynomial Modelling GPpenalty Penalized Likelihood in Gaussian Processes GPvam Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling GPvecchia Scalable Gaussian-Process Approximations GRAB Genome-Wide Robust Analysis for Biobank Data (GRAB) GRANDpriv Graph Release with Assured Node Differential Privacy GRCFE Generate Optimal Row-Column Factorial Experiments GRCRegression Modified Poisson Regression of Grouped and Right-Censored Counts GRCdesigns Generalized Row-Column Designs GREENREG Tool for Statistical and Environmental Analysis GREENeR Geospatial Regression Equation for European Nutrient Losses (GREEN) GREMLINS Generalized Multipartite Networks GRIN2 Genomic Random Interval (GRIN) GRNNs General Regression Neural Networks Package GROAN Genomic Regression Workbench GRShiny Graded Response Model GRSxE Testing Gene-Environment Interactions Through Genetic Risk Scores GRelevance Graph-Based k-Sample Comparisons and Relevance Analysis in High Dimensions GSA Gene Set Analysis GSA.UN Global Sensitivity Analysis Tool GSD Graph Signal Decomposition GSDA Gene Set Distance Analysis (GSDA) GSE Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data GSEABase Gene set enrichment data structures and methods GSED Group Sequential Enrichment Design GSEMA Gene Set Enrichment Meta-Analysis GSM Gamma Shape Mixture GSMX Multivariate Genomic Selection GSODR Global Surface Summary of the Day ('GSOD') Weather Data Client GSSE Genotype-Specific Survival Estimation GSSTDA Progression Analysis of Disease with Survival using Topological Data Analysis GSVA Gene Set Variation Analysis for Microarray and RNA-Seq Data GSbench Benchmarking Genomic Selection and Machine-Learning Prediction Models GSelection Genomic Selection GSparO Group Sparse Optimization GTAPViz Automating 'GTAP' Data Processing and Visualization GTDL The Generalized Time-Dependent Logistic Family GTEs Group Technical Effects GTFSwizard Creating, Exploring and Manipulating 'GTFS' Files GTRT Graph Theoretic Randomness Tests GTbasedIM Game Theory-Based Influence Measures GUD Bayesian Modal Regression Based on the GUD Family GUEST Graphical Models in Ultrahigh-Dimensional and Error-Prone Data via Boosting Algorithm GUILDS Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure GUTS Fast Calculation of the Likelihood of a Stochastic Survival Model GUniFrac Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis GVARX Perform Global Vector Autoregression Estimation and Inference GVS 'Geocoordinate Validation Service' GWASExactHW Exact Hardy-Weinburg Testing for Genome Wide Association Studies GWASTools Tools for Genome Wide Association Studies GWASbyCluster Identifying Significant SNPs in Genome Wide Association Studies (GWAS) via Clustering GWASinlps Non-Local Prior Based Iterative Variable Selection Tool for Genome-Wide Association Studies GWASinspector Comprehensive and Easy to Use Quality Control of GWAS Results GWEX Multi-Site Stochastic Models for Daily Precipitation and Temperature GWI Count and Continuous Generalized Variability Indexes GWLelast Geographically Weighted Logistic Elastic Net Regression GWPR.light Geographically Weighted Panel Regression GWRLASSO A Hybrid Model for Spatial Prediction Through Local Regression GWRM Generalized Waring Regression Model for Count Data GWSDAT GroundWater Spatiotemporal Data Analysis Tool (GWSDAT) GWalkR Interactive Exploratory Data Analysis Tool GWlasso Geographically Weighted Lasso GWmodel Geographically-Weighted Models GWnnegPCA Geographically Weighted Non-Negative Principal Components Analysis GWnorm G-Wishart Normalising Constants for Gaussian Graphical Models GWpcor Geographically Weighted Partial Correlation Coefficient GWsignif Estimating Genome-Wide Significance for Whole Genome Sequencing Studies, Either Single SNP Tests or Region-Based Tests GaSP Train and Apply a Gaussian Stochastic Process Model GalaxyR 'Galaxy' API Implementation GameTheory Cooperative Game Theory GammaFrailty Gamma Frailty Regression Models with Multiple Baseline Distributions Gammareg Classic Gamma Regression: Joint Modeling of Mean and Shape Parameters GapAnalysis Conservation Indicators Using Spatial Information GauPro Gaussian Process Fitting GaussSuppression Tabular Data Suppression using Gaussian Elimination GaussianHMM1d Inference, Goodness-of-Fit and Forecast for Univariate Gaussian Hidden Markov Models GeDS Geometrically Designed Spline Regression GeNetIt Spatial Graph-Theoretic Genetic Gravity Modelling GeRnika Simulation, Visualization and Comparison of Tumor Evolution Data GenAI Generative Artificial Intelligence GenAlgo Classes and Methods to Use Genetic Algorithms for Feature Selection GenBinomApps Clopper-Pearson Confidence Interval and Generalized Binomial Distribution GenEst Generalized Mortality Estimator GenHMM1d Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov Models GenMarkov Multivariate Markov Chains GenOU Sequential Change-Point Tests for Generalized Ornstein-Uhlenbeck Processes GenOrd Simulation of Discrete Random Variables with Marginal Distributions and Correlation Matrix and via a Gaussian or Student's t Copula GenSA R Functions for Generalized Simulated Annealing GenTag Generate Color Tag Sequences GenTwoArmsTrialSize Generalized Two Arms Clinical Trial Sample Size Calculation GenWin Spline Based Window Boundaries for Genomic Analyses GencoDymo2 Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs GenderInfer This is a Collection of Functions to Analyse Gender Differences GeneCycle Identification of Periodically Expressed Genes GeneF Package for Generalized F-Statistics GeneNMF Non-Negative Matrix Factorization for Single-Cell Omics GeneNet Modeling and Inferring Gene Networks GenePopStats Population Genetics Statistics for Selective Sweep GeneScape Simulation of Single Cell RNA-Seq Data with Complex Structure GeneScoreR Gene Scoring from Count Tables GeneralOaxaca Blinder-Oaxaca Decomposition for Generalized Linear Model GeneralizedHyperbolic The Generalized Hyperbolic Distribution GeneralizedUmatrix Credible Visualization for Two-Dimensional Projections of Data GeneralizedUmatrixGPU Credible Visualization for Two-Dimensional Projections of Data GeneralizedWendland Fully Parameterized Generalized Wendland Covariance Function GenerateIndexPedigree Generate Pedigrees for Index Case Based on US Census Data GenericML Generic Machine Learning Inference GeneticSubsetter Identify Favorable Subsets of Germplasm Collections GenoPop Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files GenoTriplo Genotyping Triploids (or Diploids) from Luminescence Data GenomeAdmixR Simulate Admixture of Genomes GenomeInfoDb Utilities for manipulating chromosome names, including modifying them to follow a particular naming style GenomicAlignments Representation and manipulation of short genomic alignments GenomicDataCommons NIH / NCI Genomic Data Commons Access GenomicFeatures Query the gene models of a given organism/assembly GenomicInteractions Utilities for handling genomic interaction data GenomicRanges Representation and manipulation of genomic intervals GenomicSig Computation of Genomic Signatures GenomicTools.fileHandler File Handlers for Genomic Data Analysis GeoAdjust Accounting for Random Displacements of True GPS Coordinates of Data GeoDensityR Generate Density Rasters from Polygon and Census Data GeoFIS Spatial Data Processing for Decision Making GeoModels Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis GeoMongo Geospatial Queries Using 'PyMongo' GeoRange Calculating Geographic Range from Occurrence Data GeoThinneR Efficient Spatial Thinning of Species Occurrences GeoTox Spatiotemporal Mixture Risk Assessment GeoVersa Design-Based Residual-Correction Forests for Digital Soil Mapping GeoWeightedModel User-Friendly Interface for Geographically-Weighted Models GeodRegr Geodesic Regression GeomArchetypal Finds the Geometrical Archetypal Analysis of a Data Frame GeometricMorphometricsMix Heterogeneous Methods for Shape and Other Multidimensional Data GephiForR 'Gephi' Network Visualization GerminaR Indices and Graphics for Assess Seed Germination Process GetBCBData Imports Datasets from BCB (Central Bank of Brazil) using Its Official API GetDFPData2 Reading Annual and Quarterly Financial Reports from B3 GetFREData Reading FRE Corporate Data of Public Traded Companies from B3 GetLattesData Reading Bibliometric Data from Lattes Platform GetQuandlData Fast and Cached Import of Data from 'Quandl' Using the 'json API' GetTDData Get Data for Brazilian Bonds (Tesouro Direto) GetoptLong Parsing Command-Line Arguments Ghat Quantifying Evolution and Selection on Complex Traits Ghost Missing Data Segments Imputation in Multivariate Streams GiANT Gene Set Uncertainty in Enrichment Analysis GiRaF Gibbs Random Fields Analysis Gifi Multivariate Analysis with Optimal Scaling GillespieSSA Gillespie's Stochastic Simulation Algorithm (SSA) GillespieSSA2 Gillespie's Stochastic Simulation Algorithm for Impatient People GimmeMyPlot Graphical Utilities for Visualizing and Exploring Data GimmeMyStats Statistics Utilities Gini Gini Coefficient GiniDecompLY Gini Decomposition by Income Sources GiniDistance A New Gini Correlation Between Quantitative and Qualitative Variables GitAI Extracts Knowledge from 'Git' Repositories GitStats Standardized Git Repository Data GlarmaVarSel Variable Selection in Sparse GLARMA Models Glarmadillo Solve the Graphical Lasso Problem with 'Armadillo' GlmSimulatoR Creates Ideal Data for Generalized Linear Models GlobalAncova Global test for groups of variables via model comparisons GlobalOptions Generate Functions to Get or Set Global Options Gmedian Geometric Median, k-Medians Clustering and Robust Median PCA Gmisc Descriptive Statistics, Transition Plots, and More GmooG Datasets for the Book 'Getting (more out of) Graphics' GmptzCurve Gompertz Curve Fitting GoFKernel Testing Goodness-of-Fit with the Kernel Density Estimator GoMiner Automate the Mapping Between a List of Genes and Gene Ontology Categories GofCens Goodness-of-Fit Methods for Right-Censored Data GomoGomonoMi Animate Text using the 'Animate.css' Library GoodFibes Detection and Reconstruction of Muscle Fibers from diceCT Image Data GoodFitSBM Monte Carlo Goodness-of-Fit Tests for Stochastic Block Models GoodmanKruskal Association Analysis for Categorical Variables GoogleKnowledgeGraphR Retrieve Information from 'Google Knowledge Graph' API GowerSom Self-Organizing Maps for Mixed-Attribute Data Using Gower Distance GpGp Fast Gaussian Process Computation Using Vecchia's Approximation GrFA Group Factor Analysis GrabSVG Granularity-Based Spatially Variable Genes Identifications GramQuad Gram Quadrature GraphRankTest Rank in Similarity Graph Edge-Count Two-Sample Test (RISE) GrapheR A Multi-Platform GUI for Drawing Customizable Graphs in R GreedyEPL Greedy Expected Posterior Loss GreedyExperimentalDesign Greedy Experimental Design Construction GreedyExperimentalDesignJARs GreedyExperimentalDesign JARs Greg Regression Helper Functions GregoryQuadrature Gregory Weights for Function Integration GreyModel Fitting and Forecasting of Grey Model Greymodels Shiny App for Grey Forecasting Model GridOnClusters Multivariate Joint Grid Discretization GroupBN Inferring Group Bayesian Networks using Hierarchical Feature Clustering GroupComparisons Paired/Unpaired Parametric/Non-Parametric Group Comparisons GroupSeq Group Sequential Design Probabilities - With Graphical User Interface GroupTest Multiple Testing Procedure for Grouped Hypotheses GrowthCurveME Mixed-Effects Modeling for Growth Data GrpString String Patterns and Statistical Differences Between Two Groups of Strings GsymPoint Estimation of the Generalized Symmetry Point, an Optimal Cutpoint in Continuous Diagnostic Tests Guerry Maps, Data and Methods Related to Guerry (1833) "Moral Statistics of France" GulFM General Unilateral Load Estimator for Two-Layer Latent Factor Models Gviz Plotting data and annotation information along genomic coordinates GxEScanR Run GWAS/GWEIS Scans Using Binary Dosage Files GxEprs Genotype-by-Environment Interaction in Polygenic Score Models H2x2Factorial Sample Size Calculation in Hierarchical 2x2 Factorial Trials HAC Estimation, Simulation and Visualization of Hierarchical Archimedean Copulae (HAC) HACSim Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment HAMMER High-Dimensional Factor-Analytic Representation Modeling and Metrics HARplus Enhanced R Package for 'GEMPACK' .har and .sl4 Files HARr 'HAR' ('GEMPACK') File Read/Write Utility HBSTM Hierarchical Bayesian Space-Time Models for Gaussian Space-Time Data HBV.IANIGLA Modular Hydrological Model HCD Hierarchical Community Detection by Recursive Partitioning HCPclust Hierarchical Conformal Prediction for Clustered Data with Missing Responses HCR Causal Discovery from Discrete Data using Hidden Compact Representation HCTDesign Group Sequential Design for Historical Control Trial with Survival Outcome HCUPtools Access and Work with HCUP Resources and Datasets HCmodelSets Regression with a Large Number of Potential Explanatory Variables HDANOVA High-Dimensional Analysis of Variance HDBRR High Dimensional Bayesian Ridge Regression without MCMC HDCD High-Dimensional Changepoint Detection HDCurves Hierarchical Derivative Curve Estimation HDF5Array HDF5 datasets as array-like objects in R HDGLM Tests for High Dimensional Generalized Linear Models HDInterval Highest (Posterior) Density Intervals HDLSSkST Distribution-Free Exact High Dimensional Low Sample Size k-Sample Tests HDMAADMM ADMM for High-Dimensional Mediation Models HDMFA High-Dimensional Matrix Factor Analysis HDMT A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses HDNRA High-Dimensional Location Testing with Normal-Reference Approaches HDOMDesign High-Dimensional Orthogonal Maximin Distance Designs HDRFA High-Dimensional Robust Factor Analysis HDShOP High-Dimensional Shrinkage Optimal Portfolios HDSinRdata Data for the 'Mastering Health Data Science Using R' Online Textbook HDSpatialScan Multivariate and Functional Spatial Scan Statistics HDStIM High Dimensional Stimulation Immune Mapping ('HDStIM') HDTSA High Dimensional Time Series Analysis Tools HDXBoxeR Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data HDclassif High Dimensional Supervised Classification and Clustering HDclust Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks HDcpDetect Detect Change Points in Means of High Dimensional Data HDtweedie The Lasso for Tweedie's Compound Poisson Model Using an IRLS-BMD Algorithm HEDA 'Hydropeaking Events Detection Algorithm' HEssRNA Heritability-Based Estimation of Sample Size for RNA-Seq Data HEtools Homomorphic Encryption Polynomials HGDMr Hysteretic and Gatekeeping Depressions Model HGMND Heterogeneous Graphical Model for Non-Negative Data HGNChelper Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols HGSL Heterogeneous Group Square-Root Lasso HGraph Use Graph Structure to Travel HH Statistical Analysis and Data Display: Heiberger and Holland HHBayes Bayesian Household Transmission Modeling with 'Stan' HIViz Interactive Dashboard for 'HIV' Data Visualization HK80 Conversion Tools for HK80 Geographical Coordinate System HKRbook Apps and Data for the Book "Introduction to Statistics" HLAtools Toolkit for HLA Immunogenomics HLMdiag Diagnostic Tools for Hierarchical (Multilevel) Linear Models HLSM Hierarchical Latent Space Network Model HMC High-Dimensional Mean Comparison with Projection and Cross-Fitting HMDA Holistic Multimodel Domain Analysis for Exploratory Machine Learning HMDHFDplus Read Human Mortality Database and Human Fertility Database Data from the Web HMM Hidden Markov Models HMMHSMM Inference and Estimation of Hidden Markov Models and Hidden Semi-Markov Models HMMRel Hidden Markov Models for Reliability and Maintenance HMMcopula Markov Regime Switching Copula Models Estimation and Goodness-of-Fit HMMextra0s Hidden Markov Models with Extra Zeros HMMpa Analysing Accelerometer Data Using Hidden Markov Models HMR Flux Estimation with Static Chamber Data HMTL Heterogeneous Multi-Task Feature Learning HNPclassifier Hierarchical Neyman-Pearson Classification for Ordered Classes HOIF Higher-Order Influence Function Estimators for the Average Treatment Effect HOIFCar Covariate Adjustment in RCT by Higher-Order Influence Functions HOME Harmonized Orphanhood Mortality Estimation HOasso Higher Order Assortativity for Complex Networks HPZoneAPI 'HPZone' API Interface HQM Superefficient Estimation of Future Conditional Hazards Based on Marker Information HRTnomaly Historical, Relational, and Tail Anomaly-Detection Algorithms HRW Datasets, Functions and Scripts for Semiparametric Regression Supporting Harezlak, Ruppert & Wand (2018) HSAR Hierarchical Spatial Autoregressive Model HSAUR A Handbook of Statistical Analyses Using R (1st Edition) HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition) HSAUR3 A Handbook of Statistical Analyses Using R (3rd Edition) HSEtest Homogeneity of Stratum Effects Test HSPOR Hidden Smooth Polynomial Regression for Rupture Detection HTDV Hypothesis Testing for Dependent Variables with Unbalanced Data HTGM High Throughput 'GoMiner' HTGM2D Two Dimensional High Throughput 'GoMiner' HTGM3D Three Dimensional High Throughput 'GoMiner' HTGM4D Four Dimensional High Throughput 'GoMiner' HTLR Bayesian Logistic Regression with Heavy-Tailed Priors HTMLUtils Facilitates Automated HTML Report Creation HTRX Haplotype Trend Regression with eXtra Flexibility (HTRX) HTSCluster Clustering High-Throughput Transcriptome Sequencing (HTS) Data HTSFilter Filter replicated high-throughput transcriptome sequencing data HTSeed Fitting of Hydrotime Model for Seed Germination Time Course HTSeedGLM Hydro Thermal Time Analysis of Seed Germination Using Generalised Linear Model HTT Hypothesis Testing Tree HUM Compute HUM Value and Visualize ROC Curves HVT Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis HWEintrinsic Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem HYDROCAL Hydraulic Roughness Calculator HYPEtools Tools for Processing and Analyzing Files from the Hydrological Catchment Model HYPE HZIP Likelihood-Based Inference for Joint Modeling of Correlated Count and Binary Outcomes with Extra Variability and Zeros HaDeX Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data HaDeX2 Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data HadIBDs Incomplete