* using log directory ‘/tmp/dse.Rcheck’ * using R Under development (unstable) (2024-06-24 r86824) * using platform: x86_64-pc-linux-gnu * R was compiled by Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602) ifx (IFX) 2024.2.0 20240602 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘dse/DESCRIPTION’ ... OK * this is package ‘dse’ version ‘2020.2-1’ * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘dse’ can be installed ... [29s/29s] OK * used Fortran compiler: ‘ifx (IFX) 2024.2.0 20240602’ * checking package directory ... 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 pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE File ‘dse/libs/dse.so’: Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’ It is good practice to register native routines and to disable symbol search. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking usage of KIND in Fortran files ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘dse-Ex.R’ failed The error most likely occurred in: > ### Name: DSEversion > ### Title: Print Version Information > ### Aliases: DSEversion > ### Keywords: ts > > ### ** Examples > DSEversion() Error in is.R() : 'is.R' is defunct. See help("Defunct") Calls: DSEversion -> is.R -> .Defunct Execution halted * checking tests ... [153s/245s] ERROR Running ‘TSdataTests.R’ [152s/245s] Running the tests in ‘tests/TSdataTests.R’ failed. Complete output: > ############################################################### > > #### Test TSdata methods > > ############################################################### > > Sys.getenv("R_LIBS") [1] "/tmp/dse.Rcheck:/data/gannet/ripley/R/test-Intel:/data/gannet2/ripley/R/test-MKL:/data/gannet/ripley/R/test-dev:/data/gannet/ripley/R/test-BioCdata" > library() Packages in library '/tmp/dse.Rcheck': dse Dynamic Systems Estimation (Time Series Package) Packages in library '/data/gannet/ripley/R/test-Intel': rtkore 'STK++' Core Library Integration to 'R' using 'Rcpp' Packages in library '/data/gannet2/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 ADMMsigma Penalized Precision Matrix Estimation via ADMM 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 ANN2 Artificial Neural Networks for Anomaly Detection APIS Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents 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 ASMap Linkage Map Construction using the MSTmap Algorithm 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 AcceptReject Acceptance-Rejection Method for Generating Pseudo-Random Observations ActiSleep Sleep Duration Estimate Algorithm AdMit Adaptive Mixture of Student-t Distributions AdaptGauss Gaussian Mixture Models (GMM) 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 AnaCoDa Analysis of Codon Data under Stationarity using a Bayesian Framework AntMAN Anthology of Mixture Analysis Tools Anthropometry Statistical Methods for Anthropometric Data Apoderoides Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree Apollonius 2D Apollonius Graphs 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 BANOVA Hierarchical Bayesian ANOVA Models BART Bayesian Additive Regression Trees BAS Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling BBSSL Bayesian Bootstrap Spike-and-Slab LASSO 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 BCSub A Bayesian Semiparametric Factor Analysis Model for Subtype Identification (Clustering) BCT Bayesian Context Trees for Discrete Time Series BClustLonG A Dirichlet Process Mixture Model for Clustering Longitudinal Gene Expression Data BDgraph Bayesian Structure Learning in Graphical Models using Birth-Death MCMC 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 BIFIEsurvey Tools for Survey Statistics in Educational Assessment 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 BMisc Miscellaneous Functions for Panel Data, Quantiles, and Printing Results BNPmix Bayesian Nonparametric Mixture Models BNSL Bayesian Network Structure Learning BNSP Bayesian Non- And Semi-Parametric Model Fitting BOSSreg Best Orthogonalized Subset Selection (BOSS) BPrinStratTTE Causal Effects in Principal Strata Defined by Antidrug Antibodies BRISC Fast Inference for Large Spatial Datasets using BRISC BRL Beta Record Linkage BRugs Interface to the 'OpenBUGS' MCMC Software 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 BTLLasso Modelling Heterogeneity in Paired Comparison Data BTM Biterm Topic Models for Short Text BTSR Bounded Time Series Regression BTYDplus Probabilistic Models for Assessing and Predicting your Customer Base BTtest Estimate the Number of Factors in Large Nonstationary Datasets BVSNLP Bayesian Variable Selection in High Dimensional Settings using Nonlocal Priors 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 Bayesian Quantile Elastic Net for Genetic Study BayesComm Bayesian Community Ecology Analysis BayesDLMfMRI Statistical Analysis for Task-Based Fmri Data BayesESS Determining Effective Sample Size BayesFM Bayesian Inference for Factor Modeling BayesFactor Computation of Bayes Factors for Common Designs 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 BayesPPD Bayesian Power Prior Design BayesPPDSurv Bayesian Power Prior Design for Survival Data BayesProject Fast Projection Direction for Multivariate Changepoint Detection BayesRGMM Bayesian Robust Generalized Mixed Models for Longitudinal Data BayesReversePLLH Fits the Bayesian Piecewise Linear Log-Hazard Model BayesSUR Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings BayesSurvive Bayesian Survival Models for High-Dimensional Data 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 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 Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase 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 BigQuic Big Quadratic Inverse Covariance Estimation 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 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 Biostrings Efficient manipulation of biological strings BipartiteModularityMaximization Partition Bipartite Network into Non-Overlapping Biclusters by Optimizing Bipartite Modularity BivRec Bivariate Alternating Recurrent Event Data Analysis 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 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 CAMAN Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN 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 CASMAP Detection of Statistically Significant Combinations of SNPs in Association Mapping CB2 CRISPR Pooled Screen Analysis using Beta-Binomial Test CBnetworkMA Contrast-Based Bayesian Network Meta Analysis CCMMR Minimization of the Convex Clustering Loss Function 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 Tress 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 CKLRT Composite Kernel Machine Regression Based on Likelihood Ratio Test CKMRpop Forward-in-Time Simulation and Tallying of Pairwise Relationships 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 CNEr CNE Detection and Visualization COAP High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model COMIX Coarsened Mixtures of Hierarchical Skew Kernels COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression CORElearn Classification, Regression and Feature Evaluation CPAT Change Point Analysis Tests CPE Concordance Probability Estimates in Survival Analysis CPGLIB Competing Proximal Gradients Library CRF Conditional Random Fields CRM Continual Reassessment Method (CRM) for Phase I Clinical Trials CRTConjoint Conditional Randomization Testing (CRT) Approach for Conjoint Analysis CSTools Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales CUSUMdesign Compute Decision Interval and Average Run Length for CUSUM Charts CVR Canonical Variate Regression 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 ChannelAttribution Markov Model for Online Multi-Channel Attribution Chaos01 0-1 Test for Chaos ChemmineR Cheminformatics Toolkit for R CholWishart Cholesky Decomposition of the Wishart Distribution CircSpaceTime Spatial and Spatio-Temporal Bayesian Model for Circular Data CircularDDM Circular Drift-Diffusion Model CircularSilhouette Fast Silhouette on Circular or Linear Data Clusters Ckmeans.1d.dp Optimal, Fast, and Reproducible Univariate Clustering ClickClust Model-Based Clustering of Categorical Sequences 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 ClusVis Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering 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 CoOL Causes of Outcome Learning CohensdpLibrary Cohen's D_p Computation with Confidence Intervals 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 ConConPiWiFun Optimisation with Continuous Convex Piecewise (Linear and Quadratic) Functions 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 Corbi Collection of Rudimentary Bioinformatics Tools CorrBin Nonparametrics with Clustered Binary and Multinomial Data Countr Flexible Univariate Count Models Based on Renewal Processes CovCombR Combine Partial Covariance / Relationship Matrices CovRegRF Covariance Regression with Random Forests CovTools Statistical Tools for Covariance Analysis 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 DCCA Detrended Fluctuation and Detrended Cross-Correlation Analysis DCEM Clustering Big Data using Expectation Maximization Star (EM*) Algorithm DCLEAR Distance Based Cell Lineage Reconstruction DCSmooth Nonparametric Regression and Bandwidth Selection for Spatial Models 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 DESeq2 Differential gene expression analysis based on the negative binomial distribution DEoptim Global Optimization by Differential Evolution DGM Dynamic Graphical Models DGP4LCF Dependent Gaussian Processes for Longitudinal Correlated Factors 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 DMQ Dynamic Multiple Quantile (DMQ) 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 DREGAR Regularized Estimation of Dynamic Linear Regression in the Presence of Autocorrelated Residuals (DREGAR) DRIP Discontinuous Regression and Image Processing DSL Distributed Storage and List DSSP Implementation of the Direct Sampling Spatial Prior 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 DWreg Parametric Regression for Discrete Response DatAssim Data Assimilation 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 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) DetR Suite of Deterministic and Robust Algorithms for Linear Regression DiceDesign Designs of Computer Experiments DiceKriging Kriging Methods for Computer Experiments DiceOptim Kriging-Based Optimization for Computer Experiments DirStats Nonparametric Methods for Directional Data Dire Linear Regressions