Block Designs using Hadamard Matrix (HadIBDs) HadamardR Hadamard Matrix Generation HanStat Package for Easy Interpretation of Statistical Methods HandTill2001 Multiple Class Area under ROC Curve Hapi Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells Haplin Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes HaploCatcher A Predictive Haplotyping Package HaploDiploidEquilibrium Calculate F Statistics Using Mixed Haploid and Diploid Organism Data HaploSim Functions to Simulate Haplotypes HaploVar Defining Local Haplotype Variants for Use in Trait Association and Trait Prediction Analyses HardyWeinberg Statistical Tests and Graphics for Hardy-Weinberg Equilibrium Harvest.Tree Harvest the Classification Tree Hassani.SACF Computing Lower Bound of Ljung-Box Test Hassani.Silva A Test for Comparing the Predictive Accuracy of Two Sets of Forecasts HausdorffGoF One- And Two-Sample Hausdorff Goodness-of-Fit Test HazardDiff Conditional Treatment Effect for Competing Risks HealthCal Health Calculator HealthMarkers Clinical and Metabolic Biomarker Calculation Toolkit HeatmapR Create Heatmaps Using Base Graphics Heatplus Heatmaps with row and/or column covariates and colored clusters HeckmanEM Fit Normal, Student-t or Contaminated Normal Heckman Selection Models HeckmanStan Heckman Selection Models Based on Bayesian Analysis HellCor The Hellinger Correlation HelloFrog A Quirky ASCII-Art Frog Alternative to 'print' HelpersMG Tools for Various R Functions Helpers HetSeq Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity HeterFunctionalData Test of No Main and/or Interaction Effects in Functional Data HextractoR Integrated Tool for Hairping Extraction of RNA Sequences HhP Hierarchical Heterogeneity Analysis via Penalization HiCDOC A/B compartment detection and differential analysis HiCParser Parser for HiC data in R HiCcompare HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets HiClimR Hierarchical Climate Regionalization HiCocietyExample Example HiC and Two 'HiCociety' Outputs for Demonstration and Testing HiDimDA High Dimensional Discriminant Analysis HiGarrote Nonnegative Garrote Method Incorporating Hierarchical Relationships HiResTEC Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data HiTC High Throughput Chromosome Conformation Capture analysis HiddenMarkov Hidden Markov Models HierPortfolios Hierarchical Risk Clustering Portfolio Allocation Strategies HighFive The 'HighFive' 'C++' Interface to 'HDF5' HighestMedianRules Implementation of Voting Rules Electing the Candidate with Highest Median Grade HistDAWass Histogram-Valued Data Analysis HistDat Summary Statistics for Histogram/Count Data HistData Data Sets from the History of Statistics and Data Visualization HistogramTools Utility Functions for R Histograms HiveR 2D and 3D Hive Plots for R Hmisc Harrell Miscellaneous Hmsc Hierarchical Model of Species Communities HoRM Supplemental Functions and Datasets for "Handbook of Regression Methods" HodgesTools Common Use Tools for Genomic Analysis Holomics A User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis HomeRangeR Predict Vertebrate Home-Range Sizes Using Allometric Models Homeric Doughnut Plots HomomorphicEncryption BFV, BGV, CKKS Schema for Fully Homomorphic Encryption HonestDiD Robust Inference in Difference-in-Differences and Event Study Designs Horsekicks Provide Extensions to the Prussian Army Death by Horsekick Data HospitalNetwork Building Networks of Hospitals Through Patients Transfers Hotelling Hotelling's T^2 Test and Variants HotellingEllipse Hotelling’s T-Squared Statistic and Ellipse HuraultMisc Guillem Hurault Functions' Library HurreconR Models Hurricane Wind Speed, Wind Direction, and Wind Damage HyMETT Hydrologic Model Evaluation and Time-Series Tools HyRiM Multicriteria Risk Management using Zero-Sum Games with Vector-Valued Payoffs that are Probability Distributions HybridDesign Hybrid Design for Phase I Dose-Finding Studies HybridMicrobiomes Analysis of Host-Associated Microbiomes from Hybrid Organisms HydroCode Hydrological Codes HydroMe Estimating Water Retention and Infiltration Model Parameters using Experimental Data HydroPonicsK Hydroponic Data Analysis Tools HydroPortailStats 'HydroPortail' Statistical Functions HyperG Hypergraphs in R HyperbolicDist The Hyperbolic Distribution IADT Interaction Difference Test for Prediction Models IALS Iterative Alternating Least Square Estimation for Large-Dimensional Matrix Factor Model IAPWS95 Thermophysical Properties of Water and Steam IASD Model Selection for Index of Asymmetry Distribution IATScore Scoring Algorithm for the Implicit Association Test (IAT) IATanalytics Compute Effect Sizes and Reliability for Implicit Association Test (IAT) Data IATscores Implicit Association Test Scores Using Robust Statistics IAcsSPCR Data and Functions for "An Intro. to Accept. Samp. & SPC/R" IBCF.MTME Item Based Collaborative Filtering for Multi-Trait and Multi-Environment Data IBDInfer Design-Based Causal Inference Method for Incomplete Block Designs IBFS Initial Basic Feasible Solution for Transportation Problem IBGS Iterated Block Gibbs Sampler for Ultrahigh-Dimensional Variable Selection and Model Averaging IBLM Interpretable Boosted Linear Models IBMPopSim Individual Based Model Population Simulation IBRtools Integrating Biomarker-Based Assessments and Radarchart Creation IBclust Information Bottleneck Methods for Clustering Mixed-Type Data IBrokers R API to Interactive Brokers Trader Workstation ICAOD Optimal Designs for Nonlinear Models via ICA ICBioMark Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers ICC Facilitating Estimation of the Intraclass Correlation Coefficient ICC.Sample.Size Calculation of Sample Size and Power for ICC ICCDesign Intraclass Correlation Coefficient (ICC) Design, Calculation and Interactive 'shiny' Toolkit ICCbin Facilitates Clustered Binary Data Generation, and Estimation of Intracluster Correlation Coefficient (ICC) for Binary Data ICD10gm Metadata Processing for the German Modification of the ICD-10 Coding System ICED IntraClass Effect Decomposition ICEHmeasures The Equiplot Graph and Complex Inequality Measures ICEbox Individual Conditional Expectation Plot Toolbox ICGE Estimation of Number of Clusters and Identification of Atypical Units ICGOR Fit Generalized Odds Rate Hazards Model with Interval Censored Data ICODS Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring ICS Tools for Exploring Multivariate Data via ICS/ICA ICSClust Tandem Clustering with Invariant Coordinate Selection ICSKAT Interval-Censored Sequence Kernel Association Test ICSNP Tools for Multivariate Nonparametrics ICSOutlier Outlier Detection Using Invariant Coordinate Selection ICSS ICSS Algorithm by Inclan/Tiao (1994) ICSShiny ICS via a Shiny Application ICSsmoothing Data Smoothing by Interpolating Cubic Splines ICV Indirect Cross-Validation (ICV) for Kernel Density Estimation ICcalib Cox Model with Interval-Censored Starting Time of a Covariate ICcforest An Ensemble Method for Interval-Censored Survival Data ICglm Information Criteria for Generalized Linear Regression ICompELM Independent Component Analysis Based Extreme Learning Machine ICsurv Semiparametric Regression Analysis of Interval-Censored Data ICtest Estimating and Testing the Number of Interesting Components in Linear Dimension Reduction ICvectorfields Vector Fields from Spatial Time Series of Population Abundance IDCard Update Chinese ID Card Number to Eighteen Digits IDE Integro-Difference Equation Spatio-Temporal Models IDEAFilter Agnostic, Idiomatic Data Filter Module for Shiny IDEATools Individual and Group Farm Sustainability Assessments using the IDEA4 Method IDF Estimation and Plotting of IDF Curves IDLFM Individual Dynamic Latent Factor Model IDMIR Identification of Dysregulated MiRNAs Based on MiRNA-MiRNA Interaction Network IDPSurvival Imprecise Dirichlet Process for Survival Analysis IDPmisc 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)' IDSL.CSA Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses IDSL.FSA Fragmentation Spectra Analysis (FSA) IDSL.IPA Intrinsic Peak Analysis (IPA) for HRMS Data IDSL.MXP Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data) IDSL.NPA Nominal Peak Analysis (NPA) IDSL.SUFA Simplified UFA IDSL.UFA United Formula Annotation (UFA) for HRMS Data Processing IDSL.UFAx Exhaustive Chemical Enumeration for United Formula Annotation IDSpatialStats Estimate Global Clustering in Infectious Disease IDetect Isolate-Detect Method for Multiple Change-Point Detection IDmeasurer Assessment of Individual Identity in Animal Signals IDmining Intrinsic Dimension for Data Mining IETD Inter-Event Time Definition IFC Tools for Imaging Flow Cytometry IFMCDM Intuitionistic Fuzzy Multi-Criteria Decision Making Methods IFTPredictor Predictions Using Item-Focused Tree Models IGC.CSM Simulate Impact of Different Urban Policies Through a General Equilibrium Model IGST Informative Gene Selection Tool IHSEP Inhomogeneous Self-Exciting Process IHW Independent Hypothesis Weighting IIProductionUnknown Analyzing Data Through of Percentage of Importance Indice (Production Unknown) and Its Derivations IIS Datasets to Accompany Wolfe and Schneider - Intuitive Introductory Statistics IIVpredictor Modeling Within Individual Variability as Predictor IJSE Infinitesimal Jackknife Standard Errors for 'brms' Models ILORA Indian Alien Flora Information Database Retrieval ILRCM Convert Irregular Longitudinal Data to Regular Intervals and Perform Clustering ILS Interlaboratory Study ILSAmerge Merge and Download International Large-Scale Assessments (ILSA) Data ILSAstats Statistics for International Large-Scale Assessments (ILSA) ILSM Analyze Interconnection Structure of Tripartite Interaction Networks IMD Index of Multiple Deprivation Data for the UK IMIFA Infinite Mixtures of Infinite Factor Analysers and Related Models IMIX Gaussian Mixture Model for Multi-Omics Data Integration IMP Interactive Model Performance Evaluation IMPACT The Impact of Items IMR Incomplete Matrix Regression IMTest Information Matrix Test for Generalized Partial Credit Models IMak Item Maker IMmailgun Send Emails using 'Mailgun' INCVCommunityDetection Inductive Node-Splitting Cross-Validation for Community Detection INFOSET Computing a New Informative Distribution Set of Asset Returns INLA Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations INLABMA Bayesian Model Averaging with INLA INLAjoint Multivariate Joint Modeling for Longitudinal and Time-to-Event Outcomes with 'INLA' INLAspacetime Spatial and Spatio-Temporal Models using 'INLA' INLAtools Functionalities for the 'INLA' Package INLAvaan Approximate Bayesian Latent Variable Analysis INQC Quality Control of Climatological Daily Time Series INTRIGUE Quantify and Control Reproducibility in High-Throughput Experiments INetTool Integration Network IOBR Immune Oncology Biological Research IOLS Iterated Ordinary Least Squares Regression IPAG Tools for IPAG Courses IPCWK Kendall's Tau Partial Corr. for Survival Trait and Biomarkers IPDfromKM Map Digitized Survival Curves Back to Individual Patient Data IPEC Root Mean Square Curvature Calculation IPEDS Data from the Integrated Post-Secondary Education Data System IPEDSuploadables Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload IPLGP Identification of Parental Lines via Genomic Prediction IPMRF Intervention in Prediction Measure for Random Forests IPMbook Functions and Data for the Book 'Integrated Population Models' IPPP Inhomogeneous Poisson Point Processes IPV Item Pool Visualization IPWboxplot Adapted Boxplot to Missing Observations IQCC Improved Quality Control Charts IRISMustangMetrics Statistics and Metrics for Seismic Data IRISSeismic Classes and Methods for Seismic Data Analysis IRR2FPR Computing False Positive Rate from Inter-Rater Reliability IRTBEMM Family of Bayesian EMM Algorithm for Item Response Models IRTM Theory-Driven Item Response Theory (IRT) Models IRTShiny Item Response Theory via Shiny IRTest Parameter Estimation of Item Response Theory with Estimation of Latent Distribution IRanges Foundation of integer range manipulation in Bioconductor IRdisplay 'Jupyter' Display Machinery IRexamples Collection of Practical Institutional Research Examples and Tutorials IRkernel Native R Kernel for the 'Jupyter Notebook' IRon Solving Imbalanced Regression Tasks ISAR Introduction to Sports Analytics using R (ISAR) Data ISCA Compare Heterogeneous Social Groups ISCAM Companion to the Book "Investigating Statistical Concepts, Applications, and Methods" ISCO08ConveRsions Converts ISCO-08 to Job Prestige Scores, ISCO-88 and Job Name ISEtools Ion Selective Electrodes Analysis Methods ISLR Data for an Introduction to Statistical Learning with Applications in R ISLR2 Introduction to Statistical Learning, Second Edition ISM Interpretive Structural Modelling (ISM) ISMtools Interpretive Structural Modelling Analysis Tools ISO11784Tools ISO11784 PIT Tag ID Format Converters ISO6976.2016 Calorific Values and Properties of Natural Gas per ISO 6976:2016 ISOcodes Selected ISO Codes ISOweek Week of the year and weekday according to ISO 8601 ISPYARDSWinProbabilityGSDesign Trial Design in Respiratory Disease Based on the Win Probability ISR The Iterated Score Regression-Based Estimation ISRaD Tools and Data for the International Soil Radiocarbon Database ISS Isotonic Subgroup Selection ISwR Introductory Statistics with R ITNr Analysis of the International Trade Network IVCor A Robust Integrated Variance Correlation IVDML Double Machine Learning with Instrumental Variables and Heterogeneity IVPP Invariance Partial Pruning Test IVYplot Produces an IVY Plot (Similar to Dot Plot) with/without Frequencies IceSat2R 'ICESat-2' Altimeter Data using R Icens NPMLE for Censored and Truncated Data IgAScores Score Taxon-Level IgA Binding in IgA-Seq Experiments IgorR Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data) ImCluster Efficiency of Cluster Sampling for Crop Surveys ImFoR Non-Linear Height Diameter Models for Forestry ImML Machine Learning Algorithms Fitting and Validation for Forestry ImNN Neural Networks for Predicting Volume of Forest Trees ImVol Volume Prediction of Trees Using Linear and Nonlinear Allometric Equations Immigrate Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection ImmuneSigR Immune Cell Signature Retrieval and Single-Cell Scoring Immutables Fast and Functional Data Structures Imneuron AI Powered Neural Network Solutions for Regression Tasks ImpShrinkage Improved Shrinkage Estimations for Multiple Linear Regression ImpactEffectsize Calculation and Visualization of the Impact Effect Size Measure ImportExport Import and Export Data ImportanceIndice Analyzing Data Through of Percentage of Importance Indice and Its Derivations ImprintCapASM Allele-Specific Methylation Analysis for Imprinted DMR Diagnostics ImputeLongiCovs Longitudinal Imputation of Categorical Variables via a Joint Transition Model ImputeRobust Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape InPosition Inference Tests for ExPosition InSilicoVA Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm IncDTW Incremental Calculation of Dynamic Time Warping IncidencePrevalence Estimate Incidence and Prevalence using the OMOP Common Data Model IncomPair Comparison of Means for the Incomplete Paired Data IndGenErrors Tests of Independence Between Innovations of Generalized Error Models IndTestPP Tests of Independence and Analysis of Dependence Between Point Processes in Time IndepTest Nonparametric Independence Tests Based on Entropy Estimation IndependenceTests Non-Parametric Tests of Independence Between Random Vectors IndexConstruction Index Construction for Time Series Data IndexNumR Index Number Calculation IndexNumber Index Numbers in Social Sciences IndexNumberTools Working with Index Numbers IndexWizard Constructing and Analyzing Complex Selection Indices IndiAPIs Access Indian Data via Public APIs and Curated Datasets Indicator Composite 'Indicator' Construction and Imputation Data IndonesiAPIs Access Indonesian Data via Public APIs and Curated Datasets InferenceSMR Inference About the Standardized Mortality Ratio when Evaluating the Effect of a Screening Program on Survival InfiniumPurify Estimate and Account for Tumor Purity in Cancer Methylation Data Analysis Inflation Core Inflation InflectSSP Melt Curve Fitting and Melt Shift Analysis Inflongitudinal Detecting Influential Subjects in Longitudinal Data InfluenceBorrowing Adaptive Influence-Based Borrowing for Hybrid Control Trials Information Data Exploration with Information Theory (Weight-of-Evidence and Information Value) InformativeCensoring Multiple Imputation for Informative Censoring Infusion Inference Using Simulation InjurySeverityScore Translate ICD-9 into Injury Severity Score Inquilab Dissipation Kinetics Analysis, Half Life Period, Rate Constant, Plots InsectLabelR Create Labels for Insect in Collection InspectChangepoint High-Dimensional Changepoint Estimation via Sparse Projection InspectionPlanner Phytosanitary Inspection Sampling Planner InsuSensCalc Insulin Sensitivity Indices Calculator IntCal Radiocarbon Calibration Curves IntNMF Integrative Clustering of Multiple Genomic Dataset IntegratedJM Joint Modeling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature InterNL Time Series Intervention Model Using Non-Linear Function InterSIM Simulation of Inter-Related Genomic Datasets InterVA4 Replicate and Analyse 'InterVA4' InterVA5 Replicate and Analyse 'InterVA5' InteractionPoweR Power Analyses for Interaction Effects in Cross-Sectional Regressions InteractionSet Base Classes for Storing Genomic Interaction Data InteractiveComplexHeatmap Make Interactive Complex Heatmaps Interatrix Compute Chi-Square Measures with Corrections InterfaceqPCR GUI to Analyse qPCR Results after PMA Treatment or not InterpolateR A Comprehensive Toolkit for Fast and Efficient Spatial Interpolation InterpretMSSpectrum Interpreting High Resolution Mass Spectra IntervalQuestionStat Tools to Deal with Interval-Valued Responses in Questionnaires IntervalSurgeon Operating on Integer-Bounded Intervals InvStablePrior Inverse Stable Prior for Widely-Used Exponential Models InvariantCausalPrediction Invariant Causal Prediction InvasionCorrection Invasion Correction IrishDirectorates A Dynamic Bipartite Latent Space Model to Analyse Irish Companies' Boards from 2003 to 2013 IrregLong Analysis of Longitudinal Data with Irregular Observation Times Iscores Proper Scoring Rules for Missing Value Imputation IsingFit Fitting Ising Models Using the ELasso Method IsingSampler Sampling Methods and Distribution Functions for the Ising Model Isinglandr Landscape Construction and Simulation for Ising Networks IsletCalc Calculators for Insulin and Glucagon Release Indices Iso Functions to Perform Isotonic Regression IsoCor Analyze Isotope Ratios in a 'Shiny'-App IsoMemo Retrieve Data using the 'IsoMemo' API IsoSpecR The IsoSpec Algorithm IsoplotR Statistical Toolbox for Radiometric Geochronology IsoplotRgui Web Interface to 'IsoplotR' IsoriX Isoscape Computation and Inference of Spatial Origins using Mixed Models IssueTrackeR List Things to Do ItemRest Automated Item Removal Strategies for Exploratory Factor Analysis IterativeHardThresholding Iterative Hard Thresholding Extensions to Cyclops IxPopDyMod Framework for Tick Population and Infection Modeling JADE Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria JANE Just Another Latent Space Network Clustering Algorithm JATSdecoder A Metadata and Text Extraction and Manipulation Tool Set JBrowseR An R Interface to the JBrowse 2 Genome Browser JCRImpactFactor Journal Citation Reports ('JCR') Impact Factor by 'Clarivate' 'Analytics' JDCruncheR 'JDemetra+' Quality Report Generator JFE Tools for Analyzing Time Series Data of Just Finance and Econometrics JFM Rock Mass Structural Analysis from 3D Mesh of Point Cloud JGR Java GUI for R JICO Joint and Individual Regression JLPM Joint Latent Process Models JM Joint Modeling of Longitudinal and Survival Data JM4QTN Joint Mapping for Quantitative Trait Loci JMH Joint Model of Heterogeneous Repeated Measures and Survival Data JMI Jackknife Mutual Information JMbayes Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach JMbayes2 Extended Joint Models for Longitudinal and Time-to-Event Data JMbdirect Joint Model for Longitudinal and Multiple Time to Events Data JMdesign Joint Modeling of Longitudinal and Survival Data - Power Calculation JNplots Visualize Outputs from the 'Johnson-Neyman' Technique JOPS Practical Smoothing with P-Splines JPEN Covariance and Inverse Covariance Matrix Estimation Using Joint Penalty JPSurv Joinpoint Model for Relative and Cause-Specific Survival JSDNE Estimating the Age using Auricular Surface by DNE JSM Semiparametric Joint Modeling of Survival and Longitudinal Data JSUparameters Estimate Parameters of the Best-Fitting JohnsonSU Distribution JSconsole A 'RStudio' Addin to Send 'JavaScript' Code to the 'V8' Console JSmediation Mediation Analysis Using Joint Significance JSparO Joint Sparse Optimization via Proximal Gradient Method for Cell Fate Conversion JUMP Replicability Analysis of High-Throughput Experiments JWileymisc Miscellaneous Utilities and Functions Jacquard Estimation of Jacquard's Genetic Identity Coefficients JamendoR Access to 'Jamendo' API JapanAPIs Access Japanese Data via Public APIs and Curated Datasets JavaGD Java Graphics Device Jaya Gradient-Free Optimization Algorithm for Single and Multi-Objective Problems Jcvrisk Risk Calculator for Cardiovascular Disease in Japan Jdmbs Monte Carlo Option Pricing Algorithms for Jump Diffusion Models with Correlational Companies Jmisc Julian Miscellaneous Function JoF Modelling and Simulating Judgments of Frequency JoSAE Unit-Level and Area-Level Small Area Estimation JointAI Joint Analysis and Imputation of Incomplete Data JointFPM A Parametric Model for Estimating the Mean Number of Events Julia Fractal Image Data Generator JuliaCall Seamless Integration Between R and 'Julia' JuliaConnectoR A Functionally Oriented Interface for Integrating 'Julia' with R JuliaFormulae Translate R Regression Model Formulae to 'Julia' Syntax JumpDiffSim Jump Diffusion Simulation and Calibration for Merton and Kou Models JustifyAlpha Justifying Alpha Levels for Hypothesis Tests K4PrestasiSiswa Student Achievement Data Files for TIMSS 2023 Grade 4 K4ProsesSiswa Student Process Data Files for TIMSS 2023 Grade 4 K4Sekolah School Context Data Files for TIMSS 2023 Grade 4 KCSKNNShiny K-Nearest Neighbour Classifier KCSNBShiny Naive Bayes Classifier KDEmcmc Kernel Density Estimation with a Markov Chain Monte Carlo Sample KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor KEPTED Kernel-Embedding-of-Probability Test for Elliptical Distribution KFAS Kalman Filter and Smoother for Exponential Family State Space Models KFPCA Kendall Functional Principal Component Analysis KFPLS Kernel Functional Partial Least Squares KGode Kernel Based Gradient Matching for Parameter Inference in Ordinary Differential Equations KHQ Methods for Calculating 'KHQ' Scores and 'KHQ5D' Utility Index Scores KINSIMU Panel Evaluation in Forensic Kinship Analysis KLINK Kinship Analysis with Linked Markers KLexp Kernel_lasso Expansion KMD Kernel Measure of Multi-Sample Dissimilarity KMEANS.KNN KMeans and KNN Clustering Package KMLtoSHAPE Preserving Attribute Values: Converting KML to Shapefile KMsurv Datasets from Klein and Moeschberger (1997), Survival Analysis KMunicate KMunicate-Style Kaplan–Meier Plots KNNShiny Interactive Document for Working with KNN Analysis KODAMA Knowledge Discovery by Accuracy Maximization KOFM Test the Kronecker Product Structure in Tensor Factor Models KOGMWU Functional Summary and Meta-Analysis of Gene Expression Data KOLaide Pick and Plot Key Opinion Leaders from a Network Given Constraints KONPsurv KONP Tests: Powerful K-Sample Tests for Right-Censored Data KOR.addrlink Matching Address Data to Reference Index KPC Kernel Partial Correlation Coefficient KQM K Quantiles Medoids (KQM) Clustering KRIS Keen and Reliable Interface Subroutines for Bioinformatic Analysis KRLS Kernel-Based Regularized Least Squares KRMM Kernel Ridge Mixed Model KRONX Clock of Regimes for Regime-Switching Fragility Analysis KSA Retained Component Criterion for Principal Component Analysis KSEAapp Kinase-Substrate Enrichment Analysis KSIC Korea Standard Industrial Classification (KSIC) KSPM Kernel Semi-Parametric Models KScorrect Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests KSgeneral Computing P-Values of the One-Sample K-S Test and the Two-Sample K-S and Kuiper Tests for (Dis)Continuous Null Distribution KTensorGraphs Co-Tucker3 Analysis of Two Sequences of Matrices KWCChangepoint Robust Changepoint Detection for Functional and Multivariate Data KWELA Hierarchical Adaptive 'RT-QuIC' Classification for Complex Matrices KappaGUI An R-Shiny Application for Calculating Cohen's and Fleiss' Kappa Karen Kalman Reaction Networks KarsTS An Interface for Microclimate Time Series Analysis KbMvtSkew Khattree-Bahuguna's Univariate and Multivariate Skewness Kcop Smooth Test for Equality of Copulas and Clustering Multivariate Kendall Kendall Rank Correlation and Mann-Kendall Trend Test Keng Knock Errors Off Nice Guesses KernSmoothIRT Nonparametric Item Response Theory KernelKnn Kernel k Nearest Neighbors Kernelheaping Kernel Density Estimation for Heaped and Rounded Data Keyboard Bayesian Designs for Early Phase Clinical Trials Kifidi Summary Table and Means Plots KinMixLite Inference About Relationships from DNA Mixtures KinformR Relationship-Informed Pedigree and Variant Scoring KingCountyHouses Data on House Sales in King County WA Kira Machine Learning KlerRSS Intelligent Ranked Set Sampling with 'Excel' Integration and SRS Comparison Kmedians K-Medians KnapsackSampling Generate Feasible Samples of a Knapsack Problem KneeArrower Finds Cutoff Points on Knee Curves KnockoffHybrid Hybrid Analysis of Population and Trio Data with Knockoff Statistics for FDR Control KnockoffTrio GWAS with Trio and Duo Data using Knockoff Statistics for FDR Control KnowBR Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases KoboconnectR Download Data from Kobotoolbox to R Kpart Cubic Spline Fitting with Knot Selection KrakenR Comprehensive R Interface for Accessing Kraken Cryptocurrency Exchange REST API KraljicMatrix A Quantified Implementation of the Kraljic Matrix KrigInv Kriging-Based Inversion for Deterministic and Noisy Computer Experiments Kurt Performs Kurtosis-Based Statistical Analyses L0Learn Fast Algorithms for Best Subset Selection L0TFinv A Splicing Approach to the Inverse Problem of L0 Trend Filtering L0cpt Change Point Detection with L0 Penalty L0ggm Smooth L0 Penalty Approximations for Gaussian Graphical Models L1centrality Graph/Network Analysis Based on L1 Centrality L1pack Routines for L1 Estimation L2DensityGoFtest Density Goodness-of-Fit Test L2E Robust Structured Regression via the L2 Criterion L2hdchange L2 Inference for Change Points in High-Dimensional Time Series LA Lioness Algorithm (LA) LABTNSCPSS Calculation of Comorbidity and Frailty Scores LAD Derive Leaf Angle Distribution (LAD) from Measured Leaf Inclination Angles LAGOSNE Interface to the Lake Multi-Scaled Geospatial and Temporal Database LAIr Converting NDVI to LAI of Field, Proximal and Satellite Data LAM Some Latent Variable Models LARisk Estimation of Lifetime Attributable Risk of Cancer from Radiation Exposure LATERmodel Linear Approach to Threshold with Ergodic Rate for Reaction Times LAWBL Latent (Variable) Analysis with Bayesian Learning LBBNN Latent Binary Bayesian Neural Networks Using 'torch' LBDiscover Literature-Based Discovery Tools for Biomedical Research LBI Likelihood Based Inference LBPG The Length-Biased Power Garima Distribution LBSPR Length-Based Spawning Potential Ratio LCAextend Latent Class Analysis (LCA) with Familial Dependence in Extended Pedigrees LCCR Latent Class Capture-Recapture Models LCCkNN Adaptive k-Nearest Neighbor Classifier Based on Local Curvature Estimation LCFdata Data sets for package ``LMERConvenienceFunctions'' LCMCR Bayesian Non-Parametric Latent-Class Capture-Recapture LCMSQA Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment LCPA A General Framework for Latent Classify and Profile Analysis LDAShiny Interactive Topic Modeling and Bibliometric Analysis via Shiny LDATS Latent Dirichlet Allocation Coupled with Time Series Analyses LDATree Oblique Classification Trees with Uncorrelated Linear Discriminant Analysis Splits LDAandLDAS Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS) LDAcoop Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation LDAvis Interactive Visualization of Topic Models LDM Testing Hypotheses About the Microbiome using the Linear Decomposition Model LDNN Longitudinal Data Neural Network LDRTools Tools for Linear Dimension Reduction LDcorSV Linkage Disequilibrium Corrected by the Structure and the Relatedness LDlinkR Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest LEA LEA: an R package for Landscape and Ecological Association Studies LEAVcore Constitution of Core Collections using Length of Encoded Attribute Values LEGIT Latent Environmental & Genetic InTeraction (LEGIT) Model LEdecomp Decompose Life Expectancy by Age (and Cause) LFApp Shiny Apps for Lateral Flow Assays LFDR.MLE Estimation of the Local False Discovery Rates by Type II Maximum Likelihood Estimation LFDR.MME Estimating Local False Discovery Rates Using the Method of Moments LFDREmpiricalBayes Estimating Local False Discovery Rates Using Empirical Bayes Methods LGCU Implementation of Learning Gamma CUSUM (Cumulative Sum) Control Charts LGDtoolkit Collection of Tools for LGD Rating Model Development LGEWIS Tests for Genetic Association/Gene-Environment Interaction in Longitudinal Studies LGRF Set-Based Tests for Genetic Association in Longitudinal Studies LHD Latin Hypercube Designs (LHDs) LIC The LIC Criterion for Optimal Subset Selection LINselect Selection of Linear Estimators LISTO Performing Comprehensive Overlap Assessments LJexm Extract, Convert, and Merge 'pdf' Files from 'zip' Files LJmp3converter Convert Video Files to 'mp3' Format, Merge or Trim Audio Files using 'FFmpeg' LKT Logistic Knowledge Tracing LLM Logit Leaf Model Classifier for Binary Classification LLMAgentR Language Model Agents in R for AI Workflows and Research LLMR Interface for Large Language Model APIs in R LLMTranslate 'shiny' App for TRAPD/ISPOR Survey Translation with LLMs LLMing Large Language Model (LLM) Tools for Psychological Text Analysis LLSR Data Analysis of Liquid-Liquid Systems using R LMD A Self-Adaptive Approach for Demodulating Multi-Component Signal LMERConvenienceFunctions Model Selection and Post-Hoc Analysis for (G)LMER Models LMMsolver Linear Mixed Models with Sparse Matrix Methods and Smoothing LMMstar Repeated Measurement Models for Discrete Times LMN Inference for Linear Models with Nuisance Parameters LMPdata Easy Import of the EU Labour Market Policy Data LMest Generalized Latent Markov Models LMfilteR Filter Methods for Parameter Estimation in Linear and Non Linear Regression Models LMoFit Advanced L-Moment Fitting of Distributions LNIRT LogNormal Response Time Item Response Theory Models LNPar Estimation and Testing for a Lognormal-Pareto Mixture LOCOM2 A Logistic Regression Model for Testing Microbial Differential Abundance LOCUS Low-Rank Decomposition of Brain Connectivity Matrices with Uniform Sparsity LOGAN Log File Analysis in International Large-Scale Assessments LOMAR Localization Microscopy Data Analysis LOPART Labeled Optimal Partitioning LOST Missing Morphometric Data Simulation and Estimation LPBkg Detecting New Signals under Background Mismodelling LPCM Local Principal Curve Methods LPDynR Land Productivity Dynamics Indicator LPM Linear Parametric Models Applied to Hydrological Series LPStimeSeries Learned Pattern Similarity and Representation for Time Series LPWC Lag Penalized Weighted Correlation for Time Series Clustering LPmerge Merging Linkage Maps by Linear Programming LREP Estimate and Test Exponential vs. Pareto Distributions LRMF3 Low Rank Matrix Factorization S3 Objects LRMiss Linear Regression with Missing Data LRQVB Low Rank Correction Quantile Variational Bayesian Algorithm for Multi-Source Heterogeneous Models LRTesteR Likelihood Ratio Tests and Confidence Intervals LS2W Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme LS2Wstat A Multiscale Test of Spatial Stationarity for LS2W Processes LSAMBA Lasso-SAMBA Algorithm LSAfun Applied Latent Semantic Analysis (LSA) Functions LSAmitR Daten, Beispiele und Funktionen zu 'Large-Scale Assessment mit R' LSD Lots of Superior Depictions LSDinterface Interface Tools for 'LSD' Simulation Results Files LSDirf Impulse-Response Function Analysis for Agent-Based Models LSDsensitivity Sensitivity Analysis Tools for 'LSD' Simulations LSE Constrained Least Squares and Generalized QR Factorization LSEbootLS Bootstrap Methods for Regression Models with Locally Stationary Errors LSMjml Fitting Latent Space Item Response Models using Joint Maximum Likelihood Estimation LSMonteCarlo American options pricing with Least Squares Monte Carlo method LSPFP Lysate and Secretome Peptide Feature Plotter LSRS Land Surface Remote Sensing LST Land Surface Temperature Retrieval for Landsat 8 LSTMfactors Determining the Number of Factors in Exploratory Factor Analysis by LSTM LSTS Locally Stationary Time Series LSTbook Data and Software for "Lessons in Statistical Thinking" LSVAR Estimation of Low Rank Plus Sparse Structured Vector Auto-Regressive (VAR) Model LSWPlib Simulation and Spectral Estimation of Locally Stationary Wavelet Packet Processes LSX Semi-Supervised Algorithm for Document Scaling LTASR Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R LTCDM Latent Transition Cognitive Diagnosis Model with Covariates LTFGRS Implementation of Several Phenotype-Based Family Genetic Risk Scores LTFHPlus Implementation of LT-FH++ LTPDvar LTPD and AOQL Plans for Acceptance Sampling Inspection by Variables LTRCtrees Survival Trees to Fit Left-Truncated and Right-Censored and Interval-Censored Survival Data LUCIDus LUCID with Multiple Omics Data LVGP Latent Variable Gaussian Process Modeling with Qualitative and Quantitative Input Variables LWFBrook90R Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90 LZeroSpikeInference Exact Spike Train Inference via L0 Optimization LaF Fast Access to Large ASCII Files LabApplStat Miscellaneous Scripts from the Data Science Laboratory (UCPH) LabRS Laboratorio di Ricerca Sociale con R LabourMarketAreas Identification, Tuning, Visualisation and Analysis of Labour Market Areas LactCurveModels Lactation Curve Model Fitting for Dairy Animals LadderFuelsR Automated Tool for Vertical Fuel Continuity Analysis using Airborne Laser Scanning Data LagSequential Lag-Sequential Categorical Data Analysis Lahman Sean 'Lahman' Baseball Database LakeMetabolizer Tools for the Analysis of Ecosystem Metabolism LambertW Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data LandComp Analysing Landscape Composition and Structure at Multiple Scales Landmarking Analysis using Landmark Models Langevin Langevin Analysis in One and Two Dimensions LangevinFlow Langevin Diffusion Samplers with a C++ Backend LaplacesDemon Complete Environment for Bayesian Inference Largevars Testing Large VARs for the Presence of Cointegration LassoBacktracking Modelling Interactions in High-Dimensional Data with Backtracking LassoHiDFastGibbs Fast High-Dimensional Gibbs Samplers for Bayesian Lasso Regression LassoNet 3CoSE Algorithm LassoSIR Sparsed Sliced Inverse Regression via Lasso LatSquare Analysis of Latin Square and Semi-Latin Square Designs Latamverse Latin American Data via 'RESTful' APIs and Curated Datasets LatentBMA Bayesian Model Averaging for Univariate Link Latent Gaussian Models Laterality Functions to Calculate Common Laterality Statistics in Primatology LatticeDesign Lattice-Based Space-Filling Designs LatticeKrig Multi-Resolution Kriging Based on Markov Random Fields LeArEst Border and Area Estimation of Data Measured with Additive Error LeMaRns Length-Based Multispecies Analysis by Numerical Simulation LePage LePage Type Tests LeadSense Medtronic Brain Sense Local Field Potencial Analysis LeafArea Rapid Digital Image Analysis of Leaf Area LearnBayes Functions for Learning Bayesian Inference LearnClust Learning Hierarchical Clustering Algorithms LearnGeom Learning Plane Geometry LearnNonparam 'R6'-Based Flexible Framework for Permutation Tests LearnPCA Functions, Data Sets and Vignettes to Aid in Learning Principal Components Analysis (PCA) LearnSL Learn Supervised Classification Methods Through Examples and Code