with a Latent Outcome Variable DirichletMultinomial Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data DirichletReg Dirichlet Regression DiscreteFDR Multiple Testing Procedures with Adaptation for Discrete Tests DistributionUtils Distribution Utilities DoEstRare Rare Variant Association Test Based on Position Density Estimation DoseFinding Planning and Analyzing Dose Finding Experiments DrImpute Imputing Dropout Events in Single-Cell RNA-Sequencing Data DriftBurstHypothesis Calculates the Test-Statistic for the Drift Burst Hypothesis DropletUtils Utilities for Handling Single-Cell Droplet Data DstarM Analyze Two Choice Reaction Time Data with the D*M Method DtD Distance to Default DySS Dynamic Screening Systems DynamicGP Modelling and Analysis of Dynamic Computer Experiments DysPIA Dysregulated Pathway Identification Analysis EAinference Estimator Augmentation and Simulation-Based Inference 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 EBglmnet Empirical Bayesian Lasso and Elastic Net Methods for Generalized Linear Models ECGofTestDx A Goodness-of-Fit Test for Elliptical Distributions with Diagnostic Capabilities ECOSolveR Embedded Conic Solver in R EDMeasure Energy-Based Dependence Measures 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 Evaluating Cardiac Electrophysiology Signals EL Two-Sample Empirical Likelihood ELYP Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model 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 EcoEnsemble A General Framework for Combining Ecosystem Models EcoNetGen Simulate and Sample from Ecological Interaction Networks EigenR Complex Matrix Algebra with 'Eigen' 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 EntropyEstimation Estimation of Entropy and Related Quantities EntropyMCMC MCMC Simulation and Convergence Evaluation using Entropy and Kullback-Leibler Divergence Estimation 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 EpiILMCT Continuous Time Distance-Based 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 Equalden.HD Testing the Equality of a High Dimensional Set of Densities EstMix Tumor Clones Percentage Estimations EthSEQ Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data Euclimatch Euclidean Climatch Algorithm ExactMultinom Multinomial Goodness-of-Fit Tests 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 FBCRM Phase I Optimal Dose Assignment using the FBCRM and MFBCRM Methods 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 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 FIT Transcriptomic Dynamics Models in Field Conditions FKF Fast Kalman Filter FKF.SP Fast Kalman Filtering Through Sequential Processing FKSUM Fast Kernel Sums FLLat Fused Lasso Latent Feature Model FLOPART Functional Labeled Optimal Partitioning FLORAL Fit Log-Ratio Lasso Regression for Compositional Data FLSSS Mining Rigs for Problems in the Subset Sum Family FMCCSD Efficient Estimation of Clustered Current Status Data 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 FORTLS Automatic Processing of Terrestrial-Based Technologies Point Cloud Data for Forestry Purposes FRESA.CAD Feature Selection Algorithms for Computer Aided Diagnosis FRESHD Fast Robust Estimation of Signals in Heterogeneous Data FRK Fixed Rank Kriging FSInteract Fast Searches for Interactions 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 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 Familias Probabilities for Pedigrees Given DNA Data FamilyRank Algorithm for Ranking Predictors Using Graphical Domain Knowledge FarmSelect Factor Adjusted Robust Model Selection FarmTest Factor-Adjusted Robust Multiple Testing 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 FastJM Semi-Parametric Joint Modeling of Longitudinal and Survival Data 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 FastSF Fast Structural Filtering FaultTree Fault Trees for Risk and Reliability Analysis FeatureHashing Creates a Model Matrix via Feature Hashing with a Formula Interface FiRE Finder of Rare Entities (FiRE) FisPro Fuzzy Inference System Design and Optimization 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 GAS Generalized Autoregressive Score Models GBJ Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies 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) 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 GGMselect Gaussian Graphs Models Selection 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 GLIDE Global and Individual Tests for Direct Effects GLMaSPU An Adaptive Test on High Dimensional Parameters in Generalized Linear Models GLMcat Generalized Linear Models for Categorical Responses GMCM Fast Estimation of Gaussian Mixture Copula Models GMKMcharlie Unsupervised Gaussian Mixture and Minkowski and Spherical K-Means with Constraints GMMAT Generalized Linear Mixed Model Association Tests GMSE Generalised Management Strategy Evaluation Simulator GNE Computation of Generalized Nash Equilibria GOSemSim GO-terms Semantic Similarity Measures GPBayes Tools for Gaussian Process Modeling in Uncertainty Quantification GPCERF Gaussian Processes for Estimating Causal Exposure Response Curves GPCMlasso Differential Item Functioning in Generalized Partial Credit Models GPFDA Gaussian Process for Functional Data Analysis GPGame Solving Complex Game Problems using Gaussian Processes GPM Gaussian Process Modeling of Multi-Response and Possibly Noisy Datasets GPareto Gaussian Processes for Pareto Front Estimation and Optimization GPvam Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling GPvecchia Scalable Gaussian-Process Approximations 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 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 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 GeneralizedWendland Fully Parameterized Generalized Wendland Covariance Function GeneticsPed Pedigree and genetic relationship functions GenomeAdmixR Simulate Admixture of Genomes GenomicAlignments Representation and manipulation of short genomic alignments GenomicRanges Representation and manipulation of genomic intervals GeoAdjust Accounting for Random Displacements of True GPS Coordinates of Data 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 GofKmt Khmaladze Martingale Transformation Goodness-of-Fit Test GpGp Fast Gaussian Process Computation Using Vecchia's Approximation GreedyEPL Greedy Expected Posterior Loss GreedyExperimentalDesign Greedy Experimental Design Construction GridOnClusters Cluster-Preserving Multivariate Joint Grid Discretization GxEScanR Run GWAS/GWEIS Scans Using Binary Dosage Files HACSim Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment HBV.IANIGLA Modular Hydrological Model HDCD High-Dimensional Changepoint Detection HDCurves Hierarchical Derivative Curve Estimation HDDesign Sample Size Calculation for High Dimensional Classification Study HDF5Array HDF5 backend for DelayedArray objects HDGLM Tests for High Dimensional Generalized Linear Models HDJM Penalized High-Dimensional Joint Model 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 HEMDAG Hierarchical Ensemble Methods for Directed Acyclic Graphs HKprocess Hurst-Kolmogorov Process HLMdiag Diagnostic Tools for Hierarchical (Multilevel) Linear Models HMB Hierarchical Model-Based Estimation Approach HMMEsolver A Fast Solver for Henderson Mixed Model Equation via Row Operations HMMextra0s Hidden Markov Models with Extra Zeros HMMmlselect Determine the Number of States in Hidden Markov Models via Marginal Likelihood HSMMSingleCell Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) HTLR Bayesian Logistic Regression with Heavy-Tailed Priors HTT Hypothesis Testing Tree HUM Compute HUM Value and Visualize ROC Curves Haplin Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes HardyWeinberg Statistical Tests and Graphics for Hardy-Weinberg Equilibrium HellCor The Hellinger Correlation HiCDOC A/B compartment detection and differential analysis HiClimR Hierarchical Climate Regionalization HiDimDA High Dimensional Discriminant Analysis 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 IBDsim Simulation of Chromosomal Regions Shared by Family Members IBMPopSim Individual Based Model Population Simulation ICAOD Optimal Designs for Nonlinear Statistical Models by Imperialist Competitive Algorithm (ICA) ICRanks Simultaneous Confidence Intervals for Ranks 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)' IFC Tools for Imaging Flow Cytometry IFP Identifying Functional Polymorphisms IHSEP Inhomogeneous Self-Exciting Process ILSE Linear Regression Based on 'ILSE' for Missing Data INLAspacetime Spatial and Spatio-Temporal Models using 'INLA' INSPIRE Inferring Shared Modules from Multiple Gene Expression Datasets with Partially Overlapping Gene Sets IOHanalyzer Data Analysis Part of 'IOHprofiler' IOHexperimenter Benchmarking Part of the 'IOHprofiler' IP Classes and Methods for 'IP' Addresses IRISSeismic Classes and Methods for Seismic Data Analysis IRanges Foundation of integer range manipulation in Bioconductor IRon Solving Imbalanced Regression Tasks ISOpureR Deconvolution of Tumour Profiles Immigrate Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection 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 IntegratedMRF Integrated Prediction using Uni-Variate and Multivariate Random Forests 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 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 JOUSBoost Implements Under/Oversampling for Probability Estimation JSM Semiparametric Joint Modeling of Survival and Longitudinal Data JUMP Replicability Analysis of High-Throughput Experiments JacobiEigen Classical Jacobi Eigenvalue Algorithm JavaGD Java Graphics Device JuliaCall Seamless Integration Between R and 'Julia' KERE Expectile Regression in Reproducing Kernel Hilbert Space 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 Kendall Kendall Rank Correlation and Mann-Kendall Trend Test KernSmoothIRT Nonparametric Item Response Theory KernelKnn Kernel k Nearest Neighbors Kira Machine Learning KoulMde Koul's Minimum Distance Estimation in Regression and Image Segmentation Problems L0Learn Fast Algorithms for Best Subset Selection 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 LDAandLDAS Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS) LMMsolver Linear Mixed Model Solver LMN Inference for Linear Models with Nuisance Parameters LMest Generalized Latent Markov Models LOMAR Localization Microscopy Data Analysis LOPART Labeled Optimal Partitioning LPWC Lag Penalized Weighted Correlation for Time Series Clustering LRcontrast Dose Response Signal Detection under Model Uncertainty LS2W Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme LTFHPlus