LearnVizLMM Learning and Communicating Linear Mixed Models Without Data LearningRlab Statistical Learning Functions LearningStats Elemental Descriptive and Inferential Statistics LeaveOutKSS Leave-Out Variance Component Estimation for Two-Way Fixed Effects Models LexFindR Find Related Items and Lexical Dimensions in a Lexicon LexisNexisTools Working with Files from 'LexisNexis' LexisPlotR Plot Lexis Diagrams for Demographic Purposes LiblineaR Linear Predictive Models Based on the LIBLINEAR C/C++ Library Libra Linearized Bregman Algorithms for Generalized Linear Models LifeHist Life History Models of Individuals LifeInsuranceContracts Framework for Traditional Life Insurance Contracts LifeInsureR Modelling Traditional Life Insurance Contracts LifeTableBuilder Interactive 'shiny' Application for Constructing Life Tables LifeTableFertility 'shiny' Application for Life Table and Fertility Analysis LifemapR Data Visualisation on 'Lifemap' Tree Lifertable Life and Fertility Tables Specially for Insects LiftTest A Bootstrap Proportion Test for Brand Lift Testing LightFitR Design Complex Light Regimes LightLogR Process Data from Wearable Light Loggers and Optical Radiation Dosimeters LikertEZ Easy Analysis and Visualization of Likert Scale Data LikertMakeR Synthesise and Correlate Likert Scale and Rating-Scale Data Based on Summary Statistics LilRhino For Implementation of Feed Reduction, Learning Examples, NLP and Code Management LimnoPalettes A Limnology Themed Palette Generator LinCal Static Univariate Frequentist and Bayesian Linear Calibration LinRegInteractive Interactive Interpretation of Linear Regression Models Linda Line Transect-Based Nearest Neighbor Distance Analysis LindenmayeR Functions to Explore L-Systems (Lindenmayer Systems) LindleyPowerSeries Lindley Power Series Distribution LinearRegressionMDE Minimum Distance Estimation in Linear Regression Model Linkage Clustering Communication Networks Using the Stochastic Topic Block Model Through Linkage.fr LinkedGASP Linked Emulator of a Coupled System of Simulators LinkedMatrix Column-Linked and Row-Linked Matrices Linnorm Linear model and normality based normalization and transformation method (Linnorm) LipidMS Lipid Annotation for LC-MS/MS DDA or DIA Data LipidomicsR Elegant Tools for Processing and Visualization of Lipidomics Data LipinskiFilters Computes and Visualize Lipinski's Parameters LitFetchR Automatically Fetching References Metadata from Literature Databases Lmoments L-Moments and Quantile Mixtures LncFinder LncRNA Identification and Analysis Using Heterologous Features LoBrA Generalized Spline Mixed Effect Models for Longitudinal Breath Data LoTTA Bayesian Inference in Regression Discontinuity Designs LocKer Locally Sparse Estimator of Generalized Varying Coefficient Model for Asynchronous Longitudinal Data LocaTT Geographically-Conscious Taxonomic Assignment for Metabarcoding LocalControl Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence LocalCop Local Likelihood Inference for Conditional Copula Models Lock5Data Datasets for "Statistics: UnLocking the Power of Data" LogConcDEAD Log-Concave Density Estimation in Arbitrary Dimensions LogRegEquiv Logistic Regression Equivalence LogicForest Logic Forest LogicReg Logic Regression LogisticCopula A Copula Based Extension of Logistic Regression LogisticCurveFitting Logistic Curve Fitting by Rhodes Method LogisticEnsembles Automatically Runs 18 Logistic Models-14 Individual Logistic Models and 4 Ensembles of Models LogisticRCI Linear and Logistic Regression-Based Reliable Change Index LongCART Recursive Partitioning for Longitudinal Data and Right Censored Data Using Baseline Covariates LongDat A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data LongDecompHE Longitudinal Decomposition of Health Expectancy by Age and Cause LoopAnalyst A Collection of Tools to Conduct Levins' Loop Analysis LoopDetectR Comprehensive Feedback Loop Detection in ODE Models LoopRig Integration and Analysis of Chromatin Loop Data LorMe Lightweight One-Line Resolving Microbial Ecology Program LorenzRegression Lorenz and Penalized Lorenz Regressions LowRankQP Low Rank Quadratic Programming LqG Robust Group Variable Screening Based on Maximum Lq-Likelihood Estimation Luminescence Comprehensive Luminescence Dating Data Analysis M2SMF Multi-Modal Similarity Matrix Factorization for Integrative Multi-Omics Data Analysis M2SMJF Multi-Modal Similarity Matrix Joint Factorization M3 Reading M3 Files M3C Monte Carlo Reference-based Consensus Clustering M3JF Multi-Modal Matrix Joint Factorization for Integrative Multi-Omics Data Analysis MACER Molecular Acquisition, Cleaning, and Evaluation in R 'MACER' MADMMplasso Multi Variate Multi Response ADMM with Interaction Effects MADtests Hypothesis Tests and Confidence Intervals for Median Absolute Deviations MAFLD Diagnosis of Metabolic Dysfunction Associated Fatty Liver Disease MAGEE Mixed Model Association Test for GEne-Environment Interaction MAGMA.R MAny-Group MAtching MAGNAMWAR A Pipeline for Meta-Genome Wide Association MAICtools Performing Matched-Adjusted Indirect Comparisons (MAIC) MAIHDA Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy MAINT.Data Model and Analyse Interval Data MAIVE Meta Analysis Instrumental Variable Estimator MAKL Multiple Approximate Kernel Learning (MAKL) MALDIquant Quantitative Analysis of Mass Spectrometry Data MALDIquantForeign Import/Export Routines for 'MALDIquant' MALDIrppa MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis MAMS Designing Multi-Arm Multi-Stage Studies MANOVA.RM Resampling-Based Analysis of Multivariate Data and Repeated Measures Designs MAP Multimodal Automated Phenotyping MAPA Multiple Aggregation Prediction Algorithm MAPCtools Multivariate Age-Period-Cohort (MAPC) Modeling for Health Data MARMoT Matching on Poset-Based Average Rank for Multiple Treatments (MARMoT) MARSANNhybrid MARS Based ANN Hybrid Model MARSGWR A Hybrid Spatial Model for Capturing Spatially Varying Relationships Between Variables in the Data MARSS Multivariate Autoregressive State-Space Modeling MARSSVRhybrid MARS SVR Hybrid MASSExtra Some 'MASS' Enhancements MASSTIMATE Body Mass Estimation Equations for Vertebrates MAST Model-based Analysis of Single Cell Transcriptomics MAT Multidimensional Adaptive Testing MATA Model-Averaged Tail Area (MATA) Confidence Interval and Distribution MATES Multi-View Aggregated Two Sample Tests MAVE Methods for Dimension Reduction MAZE Mediation Analysis for Zero-Inflated Mediators MAd Meta-Analysis with Mean Differences MAnorm2 Tools for Normalizing and Comparing ChIP-seq Samples MB The Use of Marginal Distributions in Conditional Forecasting MBA Multilevel B-Spline Approximation MBAnalysis Multiblock Exploratory and Predictive Data Analysis MBBEFDLite Statistical Functions for the Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of Distributions MBC Multivariate Bias Correction of Climate Model Outputs MBCbook Companion Package for the Book "Model-Based Clustering and Classification for Data Science" MBESS The MBESS R Package MBGapp Interactive 'shiny' Application for Model-Based Geostatistics MBHdesign Spatial Designs for Ecological and Environmental Surveys MBMethPred Medulloblastoma Subgroups Prediction MBNMAdose Dose-Response MBNMA Models MBNMAtime Run Time-Course Model-Based Network Meta-Analysis (MBNMA) Models MBRM Mixed Regression Models with Generalized Log-Gamma Random Effects MBSGS Multivariate Bayesian Sparse Group Selection with Spike and Slab MBSP Multivariate Bayesian Model with Shrinkage Priors MBmca Nucleic Acid Melting Curve Analysis MCARtest Optimal Nonparametric Testing of Missing Completely at Random MCAvariants Multiple Correspondence Analysis Variants MCBackscattering Monte Carlo Simulation for Surface Backscattering MCCM Mixed Correlation Coefficient Matrix MCI Multiplicative Competitive Interaction (MCI) Model MCID Estimating the Minimal Clinically Important Difference MCL Markov Cluster Algorithm MCM Estimating and Testing Intergenerational Social Mobility Effect MCMC.qpcr Bayesian Analysis of qRT-PCR Data MCMC4Extremes Posterior Distribution of Extreme Value Models in R MCMCglmm MCMC Generalised Linear Mixed Models MCMChybridGP Hybrid Markov Chain Monte Carlo Using Gaussian Processes MCMCpack Markov Chain Monte Carlo (MCMC) Package MCMCprecision Precision of Discrete Parameters in Transdimensional MCMC MCMCvis Tools to Visualize, Manipulate, and Summarize MCMC Output MCOE Creates New Folders and Loads Standard Practices for Monterey County Office of Education MCPAN Multiple Comparisons Using Normal Approximation MCPMod Design and Analysis of Dose-Finding Studies MCPModBC Improved Inference in Multiple Comparison Procedure – Modelling MCPModGeneral A Supplement to the 'DoseFinding' Package for the General Case MCPModPack Simulation-Based Design and Analysis of Dose-Finding Trials MCPtests Multiples Comparisons Procedures MCS Model Confidence Set Procedure MCSim Determine the Optimal Number of Clusters MCSimMod Working with 'MCSim' Models MCTrend Monte Carlo Trend Analysis MChtest Monte Carlo Hypothesis Tests with Sequential Stopping MCseqReplic Monte Carlo Simulations of Time Changes in Sequences MD2sample Various Methods for the Two Sample Problem in D>1 Dimensions MDCcure Martingale Dependence Tools and Testing for Mixture Cure Models MDDC Modified Detecting Deviating Cells Algorithm in Pharmacovigilance MDFS MultiDimensional Feature Selection MDMA Mathijs Deen's Miscellaneous Auxiliaries MDMR Multivariate Distance Matrix Regression MDOLS Inference of Quadratic Functional for Moderate-Dimensional OLS MDP2 Markov Decision Processes (MDPs) MDPIexploreR Web Scraping and Bibliometric Analysis of MDPI Journals MDPtoolbox Markov Decision Processes Toolbox MDSMap High Density Genetic Linkage Mapping using Multidimensional Scaling MDSPCAShiny Interactive Document for Working with Multidimensional Scaling and Principal Component Analysis MDSS Modeling Human Dentin Serial Sectioning MDgof Various Methods for the Goodness-of-Fit Problem in D>1 Dimensions MDimNormn Multi-Dimensional MA Normalization for Plate Effect MEAanalysis Analyse and Visualise Multi Electrode Array Burst Data MECfda Scalar-on-Function Regression with Measurement Error Correction MED Mediation by Tilted Balancing MEDesigns Mating Environmental Designs MEDseq Mixtures of Exponential-Distance Models with Covariates MEFM Perform MEFM Estimation on Matrix Time Series MEGB Gradient Boosting for Longitudinal Data MEMSS Data Sets from Mixed-Effects Models in S MERO Performing Monte Carlo Expectation Maximization Random Forest Imputation for Biological Data MESS Miscellaneous Esoteric Statistical Scripts MEclustnet Fit the Mixture of Experts Latent Position Cluster Model to Network Data MEsreg Generalized Maximum Entropy Estimation for Smooth Transition and Kink Regression Models MF.beta4 Measuring Ecosystem Multi-Functionality and Its Decomposition MFAg Multiple Factor Analysis (MFA) MFDFA MultiFractal Detrended Fluctuation Analysis MFF Meta Fuzzy Functions MFO Maximal Fat Oxidation and Kinetics Calculation MFPCA Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains MFRCD Optimal Row-Column Designs for Asymmetrical Factorial Experiments MFSD Multivariate Functional Spatial Data MFSIS Model-Free Sure Independent Screening Procedures MGBT Multiple Grubbs-Beck Low-Outlier Test MGDrivE Mosquito Gene Drive Explorer MGDrivE2 Mosquito Gene Drive Explorer 2 MGL Module Graphical Lasso MGLM Multivariate Response Generalized Linear Models MGMM Missingness-Aware Gaussian Mixture Models MGPSDK Interact with the Maxar 'MGP' Application Programming Interfaces MGSDA Multi-Group Sparse Discriminant Analysis MHCtools Analysis of MHC Data in Non-Model Species MHD Metric Halfspace Depth MHDA Massive Hierarchically Data Analysis MHQoL Mental Health Quality of Life Toolkit MHTdiscrete Multiple Hypotheses Testing for Discrete Data MHTmult Multiple Hypotheses Testing for Multiple Families/Groups Structure MHTrajectoryR Bayesian Model Selection in Logistic Regression for the Detection of Adverse Drug Reactions MIAmaxent A Modular, Integrated Approach to Maximum Entropy Distribution Modeling MIC Analysis of Antimicrobial Minimum Inhibitory Concentration Data MICsplines The Computing of Monotonic Spline Bases and Constrained Least-Squares Estimates MIDASim Simulating Realistic Microbiome Data using 'MIDASim' MIDN Nearly Exact Sample Size Calculation for Exact Powerful Nonrandomized Tests for Differences Between Binomial Proportions MIGEE Impute Missing Values and Fitting Linear Mixed Effect Model MIIPW IPW and Mean Score Methods for Time-Course Missing Data MIIVefa Exploratory Factor Analysis Using Model Implied Instrumental Variables MIIVsem Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models MIMER Data Wrangling for Antimicrobial Resistance Studies MIMSunit Algorithm to Compute Monitor Independent Movement Summary Unit (MIMS-Unit) MINTplates Encode "License-Plates" from Sequences and Decode Them Back MIRDD Diagnostic Tool by Multiple Imputation for Regression Discontinuity Designs MIXFIM Evaluation of the FIM in NLMEMs using MCMC MJMbamlss Multivariate Joint Models with 'bamlss' MKLE Maximum Kernel Likelihood Estimation MKMeans A Modern K-Means (MKMeans) Clustering Algorithm MKclass Statistical Classification MKdescr Descriptive Statistics MKendall Matrix Kendall's Tau and Matrix Elliptical Factor Model MKinfer Inferential Statistics MKmisc Miscellaneous Functions from M. Kohl MKomics Omics Data Analysis MKpower Power Analysis and Sample Size Calculation ML.MSBD Maximum Likelihood Inference on Multi-State Trees ML2Pvae Variational Autoencoder Models for IRT Parameter Estimation MLBC Bias Correction Methods for Models Using Synthetic Data MLCIRTwithin Latent Class Item Response Theory (LC-IRT) Models under Within-Item Multidimensionality MLCM Maximum Likelihood Conjoint Measurement MLCausal Causal Inference Methods for Multilevel and Clustered Data MLDS Maximum Likelihood Difference Scaling MLDataR Collection of Machine Learning Datasets for Supervised Machine Learning MLE Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions MLEce Asymptotic Efficient Closed-Form Estimators for Multivariate Distributions MLEcens Computation of the MLE for Bivariate Interval Censored Data MLFDR High Dimensional Mediation Analysis using Local False Discovery Rates MLFS Machine Learning Forest Simulator MLGL Multi-Layer Group-Lasso MLGdata Datasets for Use with Salvan, Sartori and Pace (2020) MLID Multilevel Index of Dissimilarity MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers MLML2R Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions MLMOI Estimating Frequencies, Prevalence and Multiplicity of Infection MLMusingR Practical Multilevel Modeling MLPUGS Multi-Label Prediction Using Gibbs Sampling (and Classifier Chains) MLSP Machine Learning Models for Soil Properties MLZ Mean Length-Based Estimators of Mortality using TMB MLeval Machine Learning Model Evaluation MLmetrics Machine Learning Evaluation Metrics MLmorph Integrating Morphological Modeling and Machine Learning for Decision Support MLpreemption Maximum Likelihood Estimation of the Niche Preemption Model MLwrap Machine Learning Modelling for Everyone MM The Multiplicative Multinomial Distribution MM4LMM Inference of Linear Mixed Models Through MM Algorithm MMAC Data for Mathematical Modeling and Applied Calculus MMAD Minorization-Maximization via Assembly-Decomposition Technology MMD Minimal Multilocus Distance (MMD) for Source Attribution and Loci Selection MMDCopula Robust Estimation of Copulas by Maximum Mean Discrepancy MMDai Multivariate Multinomial Distribution Approximation and Imputation for Incomplete Categorical Data MMDvariance Detecting Differentially Variable Genes Using the Mixture of Marginal Distributions MMGFM Multi-Study Multi-Modality Generalized Factor Model MMINP Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor MMLR Fitting Markov-Modulated Linear Regression Models MMOC Multi-Omic Spectral Clustering using the Flag Manifold MMRcaseselection Case Classification and Selection Based on Regression Results MMWRweek Convert Dates to MMWR Day, Week, and Year MMeM Multivariate Mixed Effects Model MN Matrix Normal Distribution MNARclust Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models MNB Diagnostic Tools for a Multivariate Negative Binomial Regression Model MNLR Interactive Shiny Presentation for Working with Multinomial Logistic Regression MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks MNP Fitting the Multinomial Probit Model MNS Mixed Neighbourhood Selection MNormTest Multivariate Normal Hypothesis Testing MOCCA Multi-Objective Optimization for Collecting Cluster Alternatives MODISTools Interface to the 'MODIS Land Products Subsets' Web Services MOEADr Component-Wise MOEA/D Implementation MOFA2 Multi-Omics Factor Analysis v2 MOFAT Maximum One-Factor-at-a-Time Designs MOLHD Multiple Objective Latin Hypercube Design MOM Estimation and Testing of Hypothesis MOODE Multi-Objective Optimal Design of Experiments MOQA Basic Quality Data Assurance for Epidemiological Research MOSAlloc Constraint Multiobjective Sample Allocation MOST Multiphase Optimization Strategy MOTE Effect Size and Confidence Interval Calculator MOsemiind Marshall-Olkin Shock Models with Semi-Independent Time MOutliers Multivariate Outlier Detection Methods MPBoost Treatment Allocation in Clinical Trials by the Maximal Procedure MPCI Multivariate Process Capability Indices (MPCI) MPCR Multi Precision Computing MPDiR Data Sets and Scripts for Modeling Psychophysical Data in R MPGE A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes MPI Computation of Multidimensional Poverty Index (MPI) MPN Most Probable Number and Other Microbial Enumeration Techniques MPS Estimating Through the Maximum Product Spacing Approach MPSEM Modelling Phylogenetic Signals using Eigenvector Maps MPTinR Analyze Multinomial Processing Tree Models MPV Data Sets from Montgomery, Peck and Vining MPsychoR Modern Psychometrics with R MQMF Modelling and Quantitative Methods in Fisheries MR.RGM Fitting Multivariate Bidirectional Mendelian Randomization Networks Using Bayesian Directed Cyclic Graphical Models MRAM Multivariate Regression Association Measure MRCE Multivariate Regression with Covariance Estimation MRCV Methods for Analyzing Multiple Response Categorical Variables (MRCVs) MRFA Fitting and Predicting Large-Scale Nonlinear Regression Problems using Multi-Resolution Functional ANOVA (MRFA) Approach MRFcov Markov Random Fields with Additional Covariates MRG Create Non-Confidential Multi-Resolution Grids MRHawkes Multivariate Renewal Hawkes Process MRIreduce ROI-Based Transformation of Neuroimages into High-Dimensional Data Frames MRMCaov Multi-Reader Multi-Case Analysis of Variance MRMCbinary Multi-Reader Multi-Case Analysis of Binary Diagnostic Tests MRMCsamplesize Sample Size Estimations for Planning Multi-Reader Multi-Case (MRMC) Studies Without Pilot Data MRPC PC Algorithm with the Principle of Mendelian Randomization MRQoL Minimal Clinically Important Difference and Response Shift Effect for Health-Related Quality of Life MRReg MDL Multiresolution Linear Regression Framework MRStdCRT Model-Robust Standardization in Cluster-Randomized Trials MRStdLCRT Model-Robust Standardization for Longitudinal Cluster-Randomized Trials MRTAnalysis Assessing Proximal, Distal, and Mediated Causal Excursion Effects for Micro-Randomized Trials MRTSampleSize A Sample Size Calculator for Micro-Randomized Trials MRTSampleSizeBinary Sample Size Calculator for MRT with Binary Outcomes MRZero Diet Mendelian Randomization MRgrowth Mark-Recapture Growth Models MRmediation A Causal Mediation Method with Methylated Region (MR) as the Mediator MSBStatsData Data Sets for Courses at the Münster School of Business MSCCT Multiple Survival Crossing Curves Tests MSCMT Multivariate Synthetic Control Method Using Time Series MSCquartets Analyzing Gene Tree Quartets under the Multi-Species Coalescent MSCsimtester Tests of Multispecies Coalescent Gene Tree Simulator Output MSEtool Management Strategy Evaluation Toolkit MSG Data and Functions for the Book Modern Statistical Graphics MSGARCH Markov-Switching GARCH Models MSGARCHelm Hybridization of MS-GARCH and ELM Model MSIMST Bayesian Monotonic Single-Index Regression Model with the Skew-T Likelihood MSMGOptimizer Mine Sustainability Modeling Group (MSMG) 'SimaPro' CSV Optimizer MSML Model Selection Based on Machine Learning (ML) MSMU Descriptive Statistics Functions for Numeric Data MSMwRA Multivariate Statistical Methods with R Applications MSN Multivariate Survival Data with Network Structures MSPRT A Modified Sequential Probability Ratio Test (MSPRT) MSSQL Tools to Work with Microsoft SQL Server Databases via 'RODBC' MST Multivariate Survival Trees MSTest Hypothesis Testing for Markov Switching Models MSUthemes Michigan State University (MSU) Palettes and Themes MSbox Mass Spectrometry Tools MSclassifR Automated Classification of Mass Spectra MSclust Multiple-Scaled Clustering MScombine Combine Data from Positive and Negative Ionization Mode Finding Common Entities MSigSeg Multiple SIGnal SEGmentation MSinference Multiscale Inference for Nonparametric Time Trend(s) MSnbase Base Functions and Classes for Mass Spectrometry and Proteomics MSoutcomes CORe Multiple Sclerosis Outcomes Toolkit MSwM Fitting Markov Switching Models MTA Multiscalar Territorial Analysis MTAR Multi-Trait Analysis of Rare-Variant Association Study MTE Maximum Tangent Likelihood Estimation for Robust Linear Regression and Variable Selection MTLR Survival Prediction with Multi-Task Logistic Regression MTPS Multi-Task Prediction using Stacking Algorithms MTS All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models MTSYS Methods in Mahalanobis-Taguchi (MT) System MTest A Procedure for Multicollinearity Testing using Bootstrap MUACz Generate MUAC and BMI z-Scores and Percentiles for Children and Adolescents MUGS Multisource Graph Synthesis with EHR Data MUS Monetary Unit Sampling and Estimation Methods, Widely Used in Auditing MUVR2 Multivariate Methods with Unbiased Variable Selection MVA An Introduction to Applied Multivariate Analysis with R MVET Multivariate Estimates and Tests MVN Multivariate Normality Tests MVNBayesian Bayesian Analysis Framework for MVN (Mixture) Distribution MVNGmod Matrix-Variate Non-Gaussian Linear Regression Models MVOPR Multi-View Orthogonal Projection Regression for Multi-Modality Integration MVPBT Publication Bias Tests for Meta-Analysis of Diagnostic Accuracy Test MVQuickGraphs Quick Multivariate Graphs MVR Mean-Variance Regularization MVSKmod Matrix-Variate Skew Linear Regression Models MVT Estimation and Testing for the Multivariate t-Distribution MVTests Multivariate Hypothesis Tests MVar Multivariate Analysis MVar.pt Analise multivariada (brazilian portuguese) MVisAGe Compute and Visualize Bivariate Associations MWright Mainardi-Wright Family of Distributions MaOEA Many Objective Evolutionary Algorithm MacBehaviour Behavioural Studies of Large Language Models MachineShop Machine Learning Models and Tools MacroFilters Robust Trend-Cycle Decomposition for Macroeconomic Time Series MacroZooBenthosWaterA Fresh Water Quality Analysis Based on Macrozoobenthos MaddisonData Maddison Project Data Maeswrap Wrapper Functions for MAESTRA/MAESPA MagmaClustR Clustering and Prediction using Multi-Task Gaussian Processes with Common Mean MainExistingDatasets Main Existing Human Datasets MajKMeans k-Means Algorithm with a Majorization-Minimization Method MajMinKmeans k-Means Algorithm with a Majorization-Minimization Method MakefileR Create 'Makefiles' Using R ManagedCloudProvider Providing the Kubernetes-Like Functions for the Non-Kubernetes Cloud Service MandalaR Building Mandalas from Parametric Equations of Classical Curves Mangrove Risk Prediction on Trees ManifoldOptim An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization ManlyMix Manly Mixture Modeling and Model-Based Clustering MannWhitneyCopula Computing Mann-Whitney Effect Based on Copulas MantaID A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs ManyIVsNets Environmental Phillips Curve Analysis with Multiple Instrumental Variables and Networks ManyTests Multiple Testing Procedures of Cox (2011) and Wong and Cox (2007) Map2NCBI Mapping Markers to the Nearest Genomic Feature MapGAM Mapping Smoothed Effect Estimates from Individual-Level Data Mapinguari Process-Based Biogeographical Analysis MapperAlgo Topological Data Analysis: Mapper Algorithm MappingCalc Mapping Calculator for EQ-5D Utility Scores MarZIC Marginal Mediation Effects with Zero-Inflated Compositional Mediator MareyMap Estimation of Meiotic Recombination Rates Using Marey Maps MarginalMaxTest Max-Type Test for Marginal Correlation with Bootstrap MarginalMediation Marginal Mediation MariNET Build Network Based on Linear Mixed Models from EHRs MarineChain Blockchain-Enabled Maritime Transportation System Simulator MarketMatching Market Matching and Causal Impact Inference Markovchart Markov Chain-Based Cost-Optimal Control Charts MarkowitzR Statistical Significance of the Markowitz Portfolio MassSpecWavelet Peak Detection for Mass Spectrometry data using wavelet-based algorithms MassWateR Quality Control and Analysis of Massachusetts Water Quality Data Massign Simple Matrix Construction MasterBayes Maximum Likelihood and Markov Chain Monte Carlo (MCMC) Methods for Pedigree Reconstruction and Analysis MatchGATE Estimate Group Average Treatment Effects with Matching MatchIt Nonparametric Preprocessing for Parametric Causal Inference MatchLinReg Combining Matching and Linear Regression for Causal Inference MatchThem Matching and Weighting Multiply Imputed Datasets Matching Multivariate and Propensity Score Matching with Balance Optimization MatchingPursuit Processing Time Series Data Using the Matching Pursuit Algorithm MatrixCorrelation Matrix Correlation Coefficients MatrixEQTL Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations MatrixExtra Extra Methods for Sparse Matrices MatrixGenerics S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects MatrixHMM Parsimonious Families of Hidden Markov Models for Matrix-Variate Longitudinal Data MatrixMixtures Model-Based Clustering via Matrix-Variate Mixture Models MatrixModels Modelling with Sparse and Dense Matrices MaxIntTools Testing Maximal Interaction in Two-Mode Clustering via a Permutation Based Procedure MaxMC Maximized Monte Carlo MaxPro Maximum Projection Designs MaxSkew Orthogonal Data Projections with Maximal Skewness MaxWiK Machine Learning Method Based on Isolation Kernel Mean Embedding MaxentVariableSelection Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling MaximinInfer Inference for Maximin Effects in High-Dimensional Settings MazamaCoreUtils Utility Functions for Production R Code MazamaLocationUtils Manage Spatial Metadata for Known Locations MazamaRollUtils Efficient Rolling Functions MazamaSpatialPlots Thematic Plots for Mazama Spatial Datasets MazamaSpatialUtils Spatial Data Download and Utility Functions MazamaTimeSeries Core Functionality for Environmental Time Series McMiso Multicore Multivariable Isotonic Regression Mcomp Data from the M-Competitions MeTo Meteorological Tools Meanimiles Estimation of Meanimiles MeasurementDiagnostics Diagnostics for Lists of Codes Based on Measurements MedDataSets Comprehensive Medical, Disease, Treatment, and Drug Datasets MedDietCalc Multi Calculator to Compute Scores of Adherence to Mediterranean Diet MedLEA Morphological and Structural Features of Medicinal Leaves MedZIsc Statistical Framework for Co-Mediators of Zero-Inflated Single-Cell Data MediaK Calculate MeDiA_K Distance Mediana Clinical Trial Simulations MedianaDesigner Power and Sample Size Calculations for Clinical Trials MedxR Access Drug Regulatory Data via FDA and Health Canada APIs MendelianRandomization Mendelian Randomization Package Mercator Clustering and Visualizing Distance Matrices Mestim Computes the Variance-Covariance Matrix of Multidimensional Parameters Using M-Estimation MetAlyzer Read and Analyze 'MetIDQ™' Software Output Files MetBrewer Color Palettes Inspired by Works at the Metropolitan Museum of Art MetSizeR A Shiny App for Sample Size Estimation in Metabolomic Experiments MetaAnalyser An Interactive Visualisation of Meta-Analysis as a Physical Weighing Machine MetaCycle Evaluate Periodicity in Large Scale Data MetaDose Dose-Response Meta-Regression for Meta-Analysis MetaEntropy Functional Shannon Entropy for Virome Mutational Analysis MetaHD A Multivariate Meta-Analysis Model for High-Dimensional Data MetaHunt Privacy-Preserving Meta-Analysis via Low-Rank Basis Hunting MetaIntegration Ensemble Meta-Prediction Framework MetaLandSim Landscape and Range Expansion Simulation MetaNLP Natural Language Processing for Meta Analysis MetaNet Network Analysis for Omics Data MetaRVM Meta-Population Compartmental Model for Respiratory Virus Diseases MetaSKAT Meta Analysis for SNP-Set (Sequence) Kernel Association Test MetaSubtract Subtracting Summary Statistics of One or more Cohorts from Meta-GWAS Results MetaUtility Utility Functions for Conducting and Interpreting Meta-Analyses MetaboCoreUtils Core Utils for Metabolomics Data MetaboQC Normalize Metabolomic Data using QC Signal MetabolAnalyze Probabilistic Latent Variable Models for Metabolomic Data MetabolSSMF Simplex-Structured Matrix Factorisation for Metabolomics Analysis MetabolicSurv A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature MetabolicSyndrome Diagnosis of Metabolic Syndrome MetabolomicsBasics Basic Functions to Investigate Metabolomics Data Matrices MethComp Analysis of Agreement in Method Comparison Studies MethEvolSIM Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies MethScope Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding MethodCompare Evaluating Bias and Precision in Method Comparison Studies MethodOpt Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation MetricGraph Random Fields on Metric Graphs Metrics Evaluation Metrics for Machine Learning MetricsWeighted Weighted Metrics and Performance Measures for Machine Learning MexBrewer Color Palettes Inspired by Works of Mexican Painters and Muralists MexicoDataAPI Access Mexican Data via APIs and Curated Datasets MfUSampler Multivariate-from-Univariate (MfU) MCMC Sampler Mfuzz Soft clustering of omics time series data Mhorseshoe Approximate Algorithm for Horseshoe Prior MiRKAT Microbiome Regression-Based Kernel Association Tests MiRNAQCD Micro-RNA Quality Control and Diagnosis MiRSEA 'MicroRNA' Set Enrichment Analysis MicSim Performing Continuous-Time Microsimulation MicroDatosEs Utilities for Official Spanish Microdata MicroMacroMultilevel Micro-Macro Multilevel Modeling MicroMoB Discrete Time Simulation of Mosquito-Borne Pathogen Transmission MicroNiche Microbial Niche Measurements MicrobTiSDA Microbiome Time-Series Data Analysis MicrobialGrowth Estimates Growth Parameters from Models and Plots the Curve MicrobiomeStat Statistical Methods for Microbiome Compositional Data MicrobiomeSurv Biomarker Validation for Microbiome-Based Survival Classification and Prediction Microsoft365R Interface to the 'Microsoft 365' Suite of Cloud Services MigConnectivity Estimate Migratory Connectivity for Migratory Animals MigrationDetectR Segment-Based Migration Detection Algorithm MinEDfind A Bayesian Design for Minimum Effective Dosing-Finding Trial MinTriadic Extension to the 'Lolog' Package for 'Triadic' Network Statistics MindOnStats Data sets included in Utts and Heckard's Mind on Statistics Minirand Minimization Randomization MisRepARMA Misreported Time Series Analysis MiscMath Miscellaneous Mathematical Tools MiscMetabar Miscellaneous Functions for Metabarcoding Analysis MissCP Change Point Detection with Missing Values MissMech Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random MissingHandle Handles Missing Dates and Data and Converts into Weekly and Monthly from Daily MissingPlotLSD Missing Plot in LSD MissingPlotRBD Missing Plot in RBD Missplot Missing Plot Technique in Design of Experiment MitoHEAR Quantification of Mitochondrial DNA Heteroplasmy MittagLeffleR Mittag-Leffler Family of Distributions MixFrac Fractional Factorial Designs with Alias and Trend-Free Analysis MixGHD Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions MixLFA Mixture of Longitudinal Factor Analysis Methods MixMashNet Tools for Multilayer and Single Layer Network Modeling MixMatrix Classification with Matrix Variate Normal and t Distributions MixOptim Mixture Optimization Algorithm MixRF A Random-Forest-Based Approach for Imputing Clustered Incomplete Data MixSAL Mixtures of Multivariate Shifted Asymmetric Laplace (SAL) Distributions MixSIAR Bayesian Mixing Models in R MixSemiRob Mixture Models: Parametric, Semiparametric, and Robust MixSim Simulating Data to Study Performance of Clustering Algorithms MixStable Parameter Estimation for Stable Distributions and Their Mixtures MixTwice Large-Scale Hypothesis Testing by Variance Mixing MixedIndTests Tests of Randomness and Tests of Independence MixedLevelRSDs Mixed Level Response Surface Designs MixedPoisson Mixed Poisson Models MixedPsy Statistical Tools for the Analysis of Psychophysical Data MixedTS Mixed Tempered Stable Distribution MixfMRI Mixture fMRI Clustering Analysis MixtureFitting Fitting of Univariate Mixture Distributions to Data using Various Approaches MixtureMissing Robust and Flexible Model-Based Clustering for Data Sets with Missing Values at Random Mmcsd Modeling Complex Longitudinal Data in a Quick and Easy Way MoBPS Modular Breeding Program Simulator MoEClust Gaussian Parsimonious Clustering Models with Covariates and a Noise Component MoNAn Mobility Network Analysis MoTBFs Learning Hybrid Bayesian Networks using Mixtures of Truncated Basis Functions ModEstM Mode Estimation, Even in the Multimodal Case ModLR Information-Theoretic Approach for Moderation Analysis ModStatR Statistical Modelling in Action with R ModTools Building Regression and Classification Models ModalCens Parametric Modal Regression with Right Censoring ModalForecast Parametric Modal ARIMA Models using the SKD Family Modalclust Hierarchical Modal Clustering ModelMap Modeling and Map Production using Random Forest and Related Stochastic Models ModelMatrixModel Create Model Matrix and Save the Transforming Parameters ModelMetrics Rapid Calculation of Model Metrics Modelcharts Classification Model Charts Modeler Classes and Methods for Training and Using Binary Prediction Models MolgenisArmadillo Armadillo Client for the Armadillo Service MolgenisAuth 'OpenID Connect' Discovery and Authentication MomTrunc Moments of Folded and Doubly Truncated Multivariate Distributions Mondrian A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events MonoPhy Explore Monophyly of Taxonomic Groups in a Phylogeny MonoPoly Functions to Fit Monotone Polynomials MonotoneHazardRatio Nonparametric Estimation and Inference of a Monotone Hazard Ratio Function MonotonicityTest Nonparametric Bootstrap Test for Regression Monotonicity Monte.Carlo.se Monte Carlo Standard Errors MonteCarloSEM Monte Carlo Simulation for Structural Equation Modeling MoonShineR Predict Moonlight, Sunlight, and/or Twilight Ground Illuminance MorphSim Simulate Discrete Character Data along Phylogenetic Trees Morpho Calculations and Visualisations Related to Geometric Morphometrics MorphoRegions Analysis of Regionalization Patterns in Serially Homologous Structures MorphoTools2 Multivariate Morphometric Analysis MortCast Estimation and Projection of Age-Specific Mortality Rates MortalityGaps The Double-Gap Life Expectancy Forecasting Model MortalityLaws Parametric Mortality Models, Life Tables and HMD MortalityTables A Framework for Various Types of Mortality / Life Tables MplusAutomation An R Package for Facilitating Large-Scale Latent Variable Analyses in Mplus MplusLGM Automate Latent Growth Mixture Modelling in 'Mplus' MplusTrees Decision Trees with Structural Equation Models Fit in 'Mplus' Mqrcm M-Quantile Regression Coefficients Modeling MsCoreUtils Core Utils for Mass Spectrometry Data MsExperiment Infrastructure for Mass Spectrometry Experiments MsFeatures Functionality for Mass Spectrometry Features MuChPoint Multiple Change Point MuFiMeshGP Multi-Fidelity Emulator for Computer Experiments with Tunable Fidelity Levels MuMIn Multi-Model Inference MuPETFlow Multiple Ploidy Estimation Tool for all Species Compatible with Flow Cytometry MuViCP MultiClass Visualizable Classification using Combination of Projections MultANOVA Analysis of Designed High-Dimensional Data using the Comprehensive MultANOVA Framework MultBiplotR