Implementation of LT-FH++ LTRCforests Ensemble Methods for Survival Data with Time-Varying Covariates LWFBrook90R Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90 LaF Fast Access to Large ASCII Files LaMa Fast Numerical Maximum Likelihood Estimation for Latent Markov Models 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 LassoBacktracking Modelling Interactions in High-Dimensional Data with Backtracking LassoGEE High-Dimensional Lasso Generalized Estimating Equations 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 LearningRlab Statistical Learning Functions LibOPF Design of Optimum-Path Forest Classifiers LiblineaR Linear Predictive Models Based on the LIBLINEAR C/C++ Library Libra Linearized Bregman Algorithms for Generalized Linear Models LikertMakeR Synthesise and Correlate Rating-Scale Data Linnorm Linear model and normality based normalization and transformation method (Linnorm) 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 LongMemoryTS Long Memory Time Series LorenzRegression Lorenz and Penalized Lorenz Regressions LowRankQP Low Rank Quadratic Programming LowWAFOMNX Low WAFOM Niederreiter-Xing Sequence LowWAFOMSobol Low WAFOM Sobol Sequence Luminescence Comprehensive Luminescence Dating Data Analysis MABOUST Multi-Armed Bayesian Ordinal Utility-Based Sequential Trial 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 MAPITR MArginal ePIstasis Test for Regions MAT Multidimensional Adaptive Testing 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 MBSP Multivariate Bayesian Model with Shrinkage Priors MCARtest Optimal Nonparametric Testing of Missing Completely at Random MCMCglmm MCMC Generalised Linear Mixed Models 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 MDEI Implementing the Method of Direct Estimation and Inference MDFS MultiDimensional Feature Selection MEGENA Multiscale Clustering of Geometrical Network MESS Miscellaneous Esoteric Statistical Scripts MFPCA Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains 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' MLEcens Computation of the MLE for Bivariate Interval Censored Data MLModelSelection Model Selection in Multivariate Longitudinal Data Analysis MLZ Mean Length-Based Estimators of Mortality using TMB MM4LMM Inference of Linear Mixed Models Through MM Algorithm MMVBVS Missing Multivariate Bayesian Variable Selection MNARclust Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models MNP Fitting the Multinomial Probit Model MOLHD Multiple Objective Latin Hypercube Design MPBoost Treatment Allocation in Clinical Trials by the Maximal Procedure MPCR Multi- And Mixed-Precision Computations MPSEM Modeling Phylogenetic Signals using Eigenvector Maps MPTinR Analyze Multinomial Processing Tree Models MR.RGM Multivariate Bidirectional Mendelian Randomization Networks MRCE Multivariate Regression with Covariance Estimation MRS Multi-Resolution Scanning for Cross-Sample Differences 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 MSTest Hypothesis Testing for Markov Switching Models MSclassifR Automated Classification of Mass Spectra MSmix Finite Mixtures of Mallows Models with Spearman Distance for Full and Partial Rankings 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 MassSpecWavelet Peak Detection for Mass Spectrometry data using wavelet-based algorithms 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 MatrixLDA Penalized Matrix-Normal Linear Discriminant Analysis MaxPro Maximum Projection Designs MazamaRollUtils Efficient Rolling Functions MediaK Calculate MeDiA_K Distance MedianaDesigner Power and Sample Size Calculations for Clinical Trials Mega2R Accessing and Processing a 'Mega2' Genetic Database MendelianRandomization Mendelian Randomization Package MetaHD A Multivariate Meta-Analysis Model for Metabolomics Data MetaSKAT Meta Analysis for SNP-Set (Sequence) Kernel Association Test MetaboCoreUtils Core Utils for Metabolomics Data MetricGraph Random Fields on Metric Graphs Mhorseshoe Approximate Algorithm for Horseshoe Prior MiSPU Microbiome Based Sum of Powered Score (MiSPU) Tests MicroMoB Discrete Time Simulation of Mosquito-Borne Pathogen Transmission MicrobiomeStat Statistical Methods for Microbiome Compositional Data MissCP Change Point Detection with Missing Values MixAll Clustering and Classification using Model-Based Mixture Models 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 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 MonetDB.R Connect MonetDB to R MonoPoly Functions to Fit Monotone Polynomials Morpho Calculations and Visualisations Related to Geometric Morphometrics MortCast Estimation and Projection of Age-Specific Mortality Rates MsExperiment Infrastructure for Mass Spectrometry Experiments MsFeatures Functionality for Mass Spectrometry Features MuChPoint Multiple Change Point 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 MultiscaleDTM Multi-Scale Geomorphometric Terrain Attributes MultivariateRandomForest Models Multivariate Cases Using Random Forests NAIR Network Analysis of Immune Repertoire 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 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 NVCSSL Nonparametric Varying Coefficient Spike-and-Slab Lasso NestMRMC Single Reader Between-Cases AUC Estimator in Nested Data NestedCategBayesImpute Modeling, Imputing and Generating Synthetic Versions of Nested Categorical Data in the Presence of Impossible Combinations NetDA Network-Based Discriminant Analysis Subject to Multi-Label Classes NetFACS Network Applications to Facial Communication Data NetMix Dynamic Mixed-Membership Network Regression Model NetPreProc Network Pre-Processing and Normalization NetRep Permutation Testing Network Module Preservation Across Datasets 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 NormPsy Normalisation of Psychometric Tests Numero Statistical Framework to Define Subgroups in Complex Datasets OCNet Optimal Channel Networks ODRF Oblique Decision Random Forest for Classification and 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 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. Orcs Omnidirectional R Code Snippets OwenQ Owen Q-Function PAC Partition-Assisted Clustering and Multiple Alignments of Networks PAFit Generative Mechanism Estimation in Temporal Complex Networks PAGFL Joint Estimation of Latent Groups and Group-Specific Coefficients in Panel Data Models PANACEA Personalized Network-Based Anti-Cancer Therapy Evaluation PANPRSnext Building PRS Models Based on Summary Statistics of GWAs PAsso Assessing the Partial Association Between Ordinal Variables 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 PCICt Implementation of POSIXct Work-Alike for 365 and 360 Day Calendars 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 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 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 PLMIX Bayesian Analysis of Finite Mixtures of Plackett-Luce Models for Partial Rankings/Orderings PLNmodels Poisson Lognormal Models PLSiMCpp Methods for Partial Linear Single Index Model PLordprob Multivariate Ordered Probit Model via Pairwise Likelihood 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) POSetR Partially Ordered Sets in R POT Generalized Pareto Distribution and Peaks Over Threshold POUMM The Phylogenetic Ornstein-Uhlenbeck Mixed Model 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 PPtreeViz Projection Pursuit Classification Tree Visualization PPtreeregViz Projection Pursuit Regression Tree Visualization PQLseq Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies PRDA Conduct a Prospective or Retrospective Design Analysis PRECAST Embedding and Clustering with Alignment for Spatial Datasets PRIMAL Parametric Simplex Method for Sparse Learning PRIMEplus Study Design for Immunotherapy Clinical Trials PRIMME Eigenvalues and Singular Values and Vectors from Large Matrices PROJ Generic Coordinate System Transformations Using 'PROJ' PROsetta Linking Patient-Reported Outcomes Measures PRSPGx Construct PGx PRS PRSim Stochastic Simulation of Streamflow Time Series using Phase Randomization PRTree Probabilistic Regression Trees PReMiuM Dirichlet Process Bayesian Clustering, Profile Regression PSGD Projected Subset Gradient Descent PSMatch Handling and Managing Peptide Spectrum Matches PSPManalysis Analysis of Physiologically Structured Population Models PTSR Positive Time Series Regression 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 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 Phase123 Simulating and Conducting Phase 123 Trials Phase12Compare Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes PhaseType Inference for Phase-Type Distributions PheVis Automatic Phenotyping of Electronic Health Record at Visit Resolution PhenotypeSimulator Flexible Phenotype Simulation from Different Genetic and Noise Models PhylogeneticEM Automatic Shift Detection using a Phylogenetic EM PieceExpIntensity Bayesian Model to Find Changepoints Based on Rates and Count Data Pijavski Global Univariate Minimization PlayerRatings Dynamic Updating Methods for Player Ratings Estimation PoDBAY Vaccine Efficacy Estimation Package PoissonBinomial Efficient Computation of Ordinary and Generalized 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 PreciseSums Accurate Floating Point Sums and Products ProFAST Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction ProbBreed Probability Theory for Selecting Candidates in Plant Breeding ProbitSpatial Probit with Spatial Dependence, SAR, SEM and SARAR Models ProcData Process Data Analysis ProjectionBasedClustering Projection Based Clustering PropClust Propensity Clustering and Decomposition Pursuit Projection Pursuit PwrGSD Power in a Group Sequential Design QCA Qualitative Comparative Analysis QCApro Advanced Functionality for Performing and Evaluating Qualitative Comparative Analysis QF Density, Cumulative and Quantile Functions of Quadratic Forms QFASA Quantitative Fatty Acid Signature Analysis QFeatures Quantitative features for mass spectrometry data 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 QWDAP Quantum Walk-Based Data Analysis and Prediction QZ Generalized Eigenvalues and QZ Decomposition Qest Quantile-Based Estimator QregBB Block Bootstrap Methods for Quantile Regression in Time Series Qtools Utilities for Quantiles QuadratiK Collection of Methods Constructed using Kernel-Based Quadratic Distances QuantRegGLasso Adaptively Weighted Group Lasso for Semiparametric Quantile Regression Models Quartet Comparison of Phylogenetic Trees Using Quartet and Split Measures QuickJSR Interface for the 'QuickJS' Lightweight 'JavaScript' Engine QurvE Robust and User-Friendly