Multivariate Analysis Using Biplots in R MultEq Multiple Equivalence Tests and Simultaneous Confidence Intervals MultNonParam Multivariate Nonparametric Methods MultOrdRS Model Multivariate Ordinal Responses Including Response Styles MultRegCMP Bayesian Multivariate Conway-Maxwell-Poisson Regression Model for Correlated Count Data MultSurvTests Permutation Tests for Multivariate Survival Analysis MultiATSM Multicountry Term Structure of Interest Rates Models MultiAssayExperiment Software for the integration of multi-omics experiments in Bioconductor MultiBD Multivariate Birth-Death Processes MultiCOAP High-Dimensional Covariate-Augmented Overdispersed Multi-Study Poisson Factor Model MultiClassROC ROC Curves for Multi-Class Analysis MultiDataSet Implementation of MultiDataSet and ResultSet MultiDiscreteRNG Generate Multivariate Discrete Data MultiFit Multiscale Fisher's Independence Test for Multivariate Dependence MultiGlarmaVarSel Variable Selection in Sparse Multivariate GLARMA Models MultiGrey Fitting and Forecasting of Grey Model for Multivariate Time Series Data MultiGroupO MultiGroup Method and Simulation Data Analysis MultiGroupSequential Group-Sequential Procedures with Multiple Hypotheses MultiJoin Enables Efficient Joining of Data File on Common Fields using the Unix Utility Join MultiKink Estimation and Inference for Multi-Kink Quantile Regression MultiLCIRT Multidimensional Latent Class Item Response Theory Models MultiLevelOptimalBayes Regularized Bayesian Estimator for Two-Level Latent Variable Models MultiModalR Fast Bayesian Probability Estimation for Multimodal Categorical Data MultiNMix Multi-Species N-Mixture (MNM) Models with 'nimble' MultiObjMatch Multi-Objective Matching Algorithm MultiOrd Generation of Multivariate Ordinal Variates MultiPhen A Package to Test for Multi-Trait Association MultiRFM High-Dimensional Multi-Study Robust Factor Model MultiRNG Multivariate Pseudo-Random Number Generation MultiResponseR Analysis of Data from Multiple-Response Questionnaires MultiRobust Multiply Robust Methods for Missing Data Problems MultiSkew Measures, Tests and Removes Multivariate Skewness MultiSpline Spline-Based Nonlinear Modeling for Multilevel and Longitudinal Data MultiStatM Multivariate Statistical Methods MultiTraits Analyzing and Visualizing Multidimensional Plant Traits MultipleBreakpoints Estimating Multiple Breakpoints for a Sequence of Realizations of Bernoulli Variables MultipleBubbles Test and Detection of Explosive Behaviors for Time Series MultipleRegression Multiple Regression Analysis MultiplierDEA Multiplier Data Envelopment Analysis and Cross Efficiency MultiscaleDTM Multi-Scale Geomorphometric Terrain Attributes MultiscaleSCP Multiscale Systematic Conservation Planning Across Nested H3 Grids MultisiteMediation Causal Mediation Analysis in Multisite Trials MultivariateAnalysis Pacote Para Analise Multivariada MultivariateRandomForest Models Multivariate Cases Using Random Forests MultivariateTrendAnalysis Univariate and Multivariate Trend Testing MultiwayRegression Perform Tensor-on-Tensor Regression MulvariateRandomForestVarImp Variable Importance Measures for Multivariate Random Forests MvBinary Modelling Multivariate Binary Data with Blocks of Specific One-Factor Distribution My.stepwise Stepwise Variable Selection Procedures for Regression Analysis Mychisq Chi-Squared Test for Goodness of Fit and Independence Test MyoScore Transcriptomic Scoring for Human Skeletal Muscle Health N2H4 Handling Methods for Naver News Text Crawling N2R Fast and Scalable Approximate k-Nearest Neighbor Search Methods using 'N2' Library NAC Network-Adjusted Covariates for Community Detection NACHO NanoString Quality Control Dashboard NADA Nondetects and Data Analysis for Environmental Data NADA2 Data Analysis for Censored Environmental Data NAEPirtparams IRT Parameters for the National Assessment of Education Progress NAEPprimer The NAEP Primer NAM Nested Association Mapping NAP Non-Local Alternative Priors in Psychology NAPrior Network Meta-Analytic Predictive Prior for Mid-Trial SoC Changes NAVAECI Non-Asymptotically Valid and Asymptotically Exact (NAVAE) Confidence Intervals NB.MClust Negative Binomial Model-Based Clustering NBAloveR Help Basketball Data Analysis NBBDesigns Neighbour Balanced Block Designs (NBBDesigns) NBDCtools National Institutes of Health Brain Development Cohorts Data Hub Tools NBDdirichlet NBD-Dirichlet Model of Consumer Buying Behavior for Marketing Research NBDesign Design and Monitoring of Clinical Trials with Negative Binomial Endpoint NBKP Beta Kernel Process Modeling with Negative Binomial Response NBLDA Negative Binomial Linear Discriminant Analysis NBPSeq Negative Binomial Models for RNA-Sequencing Data NBR Network-Based R-Statistics using Mixed Effects Models NBShiny Interactive Document for Working with Naive Bayes Classification NBShiny2 Interactive Document for Working with Naive Bayes Classification NBShiny3 Interactive Document for Working with Naive Bayes Classification NBtsVarSel Variable Selection in a Specific Regression Time Series of Counts NCA Necessary Condition Analysis NCC Simulation and Analysis of Platform Trials with Non-Concurrent Controls NCSCopula Non-Central Squared Copula Models Estimation NCmisc Miscellaneous Functions for Creating Adaptive Functions and Scripts NCutYX Clustering of Omics Data of Multiple Types with a Multilayer Network Representation NDP Interactive Presentation for Working with Normal Distribution NDPalette Notre Dame Color Palettes for R NEpiC Network Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals NFLSimulatoR Simulating Plays and Drives in the NFL NFWdist The Standard Distribution Functions for the 3D NFW Profile NGBVS Bayesian Variable Selection for SNP Data using Normal-Gamma NGCHM Next Generation Clustered Heat Maps NGLVieweR Interactive 3D Visualization of Molecular Structures NHANES Data from the US National Health and Nutrition Examination Study NHLData Scores for Every Season Since the Founding of the NHL in 1917 NHPoisson Modelling and Validation of Non Homogeneous Poisson Processes NHSDataDictionaRy NHS Data Dictionary Toolset for NHS Lookups NHSRdatasets NHS and Healthcare-Related Data for Education and Training NHSRplotthedots Draw XmR Charts for NHS 'Making Data Count' Programme NHSRwaitinglist Waiting List Metrics Using Queuing Theory NIMAA Nominal Data Mining Analysis NIPTeR Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing NIRStat Novel Statistical Methods for Studying Near-Infrared Spectroscopy (NIRS) Time Series Data NISTnls Nonlinear least squares examples from NIST NISTunits Fundamental Physical Constants and Unit Conversions from NIST NLP Natural Language Processing Infrastructure NLPclient Stanford 'CoreNLP' Annotation Client NLPutils Natural Language Processing Utilities NLPwavelet Bayesian Wavelet Analysis Using Non-Local Priors NMA Network Meta-Analysis Based on Multivariate Meta-Analysis and Meta-Regression Models NMADTA Network Meta-Analysis of Multiple Diagnostic Tests NMAR Estimation under not Missing at Random Nonresponse NMAforest Forest Plots for Network Meta-Analysis with Proportion for Paths and Studies NMAoutlier Detecting Outliers in Network Meta-Analysis NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) NMFN Non-Negative Matrix Factorization NMMIPW Inverse Probability Weighting under Non-Monotone Missing NMOF Numerical Methods and Optimization in Finance NMRphasing Phase Error Correction and Baseline Correction for One Dimensional ('1D') 'NMR' Data NMTox Dose-Response Relationship Analysis of Nanomaterial Toxicity NMVANOVA Novice Model Variation ANOVA NMcalc Basic Calculations for PK/PD Modeling NMdata Preparation, Checking and Post-Processing Data for PK/PD Modeling NMsim Seamless 'Nonmem' Simulation Platform NNMIS Nearest Neighbor Based Multiple Imputation for Survival Data with Missing Covariates NNMoMo Neural Network Extension to 'StMoMo' for Lee-Carter Modeling NNS Nonlinear Nonparametric Statistics NO.PING.PONG Incorporating Previous Findings When Evaluating New Data NORMAgene Data-Driven qRT-PCR Normalization Using NORMAgene NOVA Neural Output Visualization and Analysis NPBBBDAefficiency A-Efficiency for Nested Partially Balanced Bipartite Block (NPBBB) Designs NPBBBdesigns Construction and a-Efficiency of Nested Partially Balanced Bipartite Block Designs NPBayesImputeCat Non-Parametric Bayesian Multiple Imputation for Categorical Data NPCD Nonparametric Methods for Cognitive Diagnosis NPCDTools The Nonparametric Classification Methods for Cognitive Diagnosis NPCirc Nonparametric Circular Methods NPCox Nonparametric and Semiparametric Proportional Hazards Model NPFD N-Power Fourier Deconvolution NPHMC Sample Size Calculation for the Proportional Hazards Mixture Cure Model NPHazardRate Nonparametric Hazard Rate Estimation NPIstats Nonparametric Predictive Inference NPLStoolbox N-Way Partial Least Squares Modelling of Multi-Way Data NPMLEcmprsk Type-Specific Failure Rate and Hazard Rate on Competing Risks Data NPP Normalized Power Prior Bayesian Analysis NPRED Predictor Identifier: Nonparametric Prediction NPStability Rank-Based Stability Index (RSI) for Genotype by Environment Studies NPflow Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data NRMSampling Sampling Design and Estimation Methods for Natural Resource Management NRMstatsML Statistical and Machine Learning Engine for Long-Term Natural Resource Management Data NRejections Metrics for Multiple Testing with Correlated Outcomes NSM3 Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition NSMM Non-Stationary Multivariate (Copula-Based) Framework, Hydrological Applications NSO1212 National Statistical Office of Mongolia's Open Data API Handler NSR 'Native Status Resolver' NST Normalized Stochasticity Ratio NScluster Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models NTLKwIEx Computation of NTLKwIEx Distribution Properties NTS Nonlinear Time Series Analysis NTSS Nonparametric Tests in Spatial Statistics NU.Learning Nonparametric and Unsupervised Learning from Cross-Sectional Observational Data NUCOMBog NUtrient Cycling and COMpetition Model Undisturbed Open Bog Ecosystems in a Temperate to Sub-Boreal Climate NUETON Nitrogen Use Efficiency Toolkit on Numerics NUSS Mixed N-Grams and Unigram Sequence Segmentation NVAR Nonlinear Vector Autoregression Models NVCSSL Nonparametric Varying Coefficient Spike-and-Slab Lasso NaileR Interpreting Latent Variables with AI NameNeedle Using Needleman-Wunsch to Match Sample Names NatParksPalettes Color Palettes Inspired by National Parks NatureSounds Animal Sounds for Bioacustic Analysis NbClust Determining the Best Number of Clusters in a Data Set NeEDS4BigData New Experimental Design Based Subsampling Methods for Big Data NeStage Effective Population Size from Stage-Structured Populations Nebulosa Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation Necklaces Necklaces and Bracelets NegBinBetaBinreg Negative Binomial and Beta Binomial Bayesian Regression Models NegativeControlOutcomeAdjustment Estimation of Vaccine Efficacy using Negative Control Outcomes Neighboot Neighborhood Bootstrap Method for RDS NeighborFinder Find Neighbor Species of a Bacteria of Interest in the Human Gut Microbiota Nematode Ecological Indices Calculator for Nematode Communities NestMRMC Single Reader Between-Cases AUC Estimator in Nested Data NestedMenu A Nested Menu Widget for 'Shiny' Applications Nestimate Network Estimation, Bootstrap, and Higher-Order Analysis NetCluster Clustering for networks NetCoupler Inference of Causal Links Between a Network and an External Variable NetDA Network-Based Discriminant Analysis Subject to Multi-Label Classes NetExplorer Network Explorer NetGreg Network-Guided Penalized Regression (NetGreg) NetIndices Estimating Network Indices, Including Trophic Structure of Foodwebs in R NetInt Methods for Unweighted and Weighted Network Integration NetLogoR Build and Run Spatially Explicit Agent-Based Models NetMix Dynamic Mixed-Membership Network Regression Model NetOrigin Origin Estimation for Propagation Processes on Complex Networks NetPreProc Network Pre-Processing and Normalization NetRep Permutation Testing Network Module Preservation Across Datasets NetSci Calculates Basic Network Measures Commonly Used in Network Medicine NetSimR Actuarial Functions for Non-Life Insurance Modelling NetSurvProx 'NetSurvProx': Network-Based Survival Analysis via Proximal Methods NetVAR Network Structures in VAR Models NetWeaver Graphic Presentation of Complex Genomic and Network Data Analysis NetworkChange Bayesian Package for Network Changepoint Analysis NetworkComparisonTest Statistical Comparison of Two Networks Based on Several Invariance Measures NetworkComparr Statistical Comparison of Networks NetworkDistance Distance Measures for Networks NetworkExtinction Extinction Simulation in Ecological Networks NetworkInference Inferring Latent Diffusion Networks NetworkReg Generalized Linear Regression Models on Network-Linked Data with Statistical Inference NetworkRiskMeasures Risk Measures for (Financial) Networks NetworkToolbox Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis NeuDist Univariate Continuous Distributions with Model Diagnostics NeuralEstimators Likelihood-Free Parameter Estimation using Neural Networks NeuralNetTools Visualization and Analysis Tools for Neural Networks NeuralSens Sensitivity Analysis of Neural Networks NeuroDataSets A Comprehensive Collection of Neuroscience and Brain-Related Datasets NeuroDecodeR Decode Information from Neural Activity NeutroCODsAnalysis Neutrosophic Analysis Crossover Designs NeutroIBDAnalysis Neutrosophic Analysis of Incomplete Block Designs NeutroRCDsAnalysis Neutrosophic Analysis of Row Column Designs NeutroSplitStripAnalysis Neutrosophic Analysis of Split-Plot and Strip-Plot Designs Newdistns Computes Pdf, Cdf, Quantile and Random Numbers, Measures of Inference for 19 General Families of Distributions NewmanOmics Extending the Newman Studentized Range Statistic to Transcriptomics NiLeDAM Monazite Dating for the NiLeDAM Team NightDay Night and Day Boundary Plot Function NipponMap Japanese Map Data and Functions NitrogenUptake2016 Data and Source Code From: Nitrogen Uptake and Allocation Estimates for Spartina Alterniflora and Distichlis Spicata NlcOptim Solve Nonlinear Optimization with Nonlinear Constraints NlinTS Models for Non Linear Causality Detection in Time Series NlsyLinks Utilities and Kinship Information for Research with the NLSY Nmisc Miscellaneous Functions Used at 'Numeract LLC' Nmix Bayesian Inference on Univariate Normal Mixtures NoSleepR Prevent System Sleep During Long R Tasks NobBS Nowcasting by Bayesian Smoothing NonCompart Noncompartmental Analysis for Pharmacokinetic Data NonNorMvtDist Multivariate Lomax (Pareto Type II) and Its Related Distributions NonParRolCor a Non-Parametric Statistical Significance Test for Rolling Window Correlation NonProbEst Estimation in Nonprobability Sampling NonlinearDiD Staggered Difference-in-Differences with Nonlinear Outcomes NonlinearTSA Nonlinear Time Series Analysis Nonpareil Metagenome Coverage Estimation and Projections for 'Nonpareil' NormData Derivation of Regression-Based Normative Data NormExpression Normalize Gene Expression Data using Evaluated Methods NormPsy Normalisation of Psychometric Tests NormalLaplace The Normal Laplace Distribution NormalityAssessment A Graphical User Interface for Testing Normality Visually NostalgiR Advanced Text-Based Plots NovelDistns Computes PDF, CDF, Quantile, Random Numbers and Measures of Inference for 3 General Families of Distributions NoviceDeveloperResources Resources to Assist Novice Developers NoviceDeveloperResources2 Further Resources to Assist Novice Developers NumericEnsembles Automatically Runs 18 Individual and 14 Ensembles of Models Numero Statistical Framework to Define Subgroups in Complex Datasets NutrienTrackeR Food Composition Information and Dietary Assessment OAIHarvester Harvest Metadata Using OAI-PMH Version 2.0 OBASpatial Objective Bayesian Analysis for Spatial Regression Models OBIC Calculate the Open Bodem Index (OBI) Score OBL Optimum Block Length OBMbpkg Estimate the Population Size for the Mb Capture-Recapture Model OBRE Optimal B-Robust Estimator Tools OBsMD Objective Bayesian Model Discrimination in Follow-Up Designs OCNet Optimal Channel Networks OCSdata Download Data from the 'Open Case Studies' Repository ODMeans OD-Means: k-Means for Origin-Destination ODRF Oblique Decision Random Forest for Classification and Regression ODS Statistical Methods for Outcome-Dependent Sampling Designs ODT Optimal Decision Trees Algorithm ODataQuery Querying on 'OData' OECD Search and Extract Data from the OECD OEFPIL Optimal Estimation of Function Parameters by Iterated Linearization OGI Objective General Index OHPL Ordered Homogeneity Pursuit Lasso for Group Variable Selection OLCPM Online Change Point Detection for Matrix-Valued Time Series OLSengine Transparent and Assisted Linear Modeling Engine OLStrajr Ordinary Least Squares Trajectory Analysis ONAM Fitting Interpretable Neural Additive Models Using Orthogonalization ONEST Observers Needed to Evaluate Subjective Tests OOBCurve Out of Bag Learning Curve OOR Optimistic Optimization in R OORRT Estimator for Optimised Optional Randomised Response Technique OPC The Online Principal Component Estimation Method OPCreg Online Principal Component Regression for Online Datasets OPDOE Optimal Design of Experiments OPI Open Perimetry Interface OPL Optimal Policy Learning OPSR Ordered Probit Switching Regression OPTS Optimization via Subsampling (OPTS) OPTeCD Optimal Partial Tetra-Allele Cross Designs OPTtesting Optimal Testing ORCME Order Restricted Clustering for Microarray Experiments ORFID Manage and Summarize Data from Oregon RFID ORMR and ORSR Antenna Readers ORION Ordinal Relations ORIONZ.G EAP Scoring in Exploratory FA Solutions with Correlated Residuals ORKM The Online Regularized K-Means Clustering Algorithm ORTH.Ord Alternating Logistic Regression with Orthogonalized Residuals for Correlated Ordinal Outcomes ORTSC Connects to Google Cloud API for Label Detection ORscraper Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar' OSAT OSAT: Optimal Sample Assignment Tool OSCARS Global Bounded Optimization by the OSCARS-II Algorithm OSCV One-Sided Cross-Validation