Analysis of Growth and Fluorescence Curves R2BayesX Estimate Structured Additive Regression Models with 'BayesX' R2SWF Convert R Graphics to Flash Animations R2sample Two Sample Problem Routines using Permutation 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 RCDT Fast 2D Constrained Delaunay Triangulation RCSF Airborne LiDAR Filtering Method Based on Cloth Simulation 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 RFCCA Random Forest with Canonical Correlation Analysis RFpredInterval Prediction Intervals with Random Forests and Boosted Forests 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 R 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, JavaScript Object Notation RJafroc Artificial Intelligence Systems and Observer Performance RJcluster A Fast Clustering Algorithm for High Dimensional Data Based on the Gram Matrix Decomposition RKHSMetaMod Ridge Group Sparse Optimization Problem for Estimation of a Meta Model Based on Reproducing Kernel Hilbert Spaces 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 RMKdiscrete Sundry Discrete Probability Distributions RMM Revenue Management Modeling RMPSH Recursive Modified Pattern Search on Hyper-Rectangle 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 ROTS Reproducibility-Optimized Test Statistic ROptSpace Matrix Reconstruction from a Few Entries RPANDA Phylogenetic ANalyses of DiversificAtion RPEGLMEN Gamma and Exponential Generalized Linear Models with Elastic Net Penalty 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 RSGHB Functions for Hierarchical Bayesian Estimation: A Flexible Approach RSKC Robust Sparse K-Means RSNNS Neural Networks using the Stuttgart Neural Network Simulator (SNNS) RSQLite SQLite Interface for R RSSL Implementations of Semi-Supervised Learning Approaches for Classification 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' 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 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' RaschSampler Rasch Sampler RationalMatrix Exact Matrix Algebra for Rational Matrices 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 RcppAPT 'Rcpp' Interface to the APT Package Manager 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 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') RcppCensSpatial Spatial Estimation and Prediction for Censored/Missing Responses RcppClassic Deprecated 'classic' 'Rcpp' 'API' RcppClassicExamples Examples using 'RcppClassic' to Interface R and C++ RcppClock Seamless 'Rcpp' Benchmarking RcppColors Color Mappings and 'C++' Header Files for Color Conversion RcppDE Global Optimization by Differential Evolution in C++ 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 RcppLbfgsBlaze 'L-BFGS' Algorithm Based on 'Blaze' for 'R' and 'Rcpp' RcppML Rcpp Machine Learning Library 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' 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 RcppStreams 'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream Processing 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++ 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" 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 Relatedness Maximum Likelihood Estimation of Relatedness using EM Algorithm ResidualMatrix Creating a DelayedMatrix of Regression Residuals RespirAnalyzer Analysis Functions of Respiratory Data RestRserve A Framework for Building HTTP API Rexperigen R Interface to Experigen 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 Rfssa Functional Singular Spectrum Analysis Rgb The R Genome Browser Rglpk R/GNU Linear Programming Kit Interface Rgof 1d Goodness of Fit Tests Rgraphviz Provides plotting capabilities for R graph objects Rhdf5lib hdf5 library as an R package 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 An 'Rcpp' Interface for Eunjeon Project Rmixmod Classification with Mixture Modelling Rmodule Automated Markov Chain Monte Carlo for Arbitrarily Structured Correlation Matrices Rmpfr R 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 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 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 Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import Rserve Binary R server Rsomoclu Somoclu Rssa A Collection of Methods for Singular Spectrum Analysis Rsymphony SYMPHONY in R Rtsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation Rttf2pt1 'ttf2pt1' Program Rtwobitlib '2bit' 'C' Library Runuran R Interface to the 'UNU.RAN' Random Variate Generators Rvcg Manipulations of Triangular Meshes Based on the 'VCGLIB' API Rwave Time-Frequency Analysis of 1-D Signals Rwofost WOFOST Crop Growth Simulation Model Ryacas R Interface to the 'Yacas' Computer Algebra System Ryacas0 Legacy 'Ryacas' (Interface to '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 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 SBCK Statistical Bias Correction Kit SBmedian Scalable Bayes with Median of Subset Posteriors SC.MEB Spatial Clustering with Hidden Markov Random Field using Empirical Bayes SCCI Stochastic Complexity-Based Conditional Independence Test for Discrete Data 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 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 SFS Similarity-First Search Seriation Algorithm SFSI Sparse Family and Selection Index 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 SIPmg Statistical Analysis to Identify Isotope Incorporating MAGs SIRmcmc Compartmental Susceptible-Infectious-Recovered (SIR) Model of Community and Household Infection 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 SLHD Maximin-Distance (Sliced) Latin Hypercube Designs SLOPE Sorted L1 Penalized Estimation SMITIDvisu Visualize Data for Host and Viral Population from 'SMITIDstruct' using 'HTMLwidgets' SMMA Soft Maximin Estimation for Large Scale Array-Tensor Models SMME Soft Maximin Estimation for Large Scale Heterogeneous Data 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 SNPknock Knockoffs for Hidden Markov Models and Genetic Data SNSeg Self-Normalization(SN) Based Change-Point Estimation for Time Series SPARSEMODr SPAtial Resolution-SEnsitive Models of Outbreak Dynamics SPAS Stratified-Petersen Analysis System SPECIES Statistical Package for Species Richness Estimation SPSP Selection by Partitioning the Solution Paths SPlit Split a Dataset for Training and Testing SSGL Spike-and-Slab Group Lasso for Group-Regularized Generalized Linear Models SSLASSO The Spike-and-Slab LASSO SSLR Semi-Supervised Classification, Regression and Clustering Methods 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 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 SemiCompRisks Hierarchical Models for Parametric and Semi-Parametric Analyses of Semi-Competing Risks Data SenSpe Estimating Specificity at Controlled Sensitivity, or Vice Versa SeqArray Data Management of Large-Scale Whole-Genome Sequence Variant Calls SeqDetect Sequence and Latent Process Detector SeqKat Detection of Kataegis SeqNet Generate RNA-Seq Data from Gene-Gene Association Networks 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 SheetReader Parse xlsx Files ShiftConvolvePoibin Exactly Computing the Tail of the Poisson-Binomial Distribution ShortRead FASTQ input and manipulation ShrinkCovMat Shrinkage Covariance Matrix Estimators SiMRiv Simulating Multistate Movements in River/Heterogeneous Landscapes SiPhyNetwork A Phylogenetic Simulator for Reticulate Evolution Sieve Nonparametric Estimation by the Method of Sieves SigTree Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree Signac Analysis of Single-Cell Chromatin Data Sim.DiffProc Simulation of Diffusion Processes 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 SimSurvNMarker Simulate Survival Time and Markers SingleR Reference-Based Single-Cell RNA-Seq Annotation SmartSVA Fast and Robust Surrogate Variable Analysis SmoothHazard Estimation of Smooth Hazard Models for Interval-Censored Data SnowballC Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library SobolSequence Sobol Sequences with Better Two-Dimensional Projections 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 SpaCOAP High-Dimensional Spatial Covariate-Augmented Overdispersed Poisson Factor Model SpaDES.tools Additional Tools for Developing Spatially Explicit Discrete Event Simulation (SpaDES) Models 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 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 SpatialKDE Kernel Density Estimation for Spatial Data SpatialKWD Spatial KWD for Large Spatial Maps 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 SplitSoftening Softening Splits in Decision Trees Sshaped Nonparametric, Tuning-Free Estimation of S-Shaped Functions StMoSim Quantile-Quantile Plot with Several Gaussian Simulations StanHeaders C++ Header Files for Stan StempCens Spatio-Temporal Estimation and Prediction for Censored/Missing Responses StepSignalMargiLike Step-Wise Signal Extraction via Marginal Likelihood 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 StrainRanking Ranking of Pathogen Strains StrathE2E2 End-to-End Marine Food Web Model StrucDiv Spatial Structural Diversity Quantification in Raster Data SubTS Positive Tempered Stable Distributions and Related Subordinators SubTite Subgroup Specific Optimal Dose Assignment SummaryLasso Building Polygenic Risk Score Using GWAS Summary Statistics 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 SurrogateBMA Flexible Evaluation of Surrogate Markers with Bayesian Model Averaging 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 Unrooted 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 TESS Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events TFBSTools Software Package for Transcription Factor Binding Site (TFBS) Analysis 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 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' TP.idm Estimation of Transition Probabilities for the Illness-Death Model 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 TSP Traveling Salesperson Problem (TSP) TSSS Time Series Analysis with State Space Model TSdist Distance Measures for Time Series Data TSrepr Time Series Representations TTR Technical Trading Rules 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' TensorClustering Model-Based Tensor Clustering 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 TransPhylo Inference of Transmission Tree from a Dated Phylogeny 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 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 TukeyRegion Tukey Region and Median TunePareto Multi-Objective Parameter Tuning for Classifiers TwoPhaseInd Estimate Gene-Treatment Interaction Exploiting Randomization UBL An Implementation of Re-Sampling Approaches to Utility-Based Learning for Both Classification and Regression Tasks UComp Automatic Unobserved Components and Other Time Series Models UPCM Uncertainty in Partial Credit Models Umatrix Visualization of Structures in High-Dimensional Data UniExactFunTest Uniform Exact Functional Tests for Contingency Tables UniIsoRegression Unimodal and Isotonic L1, L2 and Linf Regression UtilityFrailtyPH12 Implementing EFF-TOX and Monotone Utility Based Phase 12 Trials V8 Embedded JavaScript and WebAssembly Engine for R VAJointSurv Variational Approximation for Joint Survival and Marker Models VARDetect Multiple Change Point Detection in Structural VAR Models VARSELECTEXPOSURE Variable Selection Methods Including an Exposure Variable VBJM Variational Inference for Joint Model 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 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 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 VUROCS Volume under the ROC Surface for Multi-Class ROC Analysis VarSelLCM Variable Selection for Model-Based Clustering of Mixed-Type Data Set with Missing Values VariantAnnotation Annotation of Genetic Variants Vdgraph Variance Dispersion Graphs and Fraction of Design Space Plots for Response Surface Designs VeccTMVN Multivariate Normal Probabilities using Vecchia Approximation VeryLargeIntegers Store and Operate with Arbitrarily Large Integers VineCopula Statistical Inference of Vine Copulas WGCNA Weighted Correlation Network Analysis WLreg Regression Analysis Based on Win Loss Endpoints WPKDE Weighted Piecewise Kernel Density Estimation WRI Wasserstein Regression and Inference WRS2 A Collection of Robust Statistical Methods WaveSampling Weakly Associated Vectors (WAVE) Sampling 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 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 WpProj Linear p-Wasserstein Projections XBRL Extraction of Business Financial Information from 'XBRL' Documents XML Tools for Parsing and Generating XML Within R and S-Plus XNomial Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities XVector Foundation of external vector representation and manipulation in Bioconductor 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 aRtsy Generative Art with 'ggplot2' abclass Angle-Based Large-Margin Classifiers abcrf Approximate Bayesian Computation via Random Forests abctools Tools for ABC Analyses 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 accelerometry Functions for Processing Accelerometer Data acebayes Optimal Bayesian Experimental Design using the ACE Algorithm acepack ACE and AVAS for Selecting Multiple Regression Transformations activegp Gaussian Process Based Design and Analysis for the Active Subspace Method actuar Actuarial Functions and Heavy Tailed Distributions adaHuber Adaptive Huber Estimation and Regression adaR A Fast 'WHATWG' Compliant URL Parser 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 A Fast and Flexible Group Elastic Net Solver adephylo Exploratory Analyses for the Phylogenetic Comparative Method adespatial Multivariate Multiscale Spatial Analysis adestr Estimation in Optimal Adaptive Two-Stage Designs adheRenceRX Assess Medication Adherence from Pharmaceutical Claims Data adimpro Adaptive Smoothing of Digital Images adjSURVCI Parameter and Adjusted Probability Estimation for Right-Censored Data adjclust Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix adlift An Adaptive Lifting Scheme Algorithm admisc Adrian Dusa's Miscellaneous admix Package Admix for Admixture (aka Contamination) Models 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 aftgee Accelerated Failure Time Model with Generalized Estimating Equations afttest Model Diagnostics for Accelerated Failure Time Models agcounts Calculate 'ActiGraph' Counts from Accelerometer Data ageutils Collection of Functions for Working with Age Intervals agop Aggregation Operators and Preordered Sets agtboost Adaptive and Automatic Gradient Boosting Computations ahMLE Methods for the Additive Hazard Model ahaz Regularization for Semiparametric Additive Hazards Regression ahw Calculates Continuous Time Likelihood Ratio Weights Assuming Multiplicative Intensity Models and Additive Hazard Models 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 amap Another Multidimensional Analysis Package ambient A Generator of Multidimensional Noise ambit Simulation and Estimation of Ambit Processes ampir Predict Antimicrobial Peptides anMC Compute High Dimensional Orthant Probabilities anacor Simple and Canonical Correspondence Analysis analogue Analogue and Weighted Averaging Methods for Palaeoecology aniSNA Statistical Network Analysis of Animal Social Networks anomaly Detecting Anomalies in Data 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 apeglm Approximate posterior estimation for GLM coefficients 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' arcgisutils ArcGIS Utility Functions archive Multi-Format Archive and Compression Support 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 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 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 aspect A General Framework for Multivariate Analysis with Optimal Scaling 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 astrochron A Computational Tool for Astrochronology 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 autoRasch Semi-Automated Rasch Analysis autothresholdr An R Port of the 'ImageJ' Plugin 'Auto Threshold' av Working with Audio and Video in R avar Allan Variance aws Adaptive Weights Smoothing awsMethods Class and Methods Definitions for Packages 'aws', 'adimpro', 'fmri', 'dwi' b64 Fast and Vectorized Base 64 Engine bWGR Bayesian Whole-Genome Regression babelmixr2 Use 'nlmixr2' to Interact with Open Source and Commercial Software backShift Learning Causal Cyclic Graphs from Unknown Shift Interventions backbone Extracts the Backbone from Graphs backports Reimplementations of Functions Introduced Since R-3.0.0 baggr Bayesian Aggregate Treatment Effects bain Bayes Factors for Informative Hypotheses bakR Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets baldur Bayesian Hierarchical Modeling for Label-Free Proteomics 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 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 basilisk Freezing Python Dependencies Inside Bioconductor Packages basilisk.utils Basilisk Installation Utilities 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 bayesAB Fast Bayesian Methods for AB Testing 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 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 bayescopulareg Bayesian Copula Regression bayescount Power Calculations and Bayesian Analysis of Count Distributions and FECRT Data using MCMC bayesforecast Bayesian Time Series Modeling with Stan bayesianETAS Bayesian Estimation of the ETAS Model for Earthquake Occurrences bayesianVARs MCMC Estimation of Bayesian Vectorautoregressions 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 bbdetection Identification of Bull and Bear States of the Market 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 bcgam Bayesian Constrained Generalised Linear Models bcpa Behavioral Change Point Analysis of Animal Movement bcrypt 'Blowfish' Password Hashing Algorithm bcv Cross-Validation for the SVD (Bi-Cross-Validation) bda Binned Data Analysis bdsmatrix Routines for Block Diagonal Symmetric Matrices beachmat Compiling Bioconductor to Handle Each Matrix Type beadarray Quality assessment and low-level analysis for Illumina BeadArray data beeswarm The Bee Swarm Plot, an Alternative to Stripchart belg Boltzmann Entropy of a Landscape Gradient bench High Precision Timing of R Expressions benchr High Precise Measurement of R Expressions Execution Time bennu Bayesian Estimation of Naloxone Kit Number Under-Reporting bespatial Boltzmann Entropy for Spatial Data bestglm Best Subset GLM and Regression Utilities bestridge A Comprehensive R Package for Best Subset Selection betaBayes Bayesian Beta Regression betaclust A Family of Beta Mixture Models for Clustering Beta-Valued DNA Methylation Data 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 bhpm Bayesian Hierarchical Poisson Models for Multiple Grouped Outcomes with Clustering biClassify Binary Classification Using Extensions of Discriminant Analysis biclust BiCluster Algorithms bife Binary Choice Models with Fixed Effects bigGP Distributed Gaussian Process Calculations bigMap Big Data Mapping 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 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 binGroup2 Identification and Estimation using Group Testing binaryGP Fit and Predict a Gaussian Process Model with (Time-Series) Binary Response binaryMM Flexible Marginalized Models for Binary Correlated Outcomes 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 bioPN Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets bioacoustics Analyse Audio Recordings and Automatically Extract Animal Vocalizations bioimagetools Tools for Microscopy Imaging biomartr Genomic Data Retrieval bioregion Comparison of Bioregionalisation 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 birdie Bayesian Instrumental Regression for Disparity Estimation bisque Approximate Bayesian Inference via Sparse Grid Quadrature Evaluation (BISQuE) for Hierarchical Models bit Classes and Methods for Fast Memory-Efficient Boolean Selections bit64 A S3 Class for Vectors of 64bit Integers bitops Bitwise Operations 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 blockcluster Co-Clustering Package for Binary, Categorical, Contingency and Continuous Data-Sets 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 bluster Clustering Algorithms for Bioconductor bmabasket Bayesian Model Averaging for Basket Trials 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 bonsaiforest Shrinkage Based Forest Plots boodist Some Distributions from the 'Boost' Library and More 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 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 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 bsplinePsd Bayesian Nonparametric Spectral Density Estimation Using B-Spline Priors bssm Bayesian Inference of Non-Linear and Non-Gaussian State Space Models bsts Bayesian Structural Time Series bsvars Bayesian Estimation of Structural Vector Autoregressive Models btb Beyond the Border - Kernel Density Estimation for Urban Geography 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) cIRT Choice Item Response Theory cPCG Efficient and Customized Preconditioned Conjugate Gradient Method for Solving System