OSDR Finds an Optimal System of Distinct Representatives OSFD Output Space-Filling Design OSIRCR Cosine Regression-Based Online Sliced Inverse Regression Algorithm OSLdecomposition Signal Component Analysis for Optically Stimulated Luminescence OSMscale Add a Scale Bar to 'OpenStreetMap' Plots OSNMTF Orthogonal Sparse Non-Negative Matrix Tri-Factorization OSsurvival Assessing Surrogacy with a Censored Outcome OTBsegm Apply Unsupervised Segmentation Algorithms from 'OTB' OTE Optimal Trees Ensembles for Regression, Classification and Class Membership Probability Estimation OTRselect Variable Selection for Optimal Treatment Decision OTUtable North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions OTclust Mean Partition, Uncertainty Assessment, Cluster Validation and Visualization Selection for Cluster Analysis OTrecod Data Fusion using Optimal Transportation Theory OUwie Analysis of Evolutionary Rates in an OU Framework OVL.CI Inference on the Overlap Coefficient OVtool Omitted Variable Tool OWEA Optimal Weight Exchange Algorithm for Optimal Designs for Three Models Oarray Arrays with Arbitrary Offsets OasisR Outright Tool for the Analysis of Spatial Inequalities and Segregation Observation Collect and Process Physical Activity Direct Observation Data OceanView Visualisation of Oceanographic Data and Model Output OddsPlotty Odds Plot to Visualise a Logistic Regression Model OdysseusCharacterizationModule Handy and Minimalistic Common Data Model Characterization OdysseusPathwayModule Cohort Pathway Analysis with Pre-Index Event Support OdysseusSurvivalModule Cohort-Based Single-Event Survival Utilities OenoKPM Modeling the Kinetics of Carbon Dioxide Production in Alcoholic Fermentation OhdsiReportGenerator Observational Health Data Sciences and Informatics Report Generator OhdsiShinyAppBuilder Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules Ohit OGA+HDIC+Trim and High-Dimensional Linear Regression Models OkNNE A k-Nearest Neighbours Ensemble via Optimal Model Selection for Regression OlinkAnalyze Facilitate Analysis of Proteomic Data from Olink OlinkAnalyzeVignettes Vignettes for Analyzing Data using 'OlinkAnalyze' OlympicRshiny 'Shiny' Application for Olympic Data OmegaG Omega-Generic: Composite Reliability of Multidimensional Measures OmicFlow Fast and Efficient (Automated) Analysis of Sparse Omics Data OmicKriging Poly-Omic Prediction of Complex TRaits OmicNavigator Open-Source Software for 'Omic' Data Analysis and Visualization OmicNetR Network-Based Integration of Multi-Omics Data Using Sparse CCA OmicSense Biosensor Development using Omics Data OmicsPLS Data Integration with Two-Way Orthogonal Partial Least Squares OmicsPrepR Unified Preprocessing Toolkit for Proteomics and Metabolomics OmicsQC Nominating Quality Control Outliers in Genomic Profiling Studies Omisc DeFries-Fulker Analysis and Univariate Bootstrapping OmopConstructor Build Tables in the OMOP Common Data Model OmopOnSpark Using a Common Data Model on 'Spark' OmopSketch Characterise Tables of an OMOP Common Data Model Instance OmopStudyBuilder Build Reproducible Network Studies for OMOP Common Data Model OmopViewer Visualise OMOP Results using 'shiny' Applications OnAge Test of Between-Group Differences in the Onset of Senescence OncoDataSets A Comprehensive Collection of Cancer Types and Cancer-Related Datasets OncoSubtype Predict Cancer Subtypes Based on TCGA Data using Machine Learning Method Oncofilterfast Aids in the Analysis of Genes Influencing Cancer Survival Oncotree Estimating Oncogenetic Trees One4All Validate, Share, and Download Data OneArm2stage Phase II Single-Arm Two-Stage Designs with Time-to-Event Outcomes OneArmTTE One-Arm Clinical Trial Designs for Time-to-Event Endpoint OneR One Rule Machine Learning Classification Algorithm with Enhancements OneSampleLogRankTest One-Sample Log-Rank Test OneSampleMR One Sample Mendelian Randomization and Instrumental Variable Analyses OneStep One-Step Estimation OneTwoSamples Deal with One and Two (Normal) Samples OnlineSurr Surrogate Evaluation for Jointly Longitudinal Outcome and Surrogate OnomasticDiversity Onomastic Diversity Measures OofAExp Order-of-Addition Experiments OpEnCAST Optimized Ensemble Model for C and A Methylation Search in Plant OpEnHiMR Optimization Based Ensemble Model for Prediction of Histone Modifications in Rice OpeNoise Environmental Noise Pollution Data Analysis Open.Visualization.Academy Content to Support Classes Taught Through the Open Visualization Academy OpenBARD Open British Arboricultural Record Dataset OpenCL Interface allowing R to use OpenCL OpenImageR An Image Processing Toolkit OpenLand Quantitative Analysis and Visualization of LUCC OpenML Open Machine Learning and Open Data Platform OpenMindat Quickly Retrieve Datasets from the 'Mindat' API OpenMx Extended Structural Equation Modelling OpenRange Code to Access Open Access Species Range Maps OpenRepGrid Tools to Analyze Repertory Grid Data OpenRepGrid.ic Interpretive Clustering for Repertory Grids OpenSourceAP.DownloadR Download Open Source Asset Pricing (OpenAP) Data Directly OpenSpecy Analyze, Process, Identify, and Share Raman and (FT)IR Spectra OpenStreetMap Access to Open Street Map Raster Images Opportunistic Routing Distribution, Broadcasts, Transmissions and Receptions in an Opportunistic Network Opt5PL Optimal Designs for the 5-Parameter Logistic Model OptCirClust Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible OptGS Near-Optimal Group-Sequential Designs for Continuous Outcomes OptHedging Estimation of value and hedging strategy of call and put options. OptHoldoutSize Estimation of Optimal Size for a Holdout Set for Updating a Predictive Score OptM Estimating the Optimal Number of Migration Edges from 'Treemix' OptOTrials Optimal Two-Stage Designs for Ordered Categorical Outcomes OptSig Optimal Level of Significance for Regression and Other Statistical Tests OptSurvCutR Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with 'OptSurvCutR' OptimModel Perform Nonlinear Regression Using 'optim' as the Optimization Engine OptimaRegion Confidence Regions for Optima of Response Surfaces OptimalBinningWoE Optimal Binning and Weight of Evidence Framework for Modeling OptimalCutpoints Computing Optimal Cutpoints in Diagnostic Tests OptimalDesign A Toolbox for Computing Efficient Designs of Experiments OptimalRerandExpDesigns Optimal Rerandomization Experimental Designs OptimalSurrogate Model Free Approach to Quantifying Surrogacy OptimalTiming Optimal Timing Identification OptionPricing Option Pricing with Efficient Simulation Algorithms OralOpioids Retrieving Oral Opioid Information Orangutan Automated Analysis of Phenotypic Data Orcs Omnidirectional R Code Snippets OrdCD Ordinal Causal Discovery OrdFacReg Least Squares, Logistic, and Cox-Regression with Ordered Predictors OrdMonReg Compute Least Squares Estimates of One Bounded or Two Ordered Isotonic Regression Curves OrdNor Concurrent Generation of Ordinal and Normal Data with Given Correlation Matrix and Marginal Distributions OrdinalCompositions Wasserstein-Based Regression for Ordinal Compositional Data OrgHeatmap Visualization Tool for Numerical Data on Human/Mouse Organs and Organelles OrgMassSpecR Organic Mass Spectrometry OrganismDbi Software to enable the smooth interfacing of different database packages OrigamiPlot A Visualization Tool Enhancing Radar Plot Visualizations for Multivariate Data OrthoPanels Dynamic Panel Models with Orthogonal Reparameterization of Fixed Effects OryzaProbe Rice Microarray Probe ID Conversion, from Probe ID to RAP-DB ID OscillatorGenerator Generation of Customizable, Discretized Time Series of Oscillating Species OssaNMA Optimal Sample Size and Allocation with a Network Meta-Analysis Ostats O-Stats, or Pairwise Community-Level Niche Overlap Statistics OtsuFire Fire Scars, Severity and Regeneration Mapping Using 'Otsu' Thresholding OtsuSeg Raster Thresholding Using Otsu´s Algorithm OutSeekR Statistical Approach to Outlier Detection in RNA-Seq and Related Data OutcomeWeights Outcome Weights of Treatment Effect Estimators OutliersLearn Educational Outlier Package with Common Outlier Detection Algorithms OutliersO3 Draws Overview of Outliers (O3) Plots OwenQ Owen Q-Function OxSR Soil Iron Oxides via Diffuse Reflectance OxyBS Processing of Oxy-Bisulfite Microarray Data PAC Partition-Assisted Clustering and Multiple Alignments of Networks PACVr Plastome Assembly Coverage Visualization PADOG Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) PAFit Generative Mechanism Estimation in Temporal Complex Networks PAGE Predictor-Assisted Graphical Models under Error-in-Variables PAGFL Joint Estimation of Latent Groups and Group-Specific Coefficients in (Time-Varying) Panel Data Models PAGWAS Pathway Analysis Methods for Genomewide Association Data PAICE Phylogeographic Analysis of Island Colonization Events PAMhm Generate Heatmaps Based on Partitioning Around Medoids (PAM) PAMmisc Miscellaneous Functions for Passive Acoustic Analysis PAMpal Load and Process Passive Acoustic Data PAMscapes Tools for Summarising and Analysing Soundscape Data PANACEA Personalized Network-Based Anti-Cancer Therapy Evaluation PANPRSnext Building PRS Models Based on Summary Statistics of GWAs PAS Polygenic Analysis System (PAS) PASSED Calculate Power and Sample Size for Two Sample Mean Tests PASWR Probability and Statistics with R PASWR2 Probability and Statistics with R, Second Edition PAutilities Streamline Physical Activity Research PBD Protracted Birth-Death Model of Diversification PBIBD Partially Balanced Incomplete Block Designs PBIR Estimating the Probability of Being in Response and Related Outcomes PBImisc A Set of Datasets Used in My Classes or in the Book 'Modele Liniowe i Mieszane w R, Wraz z Przykladami w Analizie Danych' PBNPA Permutation Based Non-Parametric Analysis of CRISPR Screen Data PBSadmb ADMB for R Using Scripts or GUI PBSddesolve Solver for Delay Differential Equations PBSmapping Mapping Fisheries Data and Spatial Analysis Tools PBSmodelling GUI Tools Made Easy: Interact with Models and Explore Data PBtDesigns Partially Balanced t-Designs (PBtDesigns) PCADSC Tools for Principal Component Analysis-Based Data Structure Comparisons PCAPAM50 Enhanced 'PAM50' Subtyping of Breast Cancer PCAmatchR Match Cases to Controls Based on Genotype Principal Components PCAmixdata Multivariate Analysis of Mixed Data PCBN Inference of Pair-Copula Bayesian Networks PCBS Principal Component BiSulfite PCDimension Finding the Number of Significant Principal Components PCFAM Computation of Ancestry Scores with Mixed Families and Unrelated Individuals PCGII Partial Correlation Graph with Information Incorporation PCGSE Principal Component Gene Set Enrichment PCL Proximal Causal Learning PCLassoReg Group Regression Models for Risk Protein Complex Identification PCMBase Simulation and Likelihood Calculation of Phylogenetic Comparative Models PCMBaseCpp Fast Likelihood Calculation for Phylogenetic Comparative Models PCMRS Model Response Styles in Partial Credit Models PCObw Bandwidth Selector with Penalized Comparison to Overfitting Criterion PCPS Principal Coordinates of Phylogenetic Structure PCRA Companion to Portfolio Construction and Risk Analysis PCRedux Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit as Described in Burdukiewicz (2022) PCS Calculate the Probability of Correct Selection (PCS) PCSinR Parallel Constraint Satisfaction Networks in R PCovR Principal Covariates Regression PCpluS Piecewise Constant Plus Smooth Regression PDE Extract Tables and Sentences from PDFs with User Interface PDEnaiveBayes Plausible Naive Bayes Classifier Using PDE PDFEstimator Multivariate Nonparametric Probability Density Estimator PDIndex Disease Intensity and Progress Curve Indices for Plant Pathology PDM Photogrammetric Distances Measurer PDMIF Fits Heterogeneous Panel Data Models PDN Personalized Disease Network PDQutils PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher Approximations PDSCE Positive Definite Sparse Covariance Estimators PDShiny 'Probability Distribution Shiny' PDXpower Time to Event Outcome in Experimental Designs of Pre-Clinical Studies PDtoolkit Collection of Tools for PD Rating Model Development and Validation PEAXAI Probabilistic Efficiency Analysis Using Explainable Artificial Intelligence PEGroupTesting Population Proportion Estimation using Group Testing PEIMAN2 Post-Translational Modification Enrichment, Integration, and Matching Analysis PEIP Geophysical Inverse Theory and Optimization PELVIS Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae PEPBVS Bayesian Variable Selection using Power-Expected-Posterior Prior PERK Predicting Environmental Concentration and Risk PERMANOVA Multivariate Analysis of Variance Based on Distances and Permutations PERSUADE Parametric Survival Model Selection for Decision-Analytic Models PEkit Partition Exchangeability Toolkit PEtests Power-Enhanced (PE) Tests for High-Dimensional Data PFCI Penalized Fast Causal Inference for High-Dimensional Structure Learning PFIM Population Fisher Information Matrix PFLR Estimating Penalized Functional Linear Regression PFW Filtering and Processing Data from Project FeederWatch PGM2 Recursive Construction of Nested Resolvable Designs and Associated Uniform Designs PGRdup Discover Probable Duplicates in Plant Genetic Resources Collections PGaGEV Power Garima-Generalized Extreme Value Distribution PGaovR Analysis of Experimental Data using ANOVA and Mean Comparison PH1XBAR Phase I Shewhart X-Bar Chart PHENIX Phenotypic Integration Index PHENTHAUproc Phenology Modelling of Thaumetopoea Processionea PHEindicatormethods Common Public Health Statistics and their Confidence Intervals PHInfiniteEstimates Tools for Inference in the Presence of a Monotone Likelihood PHSMM Penalised Maximum Likelihood Estimation for Hidden Semi-Markov Models PHYLOGR Functions for Phylogenetically Based Statistical Analyses PHclust Poisson Hurdle Clustering for Sparse Microbiome Data PHeval Evaluation of the Proportional Hazards Assumption and Test for Comparing Survival Curves with a Standardized Score Process PICBayes Bayesian Models for Partly Interval-Censored Data PIE A Partially Interpretable Model with Black-Box Refinement PINMA Improved Methods for Constructing Prediction Intervals for Network Meta-Analysis PINSPlus Clustering Algorithm for Data Integration and Disease Subtyping PINstimation Estimation of the Probability of Informed Trading PITS Power of Interrupted Time Series (ITS) Studies PJCcalculator PROs-Joint Contrast (PJC) Calculator PJFM Variational Inference for High-Dimensional Joint Frailty Model PK Basic Non-Compartmental Pharmacokinetics PKI Public Key Infrastucture for R Based on the X.509 Standard PKLMtest Classification Based MCAR Test PKNCA Perform Pharmacokinetic Non-Compartmental Analysis PKPDindex Optimal PK/PD Index Finder PKPDsim Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations PKbioanalysis Pharmacokinetic Bioanalysis Experiments Design and Exploration PKconverter The Parameter Converter of the Pharmacokinetic Models PL94171 Tabulate P.L. 94-171 Redistricting Data Summary Files PLEXI Multiplex Network Analysis PLFD Portmanteau Local Feature Discrimination for Matrix-Variate Data PLIS Multiplicity Control using Pooled LIS Statistic PLNmodels Poisson Lognormal Models PLORN Prediction with Less Overfitting and Robust to Noise PLRModels Statistical Inference in Partial Linear Regression Models PLUCR Policy Learning Under Constraint PLindleyROC Receiver Operating Characteristic Based on Power Lindley Distribution PLmixed Estimate (Generalized) Linear Mixed Models with Factor Structures PLreg Power Logit Regression for Modeling Bounded Data PMA Penalized Multivariate Analysis PMCMR Calculate Pairwise Multiple Comparisons of Mean Rank Sums PMCMRplus Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended PMEvapotranspiration Calculation of the Penman-Monteith Evapotranspiration using Weather Variables PMLE4SCR Pseudo Maximum Likelihood Estimation for Semi-Competing Risks Data PMwR Portfolio Management with R PNADCperiods Identify Reference Periods in Brazil's PNADC Survey Data PNADcIBGE Downloading, Reading and Analyzing PNADC Microdata PNAR Poisson Network Autoregressive Models PNC Phylogenetic Niche Conservatism Analysis for Ecological Communities PND.heter.cluster Estimating the Cluster Specific Treatment Effects in Partially Nested Designs PNDSIBGE Downloading, Reading and Analyzing PNDS Microdata - Package in Development PNSIBGE Downloading, Reading and Analyzing PNS Microdata PNWColors Color Palettes Inspired by Nature in the US Pacific Northwest POCRE Penalized Orthogonal-Components Regression POD Probability of Detection for Qualitative PCR Methods POET Principal Orthogonal ComplEment Thresholding (POET) Method POINT Protein Structure Guided Local Test POMADE Power for Meta-Analysis of Dependent Effects POMS Phylogenetic Organization of Metagenomic Signals POMaSPU Adaptive Association Tests for Multiple Phenotypes using Proportional Odds Model (POM-aSPU) PONG2 KIR Genotype Imputation and Model Training from SNP Array Data POPInf Assumption-Lean and Data-Adaptive Post-Prediction Inference POSSA Power Simulation for Sequential Analyses and Multiple Hypotheses POSTm Phylogeny-Guided OTU-Specific Association Test for Microbiome Data POSetR Partially Ordered Sets in R POT Generalized Pareto Distribution and Peaks Over Threshold POV Partition of Variation Variance Component Analysis Method PP Person Parameter Estimation PPCDT An Optimal Subset Selection for Distributed Hypothesis Testing PPCI Projection Pursuit for Cluster Identification PPCSexRx Prescribe Sub-Symptom Exercise for Adolescent Concussion PPMR Probabilistic Two Sample Mendelian Randomization PPMiss Copula-Based Estimator for Long-Range Dependent Processes under Missing Data PPQplan Process Performance Qualification (PPQ) Plans in Chemistry, Manufacturing and Controls (CMC) Statistical Analysis PPRL Privacy Preserving Record Linkage PPSFS Partial Profile Score Feature Selection in High-Dimensional Generalized Linear Interaction Models PPTS Point Process Time Series PPTcirc Projected Polya Tree for Circular Data PPbigdata Projection Pursuit for Big Data Based on Data Nuggets PPforest Projection Pursuit Classification Forest PPtreeExt Projection Pursuit Classification Tree