of Linear Equations caTools Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc cachem Cache R Objects with Automatic Pruning calculus High Dimensional Numerical and Symbolic Calculus calibrationband Calibration Bands 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 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 cauphy Trait Evolution on Phylogenies Using the Cauchy Process causalOT Optimal Transport Weights for Causal Inference causalSLSE Semiparametric Least Squares Inference for Causal Effects causaloptim An Interface to Specify Causal Graphs and Compute Bounds on Causal Effects caviarpd Cluster Analysis via Random Partition Distributions cba Clustering for Business Analytics cbinom Continuous Analog of a Binomial Distribution ccaPP (Robust) Canonical Correlation Analysis via Projection Pursuit cccp Cone Constrained Convex Problems cclust Convex Clustering Methods and Clustering Indexes ccrs Correct and Cluster Response Style Biased Data 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 cellWise Analyzing Data with Cellwise Outliers cenROC Estimating Time-Dependent ROC Curve and AUC for Censored Data cepreader Read 'CEP' and Legacy 'CANOCO' Files cequre Censored Quantile Regression & Monotonicity-Respecting Restoring ceser Cluster Estimated Standard Errors cfa Configural Frequency Analysis (CFA) 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 cglm Fits Conditional Generalized Linear Models changepoint Methods for Changepoint Detection changepoint.np Methods for Nonparametric Changepoint Detection 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 chopthin The Chopthin Resampler chouca A Stochastic Cellular Automaton Engine chromVAR Chromatin Variation Across Regions chron Chronological Objects which Can Handle Dates and Times chunkR Read Tables in Chunks cinterpolate Interpolation From C 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 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 cluscov Clustered Covariate Regression clusrank Wilcoxon Rank Tests for Clustered Data clustAnalytics Cluster Evaluation on Graphs clusterCrit Clustering Indices clusterHD Tools for Clustering High-Dimensional Data 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 (LSF, SGE, SLURM, PBS/Torque) clv Cluster Validation Techniques cmbClust Conditional Mixture Modeling and Model-Based Clustering cmenet Bi-Level Selection of Conditional Main Effects cmfrec Collective Matrix Factorization for Recommender Systems 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 cna Causal Modeling with Coincidence Analysis cnaOpt Optimizing Consistency and Coverage in Configurational Causal Modeling cnum Chinese Numerals Processing coRanking Co-Ranking Matrix coala A Framework for Coalescent Simulation coalescentMCMC MCMC Algorithms for the Coalescent cobs Constrained B-Splines (Sparse Matrix Based) coconots Convolution-Closed Models for Count Time Series 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 collUtils Auxiliary Package for Package 'CollapsABEL' 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 colorspace A Toolbox for Manipulating and Assessing Colors and Palettes colourvalues Assigns Colours to Values comat Creates Co-Occurrence Matrices of Spatial Data combinIT A Combined Interaction Test for Unreplicated Two-Way Tables combiter Combinatorics Iterators cometExactTest Exact Test from the Combinations of Mutually Exclusive Alterations (CoMEt) Algorithm commonmark High Performance CommonMark and Github Markdown Rendering in R communication Feature Extraction and Model Estimation for Audio of Human Speech compHclust Complementary Hierarchical Clustering 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 conTree Contrast Trees and Boosting concom Connected Components of an Undirected Graph 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 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 contoureR Contouring of Non-Regular Three-Dimensional Data 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 corTESTsrd Significance Testing of Rank Cross-Correlations under SRD cord Community Estimation in G-Models via CORD coreCollection Core Collection corels R Binding for the 'Certifiably Optimal RulE ListS (Corels)' Learner corpustools Managing, Querying and Analyzing Tokenized Text corrcoverage Correcting the Coverage of Credible Sets from Bayesian Genetic Fine Mapping cosimmr Fast Fitting of Stable Isotope Mixing Models with Covariates 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 covBM Brownian Motion Processes for 'nlme'-Models covTestR Covariance Matrix Tests covafillr Local Polynomial Regression of State Dependent Covariates in State-Space Models covdepGE Covariate Dependent Graph Estimation 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 coxrt Cox Proportional Hazards Regression for Right-Truncated Data coxsei Fitting a CoxSEI Model 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 cppRouting Algorithms for Routing and Solving the Traffic Assignment Problem cppdoubles Fast Relative Comparisons of Floating Point Numbers in 'C++' cpr Control Polygon Reduction cpss Change-Point Detection by Sample-Splitting Methods cqrReg Quantile, Composite Quantile Regression and Regularized Versions 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 credule Credit Default Swap Functions crfsuite Conditional Random Fields for Labelling Sequential Data in Natural Language Processing crimCV Group-Based Modelling of Longitudinal Data crmReg Cellwise Robust M-Regression and SPADIMO crosstalkr Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks 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 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 ctsem Continuous Time Structural Equation Modelling 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 curstatCI Confidence Intervals for the Current Status Model curvHDR Filtering of Flow Cytometry Samples curveDepth Tukey Curve Depth and Distance in the Space of Curves cusp Cusp-Catastrophe Model Fitting Using Maximum Likelihood cusum Cumulative Sum (CUSUM) Charts for Monitoring of Hospital Performance cutpointr Determine and Evaluate Optimal Cutpoints in Binary Classification Tasks cvasi Calibration, Validation, and Simulation of TKTD Models cxhull Convex Hull cycleRtools Tools for Cycling Data Analysis 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 dada2 Accurate, high-resolution sample inference from amplicon sequencing data dang 'Dang' Associated New Goodies dann Discriminant Adaptive Nearest Neighbor Classification data.table Extension of `data.frame` datafsm Estimating Finite State Machine Models from Data datasailr Row by Row Data Processing Tool, Using 'DataSailr' Script 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 dauphin Compact Standard for Australian Phone Numbers dawai Discriminant Analysis with Additional Information 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 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 dcortools Providing Fast and Flexible Functions for Distance Correlation Analysis dcov A Fast Implementation of Distance Covariance dcurver Utility Functions for Davidian Curves 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') 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 decon Deconvolution Estimation in Measurement Error Models decor Retrieve Code Decorations deductive Data Correction and Imputation Using Deductive Methods deepgp Bayesian Deep Gaussian Processes using MCMC deforestable Classify RGB Images into Forest or Non-Forest deform Spatial Deformation and Dimension Expansion Gaussian Processes deformula Integration of One-Dimensional Functions with Double Exponential Formulas degreenet Models for Skewed Count Distributions Relevant to Networks deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation demu Optimal Design Emulators via Point Processes denim Generate and Simulate Deterministic Discrete-Time Compartmental Models densEstBayes Density Estimation via Bayesian Inference Engines densityClust Clustering by Fast Search and Find of Density Peaks densvis Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction depcache Cache R Expressions, Taking Their Dependencies into Account depcoeff Dependency Coefficients depmix Dependent Mixture Models depmixS4 Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4 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 devoid A Graphic Device that Does Nothing dexter Data Management and Analysis of Tests dexterMST CML and Bayesian Calibration of Multistage 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 dfped Extrapolation and Bridging of Adult Information in Early Phase Dose-Finding Paediatrics Studies 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 dgumbel The Gumbel Distribution Functions and Gradients diagis Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling diceR Diverse Cluster Ensemble in R didimputation Imputation Estimator from Borusyak, Jaravel, and Spiess (2021) diffIRT Diffusion IRT Models for Response and Response Time Data diffmatchpatch String Diff, Match, and Patch Utilities diffobj Diffs for R Objects diffudist Diffusion Distance for Complex Networks 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 dir.expiry Managing Expiration for Cache Directories disaggregation Disaggregation Modelling disbayes Bayesian Multi-State Modelling of Chronic Disease Burden Data 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 disk.frame Larger-than-RAM Disk-Based Data Manipulation Framework dismo Species Distribution Modeling dispRity Measuring Disparity dispeRse Simulation of Demic Diffusion with Environmental Constraints distances Tools for Distance Metrics 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 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 dmri.tracking DiST - Diffusion Direction Smoothing and Tracking 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 dodgr Distances on Directed Graphs 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 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 drake A Pipeline Toolkit for Reproducible Computation at Scale drclust Simultaneous Clustering and (or) Dimensionality Reduction drf Distributional Random Forests drgee Doubly Robust Generalized Estimating Equations dropout Handling Incomplete Responses in Survey Data Analysis drugDemand Drug Demand Forecasting dscore D-Score for Child Development dsdp Density Estimation with Semidefinite Programming dsem Fit Dynamic Structural Equation Models dslice Dynamic Slicing dsmisc Data Science Box of Pandora Miscellaneous dsmmR Estimation and Simulation of Drifting Semi-Markov Models dst Using the Theory of Belief Functions 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 dual Automatic Differentiation with Dual Numbers dualtrees Decimated and Undecimated 2D Complex Dual-Tree Wavelet Transform duckdb DBI Package for the DuckDB Database Management System dvmisc Convenience Functions, Moving Window Statistics, and Graphics 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 dynpred Companion Package to "Dynamic Prediction in Clinical Survival Analysis" dynr Dynamic Models with Regime-Switching 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 eBsc "Empirical Bayes Smoothing Splines with Correlated Errors" eCAR Eigenvalue CAR Models eDITH Model Transport of Environmental DNA in River Networks eDMA Dynamic Model Averaging with Grid Search eNchange Ensemble Methods for Multiple Change-Point Detection eRm Extended Rasch Modeling eaf Plots of the Empirical Attainment Function 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 echoice2 Choice Models with Economic Foundation ecodist Dissimilarity-Based Functions for Ecological Analysis ecolMod "A Practical Guide to Ecological Modelling - Using R as a Simulation Platform" econetwork Analyzing Ecological Networks 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 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 edmcr Euclidean Distance Matrix Completion Tools eds eds: Low-level reader for Alevin EDS format ef Modelling Framework for the Estimation of Salmonid Abundance 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 elections.dtree Ranked Voting Election Audits with Dirichlet-Trees 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 em Generic EM Algorithm emBayes Robust Bayesian Variable Selection via Expectation-Maximization 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 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 enerscape Compute Energy Landscapes enmpa Ecological Niche Modeling using Presence-Absence Data enviPat Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry envirem Generation of ENVIREM Variables envnames Keep Track of User-Defined Environment Names epanet2toolkit Call 'EPANET' Functions to Simulate Pipe Networks 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 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 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 ergmgp Tools for Modeling ERGM Generating Processes ergmito Exponential Random Graph Models for Small Networks 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 essentials Essential Functions not Included in Base R estimatr Fast Estimators for Design-Based Inference etasFLP Mixed FLP and ML Estimation of ETAS Space-Time Point Processes for Earthquake Description etm Empirical Transition Matrix eulerr Area-Proportional Euler and Venn Diagrams with Ellipses eummd Efficient Univariate Maximum Mean Discrepancy 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 event Event History Procedures and Models eventglm Regression Models for Event History Outcomes evgam Generalised Additive Extreme Value Models evinf Inference with Extreme Value Inflated Count Data evolqg Evolutionary Quantitative Genetics evtree Evolutionary Learning of Globally Optimal Trees exactRankTests Exact Distributions for Rank and Permutation Tests exactextractr Fast Extraction from Raster Datasets using Polygons exceedProb Confidence Intervals for Exceedance Probability excursions Excursion Sets and Contour Credibility Regions for Random Fields exdex Estimation of the Extremal Index 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 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 extRemes Extreme Value Analysis extraDistr Additional Univariate and Multivariate Distributions 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 fCWTr Fast Continuous Wavelet Transform fDMA Dynamic Model Averaging and Dynamic Model Selection for Continuous Outcomes 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 factor256 Use Raw Vectors to Minimize Memory Consumption of Factors 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 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 fastSOM Fast Calculation of Spillover Measures 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 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' fastcmh Significant Interval Discovery with Categorical Covariates fastcmprsk Fine-Gray Regression via Forward-Backward Scan 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 fastdigest Fast, Low Memory Footprint Digests of R Objects fasterElasticNet An Amazing Fast Way to Fit Elastic Net fasterize Fast Polygon to Raster Conversion 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 fastmap Fast Data Structures fastmatch Fast 'match()' Function fastmatrix Fast Computation of some Matrices Useful in Statistics fastmit Fast Mutual Information Based Independence Test fastpos Finds the Critical Sequential Point of Stability for a Pearson Correlation fastqq Faster Generation of Quantile Quantile Plots with Large Samples fastshap Fast Approximate Shapley Values fasttime Fast Utility Function for Time Parsing and Conversion 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 fctbases Functional Bases fda Functional Data Analysis 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 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 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 Counterfactuals 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 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 Sediment Source Fingerprinting fingerprint Functions to Operate on Binary Fingerprint Data finity Test for Finiteness of Moments in a Distribution fipp Induced Priors in Bayesian Mixture Models fishMod Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models fishmethods Fishery Science Methods and Models fixest Fast Fixed-Effects Estimations flam Fits Piecewise Constant Models with Data-Adaptive Knots flamingos Functional Latent Data Models for Clustering Heterogeneous Curves ('FLaMingos') flan FLuctuation ANalysis on Mutation Models flare Family of Lasso Regression flashClust Implementation of optimal hierarchical clustering flexclust Flexible Cluster Algorithms flexiblas 'FlexiBLAS' API Interface flexpolyline Flexible Polyline Encoding flexrsurv Flexible Relative Survival Analysis flexsurv Flexible Parametric Survival and Multi-State Models flightsbr Download Flight and Airport Data from Brazil 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 flsa Path Algorithm for the General Fused Lasso Signal Approximator fluidsynth Read and Play Digital Music (MIDI) flying Simulation of Bird Flight Range fmcsR Mismatch Tolerant Maximum Common Substructure Searching fmdu (Restricted) [external] Multidimensional Unfolding fmerPack Tools of Heterogeneity Pursuit via Finite Mixture Effects Model fmesher Triangle Meshes and Related Geometry Tools fmf Fast Class Noise Detector with Multi-Factor-Based Learning fmri Analysis of fMRI Experiments fmrs Variable Selection in Finite Mixture of AFT Regression and FMR Models fmtr Easily Apply Formats to Data foreSIGHT Systems Insights from Generation of Hydroclimatic Timeseries forecast Forecasting Functions for Time Series and Linear Models forecastSNSTS Forecasting for Stationary and Non-Stationary Time Series forestControl Approximate False Positive Rate Control in Selection Frequency for Random Forest fourPNO Bayesian 4 Parameter Item Response Model fourierin Computes Numeric Fourier Integrals fpcb Predictive Confidence Bands for Functional Time Series Forecasting fpeek Check Text Files Content at a Glance fplot Automatic Distribution Graphs Using Formulas 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 free Flexible Regularized Estimating Equations freealg The Free Algebra freebird Estimation and Inference for High Dimensional Mediation and Surrogate Analysis fromo Fast Robust Moments frontier Stochastic Frontier Analysis frontiles Partial Frontier Efficiency Analysis froth Emulate a 'Forth' Programming Environment fs Cross-Platform File System Operations Based on 'libuv' fso Fuzzy Set Ordination fssemR Fused Sparse Structural Equation Models to Jointly Infer Gene Regulatory Network fst Lightning Fast Serialization of Data Frames fstcore R Bindings to the 'Fstlib' Library func2vis Clean and Visualize Over Expression Results from 'ConsensusPathDB' fuser Fused Lasso for High-Dimensional Regression over Groups fuzzyRankTests Fuzzy Rank Tests and Confidence Intervals fwsim Fisher-Wright Population Simulation 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 Graphical Independence Networks gRbase A Package for Graphical Modelling in R gRc Inference in Graphical Gaussian Models with Edge and Vertex Symmetries gRim Graphical Interaction Models gadget2 Gadget is the Globally-Applicable Area Disaggregated General Ecosystem Toolbox gafit Genetic Algorithm for Curve Fitting 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 gamreg Robust and Sparse Regression via Gamma-Divergence 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 gapfill Fill Missing Values in Satellite Data 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 gb Generalize Lambda Distribution and Generalized Bootstrapping gbeta Generalized Beta and Beta Prime Distributions gbm Generalized Boosted Regression Models gbp A Bin Packing Problem Solver 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 gdalcubes Earth Observation Data Cubes from Satellite Image Collections gdalraster Bindings to the 'Geospatial Data Abstraction Library' Raster API gdm Generalized Dissimilarity Modeling gdpc Generalized Dynamic Principal Components gdsfmt R Interface to CoreArray Genomic Data Structure (GDS) Files gdtools Utilities for Graphical Rendering and Fonts Management gear Geostatistical Analysis in R gee Generalized Estimation Equation Solver geeVerse A Comprehensive Analysis of High Dimensional Longitudinal Data geepack Generalized Estimating Equation Package 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 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 Fast and Robust Hierarchical Clustering with Noise Points Detection 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 geoFKF Kriging Method for Spatial Functional Data geoFourierFDA Ordinary Functional Kriging Using Fourier Smoothing and Gaussian Quadrature geoR Analysis of Geostatistical Data geoarrow Extension Types for Spatial Data for Use with 'Arrow' geocmeans Implementing Methods for Spatial Fuzzy Unsupervised Classification geodist Fast, Dependency-Free Geodesic Distance Calculations geodiv Methods for Calculating Gradient Surface Metrics 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 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 gesso Hierarchical GxE Interactions in a Regularized Regression Model