Extensions PPtreeViz Projection Pursuit Classification Tree Visualization PQA Perform the Pearson-Quetelet Analysis on Two-Way Contingency Tables PRANA Pseudo-Value Regression Approach for Network Analysis (PRANA) PRBMSdesigns Partially Residual Balanced Multi-Session Designs PRDA Conduct a Prospective or Retrospective Design Analysis PRECAST Embedding and Clustering with Alignment for Spatial Omics Datasets PREPShiny Interactive Document for Preprocessing the Dataset PRIMAL Parametric Simplex Method for Sparse Learning PRIMEplus Study Design for Immunotherapy Clinical Trials PRISM.forecast Penalized Regression with Inferred Seasonality Module - Forecasting Unemployment Initial Claims using 'Google Trends' Data PRISMA Protocol Inspection and State Machine Analysis PRISMA2020 Make Interactive 'PRISMA' Flow Diagrams PRMethods D-Hondt, Sainte-Lague, and Modified Sainte-Lague Methods for Seat Allocation PRNG A Pseudo-Random Number Generator PROJ Generic Coordinate System Transformations Using 'PROJ' PROMETHEE Preference Ranking Organization METHod for Enrichment of Evaluations PROSPER Simulation of Weed Population Dynamics PROreg Patient Reported Outcomes Regression Analysis PROscorer Functions to Score Commonly-Used Patient-Reported Outcome (PRO) Measures and Other Psychometric Instruments PROscorerTools Tools to Score Patient-Reported Outcome (PRO) and Other Psychometric Measures PROsetta Linking Patient-Reported Outcomes Measures PRP Bayesian Prior and Posterior Predictive Replication Assessment PRROC Precision-Recall and ROC Curves for Weighted and Unweighted Data PRTree Probabilistic Regression Trees PReMiuM Dirichlet Process Bayesian Clustering, Profile Regression PResiduals Probability-Scale Residuals and Residual Correlations PSAWR 'Pushshift' API Wrapper for 'Reddit' Submission and Comment Search PSAboot Bootstrapping for Propensity Score Analysis PSAgraphics Propensity Score Analysis Graphics PSCBS Analysis of Parent-Specific DNA Copy Numbers PSDistr Distributions Derived from Normal Distribution PSF Forecasting of Univariate Time Series Using the Pattern Sequence-Based Forecasting (PSF) Algorithm PSGD Projected Subset Gradient Descent PSGoft Modified Lilliefors Goodness-of-Fit Normality Test PSIM Preference Selection Index Method (PSIM) PSIndependenceTest Independence Tests for Two-Way, Three-Way and Four-Way Contingency Tables PSLM2015 Pakistan Social and Living Standards Measurement Survey 2014-15 PSMatch Handling and Managing Peptide Spectrum Matches PSPI Propensity Score Predictive Inference for Generalizability PSPManalysis Analysis of Physiologically Structured Population Models PSRICalc Plant Stress Response Index Calculator PSRICalcSM Plant Stress Response Index Calculator - Softmax Method PSSIM Test of Independence & Image Structural Similarity Measure PSSIM PSSMCOOL Features Extracted from Position Specific Scoring Matrix (PSSM) PSTR Panel Smooth Transition Regression Modelling PSW Propensity Score Weighting Methods for Dichotomous Treatments PScr Estimation for the Power Series Cure Rate Model PSinference Inference for Released Plug-in Sampling Synthetic Dataset PSor Semiparametric Principal Stratification Analysis Beyond Monotonicity PSpower Sample Size and Power for Propensity Score Weighted Estimators PSsurvival Propensity Score Methods for Survival Analysis PStrata Principal Stratification Analysis in R PSweight Propensity Score Weighting for Causal Inference with Observational Studies and Randomized Trials PTAk Principal Tensor Analysis on k Modes PTE Personalized Treatment Evaluator PTERP PTE and RP for Optimally-Transformed Surrogate PTMods Managing Post-Translational Modifications in R PTSDdiag Optimize PTSD Diagnostic Criteria PTSR Positive Time Series Regression PTXQC Quality Report Generation for MaxQuant and mzTab Results PTwins Percentile Estimation of Fetal Weight for Twins by Chorionicity PUGMM Parsimonious Ultrametric Gaussian Mixture Models PUMP Power Under Multiplicity Project PUPAK Parameter Estimation, and Plot Visualization of Adsorption Kinetic Models PUPMCR Image-Based Identification of Color Based on Rayner (1970) Terminology and Known Fungal Pigments PUPMSI Moisture Sorption Isotherm Modeling Program PUlasso High-Dimensional Variable Selection with Presence-Only Data PVAClone Population Viability Analysis with Data Cloning PVBcorrect Partial Verification Bias Correction for Diagnostic Accuracy PVR Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve PWEALL Design and Monitoring of Survival Trials Accounting for Complex Situations PWEV PSO Based Weighted Ensemble Algorithm for Volatility Modelling PWEXP Piecewise Exponential Distribution Prediction Model PWIR Provides a Function to Calculate Prize Winner Indices Based on Bibliometric Data PaLMr Interface for 'Google Pathways Language Model 2 (PaLM 2)' PaRe A Way to Perform Code Review or QA on Other Packages PacketLLM AI Assistant Gadget for 'RStudio' Pade Padé Approximant Coefficients PairViz Visualization using Graph Traversal PairedData Paired Data Analysis PakPC2017 Pakistan Population Census 2017 PakPC2023 Pakistan Population Census 2023 PakPMICS2014Ch Multiple Indicator Cluster Survey (MICS) 2014 Child Questionnaire Data for Punjab, Pakistan PakPMICS2014HH Multiple Indicator Cluster Survey (MICS) 2014 Household Questionnaire Data for Punjab, Pakistan PakPMICS2014HL Multiple Indicator Cluster Survey (MICS) 2014 Household Listing Questionnaire Data for Punjab, Pakistan PakPMICS2014Wm Multiple Indicator Cluster Survey (MICS) 2014 Women Questionnaire Data for Punjab, Pakistan PakPMICS2018 Multiple Indicator Cluster Survey (MICS) 2017-18 Data for Punjab, Pakistan PakPMICS2018bh Multiple Indicator Cluster Survey (MICS) 2017-18 Birth History of Children Questionnaire Data for Punjab, Pakistan PakPMICS2018fs Multiple Indicator Cluster Survey (MICS) 2017-18 Children Age 5-17 Questionnaire Data for Punjab, Pakistan PakPMICS2018hh Multiple Indicator Cluster Survey (MICS) 2017-18 Household Questionnaire Data for Punjab, Pakistan PakPMICS2018mm Multiple Indicator Cluster Survey (MICS) 2017-18 Maternal Mortality Questionnaire Data for Punjab, Pakistan PakPMICS2018mn Multiple Indicator Cluster Survey (MICS) 2017-18 Men Questionnaire Data for Punjab, Pakistan PamBinaries Read and Process 'Pamguard' Binary Data PanJen A Semi-Parametric Test for Specifying Functional Form PanelCount Random Effects and/or Sample Selection Models for Panel Count Data PanelMatch Matching Methods for Causal Inference with Time-Series Cross-Sectional Data PanelSelect Panel Sample Selection Models PanelTM Two- And Three-Way Dynamic Panel Threshold Regression Model for Change Point Detection PantaRhei Plots Sankey Diagrams ParCC Parameter Converter and Calculator for Health Technology Assessment ParDNAcopy Parallel implementation of the "segment" function of package "DNAcopy" ParallelLogger Support for Parallel Computation, Logging, and Function Automation ParallelTree Visualizing Multilevel Data with Parallel Tree Plots ParamANOVA Fully Parameterizable ANOVA Tests ParamHelpers Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning Pareto The Pareto, Piecewise Pareto and Generalized Pareto Distribution ParetoPosStable Computing, Fitting and Validating the PPS Distribution Paris2024Colours Color Palettes Inspired by Paris 2024 Olympic and Paralympic Games ParmOff Complex Argument Matching PartCensReg Estimation and Diagnostics for Partially Linear Censored Regression Models Based on Heavy-Tailed Distributions PartialNetwork Estimating Peer Effects Using Partial Network Data PartialTL Partial Transfer Learning for Causal Estimation Partiallyoverlapping Partially Overlapping Samples Tests Path.Analysis Path Coefficient Analysis PathwaySpace Spatial Projection of Network Signals along Geodesic Paths PathwayVote Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting PatientGenerator Generator of Synthetic Patient Data for the OMOP Common Data Model PatientLevelPrediction Develop Clinical Prediction Models Using the Common Data Model PatientProfiles Identify Characteristics of Patients in the OMOP Common Data Model Patterns Deciphering Biological Networks with Patterned Heterogeneous Measurements PeakError Compute the Label Error of Peak Calls PeakSegDP Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data PeakSegDisk Disk-Based Constrained Change-Point Detection PeakSegJoint Joint Peak Detection in Several ChIP-Seq Samples PeakSegOptimal Optimal Segmentation Subject to Up-Down Constraints PearsonDS Pearson Distribution System PearsonICA Independent Component Analysis using Score Functions from the Pearson System Pedixplorer Pedigree Functions PeerPerformance Luck-Corrected Peer Performance Analysis in R PenCoxFrail Regularization in Cox Frailty Models PenIC Semiparametric Regression Analysis of Interval-Censored Data using Penalized Splines PenguinR A Comprehensive Collection of Penguin Datasets for Statistical Analysis and Experimental Design PepMapViz A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration Peptides Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences PerFit Person Fit PerMat Performance Metrics in Predictive Modeling PerRegMod Fitting Periodic Coefficients Linear Regression Models Perc Using Percolation and Conductance to Find Information Flow Certainty in a Direct Network PerfMeas Performance Measures for Ranking and Classification Tasks PerformanceAnalytics Econometric Tools for Performance and Risk Analysis PeriodicTable Periodic Table of the Elements PermAlgo Permutational Algorithm to Simulate Survival Data PermCor Robust Permutation Tests of Correlation Coefficients PermutationR Conduct Permutation Analysis of Variance in R PersomicsArray Automated Persomics Array Image Extraction PeruAPIs Access Peruvian Data via Public APIs and Curated Datasets PesticideLoadIndicator Computes Danish Pesticide Load Indicator PhaseGMM Phase-Function Based Estimation and Inference for Linear Errors-in-Variables (EIV) Models PhaseType Inference for Phase-Type Distributions PhaseTypeR General-Purpose Phase-Type Functions PheCAP High-Throughput Phenotyping with EHR using a Common Automated Pipeline PheNorm Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data PheVis Automatic Phenotyping of Electronic Health Record at Visit Resolution PhenoSpectra Multispectral Data Analysis and Visualization Phenotype A Tool for Phenotypic Data Processing PhenotypeR Assess Study Cohorts Using a Common Data Model Phi2rho Owen's T Function and Bivariate Normal Integral PhilipsHue R Interface to the Philips Hue API PhoneValidator Client for 'GenderAPI.io' Phone Number Validation and Formatter API PhotoGEA Photosynthetic Gas Exchange Analysis PhotosynQ Connect to PhotosynQ PhySortR A Fast, Flexible Tool for Sorting Phylogenetic Trees PhylogeneticEM Automatic Shift Detection using a Phylogenetic EM PhysActBedRest Marks Periods of 'Bedrest' in Actigraph Accelerometer Data PhysicalActivity Process Accelerometer Data for Physical Activity Measurement PhysioIndexR Physiological and Stress Indices for Crop Evaluation PhytoIn Vegetation Analysis and Forest Inventory PhytosanitaryCalculator Phytosanitary Calculator for Inspection Plans Based on Risks PiC Interactive Processing and Segmentation of Forest TLS Point-Cloud Data PieGlyph Axis Invariant Scatter Pie Plots Pijavski Global Univariate Minimization Pinference Probability Inference for Propositional Logic PivotalP Prediction for Future Data from Mixture Distributions Gamma, Beta, Weibull and Normal PlackettLuce Plackett-Luce Models for Rankings Planesmuestra Functions for Calculating Dodge Romig, MIL STD 105E and MIL STD 414 Acceptance Sampling Plan PlanetNICFI Processing of the 'Planet NICFI' Satellite Imagery PlasmaMutationDetector Tumor Mutation Detection in Plasma PlateVision Automated qPCR Analysis and Visual Quality Control PlatformDesign Optimal Two-Period Multiarm Platform Design with New Experimental Arms Added During the Trial PlayerChart Generate Pizza Chart: Player Stats 0-100 PlayerRatings Dynamic Updating Methods for Player Ratings Estimation PlotBivInvGaus Density Contour Plot for Bivariate Inverse Gaussian Distribution PlotContour Plot Contour Line PlotFTIR Plot FTIR Spectra PlotNormTest Graphical Univariate/Multivariate Assessments for Normality Assumption PlotPrjNetworks Useful Networking Tools for Project Management PlotTools Extended Tools for Continuous Legends, Polygon Manipulation, and Visual Display of Categorical Data PnT Peak Finder PoDBAY Vaccine Efficacy Estimation Package PoPdesign Posterior Predictive (PoP) Design for Phase I Clinical Trials PoSI Valid Post-Selection Inference for Linear LS Regression PoSIAdjRSquared Post-Selection Inference for Adjusted R Squared PogromcyDanych DataCrunchers (PogromcyDanych) is the Massive Online Open Course that Brings R and Statistics to the People PoiClaClu Classification and Clustering of Sequencing Data Based on a Poisson Model PointFore Interpretation of Point Forecasts as State-Dependent Quantiles and Expectiles PointedSDMs Fit Models Derived from Point Processes to Species Distributions using 'inlabru' PoisBinNonNor Data Generation with Poisson, Binary and Continuous Components PoisBinOrd Data Generation with Poisson, Binary and Ordinal Components PoisBinOrdNonNor Generation of Up to Four Different Types of Variables PoisBinOrdNor Data Generation with Poisson, Binary, Ordinal and Normal Components PoisNonNor Simultaneous Generation of Count and Continuous Data PoisNor Simultaneous Generation of Multivariate Data with Poisson and Normal Marginals PoissonBinomial Efficient Computation of Ordinary and Generalised Poisson Binomial Distributions PoissonMultinomial The Poisson-Multinomial Distribution PoissonPCA Poisson-Noise Corrected PCA PolarCAP Access the Polarization in Comparative Attitudes Project PolicyPortfolios Tools for Managing, Measuring and Visualizing Policy Portfolios PolisheR Interfacing 'NaileR' with 'Shiny' Poly4AT Access 'INVEKOS' API for Field Polygons PolyHaplotyper Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids PolyMigR Analysis of Polyphenol Migration from Packaging Films PolyPatEx Paternity Exclusion in Autopolyploid Species PolyTree Estimate Causal Polytree from Data Polychrome Qualitative Palettes with Many Colors PolycrossDesigns Polycross Designs ("PolycrossDesigns") PolynomF Polynomials in R Pomic Pattern Oriented Modelling Information Criterion PoolBal Balancing Central and Marginal Rejection of Pooled p-Values PoolDilutionR Calculate Gross Biogeochemical Flux Rates from Isotope Pool Dilution Data PooledCohort Predicted Risk for CVD using Pooled Cohort Equations, PREVENT Equations, and Other Contemporary CVD Risk Calculators PooledMeanGroup Pooled Mean Group Estimation of Dynamic Heterogenous Panels PopComm Population-Level Cell-Cell Communication Analysis Tools PopED Population (and Individual) Optimal Experimental Design PopGenHelpR Streamline Population Genomic and Genetic Analyses PopGenReport A Simple Framework to Analyse Population and Landscape Genetic Data PopPsiSeqR Process and Visualize Evolve & Resequence Experiments PopVar Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation PopulateR Create Data Frames for the Micro-Simulation of Human Populations PopulationGrowthR Linear Population Growth Scenarios PortalHacienda Acceder Con R a Los Datos Del Portal De Hacienda PortfolioAnalytics Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios PortfolioOptim Small/Large Sample Portfolio Optimization PortfolioTesteR Test Investment Strategies with English-Like Code PosRatioDist Quotient of Random Variables Conditioned to the Positive Quadrant PosiR Post-Selection Inference via Simultaneous Confidence Intervals PostcodesioR API Wrapper Around 'Postcodes.io' PosteriorBootstrap Non-Parametric Sampling with Parallel Monte Carlo PottsUtils Utility Functions of the Potts Models PowRPriori Power Analysis via Data Simulation for (Generalized) Linear Mixed Effects Models PoweR Computation of Power and Level Tables for Hypothesis Tests PoweREST A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics Power2Stage Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies PowerSDI Calculate Standardised Drought Indices Using NASA POWER Data PowerTOST Power and Sample Size for (Bio)Equivalence Studies PrInDT Prediction and Interpretation in Decision Trees for Classification and Regression PracTools Designing and Weighting Survey Samples PracticalEquiDesign Design of Practical Equivalence Trials PreKnitPostHTMLRender Pre-Knitting Processing and Post HTML-Rendering Processing PreProcess Basic Functions for Pre-Processing Microarrays PreProcessRecordLinkage Preprocessing Record Linkage PreProcessing Various Preprocessing Transformations of Numeric Data Matrices PreciseSums Accurate Floating Point Sums and Products PredPsych Predictive Approaches in Psychology PredTest Preparing Data For, and Calculating the Prediction Test PredictABEL Assessment of Risk Prediction Models PredictionR Prediction for Future Data from any Continuous Distribution PredictorSelect Out-of-Sample Predictability in Predictive Regressions with Many Predictor Candidates PresenceAbsence Presence-Absence Model Evaluation PressPurt Indeterminacy of Networks via Press Perturbations PrettyCols Pretty Colour Palettes PriceIndices Calculating Bilateral and Multilateral Price Indexes PriorGen Generates Prior Distributions for Proportions PrivateLR Differentially Private Regularized Logistic Regression ProAE PRO-CTCAE Scoring, Analysis, and Graphical Tools ProActive Detect Elevations and Gaps in Mapped Sequencing Read Coverage ProDenICA Product Density Estimation for ICA using Tilted Gaussian Density Estimates ProFAST Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction ProPublicaR Access Functions for ProPublica's APIs ProSGPV Penalized Regression with Second-Generation P-Values ProSportsDraftData Professional Sports Draft Data ProTrackR Manipulate and Play 'ProTracker' Modules ProTrackR2 Manipulate and Play 'ProTracker' Modules ProbBayes Probability and Bayesian Modeling ProbBreed Probability Theory for Selecting Candidates in Plant Breeding ProbMarg Computing Logit & Probit Predicted Probabilities & Marginal Effects ProbSVMs Probabilistic Support Vector Machines ProbSamplingI Probabilistic Sampling Design and Strategies ProbYX Inference for the Stress-Strength Model R = P(Y