getPass Masked User Input getip 'IP' Address 'Lookup' gettz Get the Timezone Information gfiExtremes Generalized Fiducial Inference for Extremes gfilmm Generalized Fiducial Inference for Normal Linear Mixed Models gfilogisreg Generalized Fiducial Inference for Binary Logistic Regression Models ggbrain Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax ggdist Visualizations of Distributions and Uncertainty ggdmc Cognitive Models ggforce Accelerating 'ggplot2' gghilbertstrings A Fast 'ggplot2'-Based Implementation of Hilbert Curves ggip Data Visualization for IP Addresses and Networks ggiraph Make 'ggplot2' Graphics Interactive gglasso Group Lasso Penalized Learning Using a Unified BMD Algorithm 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' 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' 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 glamlasso Penalization in Large Scale Generalized Linear Array Models 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 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 glmmPen High Dimensional Penalized Generalized Linear Mixed Models (pGLMM) glmmTMB Generalized Linear Mixed Models using Template Model Builder glmmrBase Generalised Linear Mixed Models in R glmmrOptim Approximate Optimal Experimental Designs Using Generalised Linear Mixed Models 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 glow Make Plots that Glow glpkAPI R Interface to C API of GLPK 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 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 googlePolylines Encoding Coordinates into 'Google' Polylines gower Gower's Distance gpboost Combining Tree-Boosting with Gaussian Process and Mixed Effects Models gpg GNU Privacy Guard for R gplite General Purpose Gaussian Process Modelling gplm Generalized Partial Linear Models (GPLM) gps General P-Splines 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 graphicalVAR Graphical VAR for Experience Sampling Data graphkernels Graph Kernels graphlayouts Additional Layout Algorithms for Network Visualizations graphql A GraphQL Query Parser 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 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 gridtext Improved Text Rendering Support for 'Grid' Graphics groc Generalized Regression on Orthogonal Components groupTesting Simulating and Modeling Group (Pooled) Testing Data 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 growfunctions Bayesian Non-Parametric Dependent Models for Time-Indexed Functional Data 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 grr Alternative Implementations of Base R Functions 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 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 gsmoothr Smoothing tools gss General Smoothing Splines gstat Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation gsw Gibbs Sea Water Functions gsynth Generalized Synthetic Control Method gte Generalized Turnbull's Estimator gtfs2gps Converting Transport Data from GTFS Format to GPS-Like Records 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 gyro Hyperbolic Geometry h3lib Exposes the 'Uber' 'H3' Library to R Packages h3r Hexagonal Hierarchical Geospatial Indexing System hSDM Hierarchical Bayesian Species Distribution Models habCluster Detecting Spatial Clustering Based on Connection Cost Between Grids hahmmr Haplotype-Aware Hidden Markov Model for RNA hal9001 The Scalable Highly Adaptive Lasso handwriter Handwriting Analysis in R 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 hapsim Haplotype Data Simulation harmony Fast, Sensitive, and Accurate Integration of Single Cell Data hashr Hash R Objects to Integers Fast 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 hdbinseg Change-Point Analysis of High-Dimensional Time Series via Binary Segmentation hdbm High Dimensional Bayesian Mediation Analysis 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 hdrcde Highest Density Regions and Conditional Density Estimation healthyAddress Convert Addresses to Standard Inputs 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 heuristicsmineR Discovery of Process Models with the Heuristics Miner hexbin Hexagonal Binning Routines hgm Holonomic Gradient Method and Gradient Descent hgwrr Hierarchical and Geographically Weighted Regression hhsmm Hidden Hybrid Markov/Semi-Markov Model Fitting hibayes Individual-Level, Summary-Level and Single-Step Bayesian Regression Model 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 higlasso Hierarchical Integrative Group LASSO hilbert Coordinate Indexing on Hilbert Curves 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 hmm.discnp Hidden Markov Models with Discrete Non-Parametric Observation Distributions hmmTMB Fit Hidden Markov Models using Template Model Builder homals Gifi Methods for Optimal Scaling hommel Methods for Closed Testing with Simes Inequality, in Particular Hommel's Method hopit Hierarchical Ordered Probit Models with Application to Reporting Heterogeneity 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 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 iBBiG Iterative Binary Biclustering of Genesets iBST Improper Bagging Survival Tree iCellR Analyzing High-Throughput Single Cell Sequencing Data 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 iRafNet Integrative Random Forest for Gene Regulatory Network Inference iapws Formulations of the International Association for the Properties of Water and Steam 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 icRSF A Modified Random Survival Forest Algorithm 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 icosa Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra icr Compute Krippendorff's Alpha icrf Interval Censored Recursive Forests idar Individual Diversity-Area Relationships idefix Efficient Designs for Discrete Choice Experiments ieeeround Functions to set and get the IEEE rounding mode ifctools Italian Fiscal Code ('Codice Fiscale') Utilities ifs Iterated Function Systems igcop Computational Tools for the IG and IGL Copula Families 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.dlib Image Processing Functionality using the 'dlib' Package image.libfacedetection Convolutional Neural Network for Face Detection image.textlinedetector Segment Images in Text Lines and Words imager Image Processing Library Based on 'CImg' imagerExtra Extra Image Processing Library Based on 'imager' imagine IMAGing engINEs, Tools for Application of Image Filters to Data Matrices imbalance Preprocessing Algorithms for Imbalanced Datasets imbibe A Pipe-Friendly Image Calculator immer Item Response Models for Multiple Ratings immunarch Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires imp4p Imputation for Proteomics impactflu Quantification of Population-Level Impact of Vaccination impactr Mechanical Loading Prediction Through Accelerometer Data imptree Classification Trees with Imprecise Probabilities impute impute: Imputation for microarray data imputeMulti Imputation Methods for Multivariate Multinomial Data imputeTS Time Series Missing Value Imputation inca Integer Calibration incgraph Incremental Graphlet Counting for Network Optimisation indelmiss Insertion Deletion Analysis While Accounting for Possible Missing Data indexthis Quick Indexation inferCSN Inferring Cell-Specific Gene Regulatory Network inferr Inferential Statistics infinitefactor Bayesian Infinite Factor Models influenceR Software Tools to Quantify Structural Importance of Nodes in a Network infotheo Information-Theoretic Measures inplace In-place Operators for R inspectdf Inspection, Comparison and Visualisation of Data Frames instantiate Pre-Compiled 'CmdStan' Models in R Packages intRegGOF Integrated Regression Goodness of Fit intRinsic Likelihood-Based Intrinsic Dimension Estimators intcensROC AUC Estimation of Interval Censored Survival Data interep Interaction Analysis of Repeated Measure Data interflex Multiplicative Interaction Models Diagnostics and Visualization interleave Converts Tabular Data to Interleaved Vectors interp Interpolation Methods interpolation Interpolation of Bivariate Functions interpolators Some Interpolation Methods interpret Fit Interpretable Machine Learning Models intervalaverage Time-Weighted Averaging for Interval Data 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 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 isoband Generate Isolines and Isobands from Regularly Spaced Elevation Grids isocir Isotonic Inference for Circular Data isodistrreg Isotonic Distributional Regression (IDR) isotone Active Set and Generalized PAVA for Isotone Optimization isotree Isolation-Based Outlier Detection itdr Integral Transformation Methods for SDR in Regression iterLap Approximate Probability Densities by Iterated Laplace Approximations itp The Interpolate, Truncate, Project (ITP) Root-Finding Algorithm ivdoctr Ensures Mutually Consistent Beliefs When Using IVs ivsacim Structural Additive Cumulative Intensity Models with IV ivtools Instrumental Variables ivx Robust Econometric Inference jSDM Joint Species Distribution Models jaccard Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients jack Jack, Zonal, and Schur Polynomials jackalope A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator jacobi Jacobi Theta Functions and Related Functions jfa Statistical Methods for Auditing jiebaR Chinese Text Segmentation jinjar Template Engine Inspired by 'Jinja' 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 jsonStrings Manipulation of JSON Strings 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 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 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 kdpee Fast Multidimensional Entropy Estimation by k-d Partitioning kerSeg New Kernel-Based Change-Point Detection kergp Gaussian Process Laboratory kerndwd Distance Weighted Discrimination (DWD) and Kernel Methods kernelboot Smoothed Bootstrap and Random Generation from Kernel Densities kernlab Kernel-Based Machine Learning Lab keyATM Keyword Assisted Topic Models 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 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 kmer Fast K-Mer Counting and Clustering for Biological Sequence Analysis kml K-Means for Longitudinal Data 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 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 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 langevitour Langevin Tour languageserver Language Server Protocol lars Least Angle Regression, Lasso and Forward Stagewise lassoshooting L1 Regularized Regression (Lasso) Solver using the Cyclic Coordinate Descent Algorithm aka Lasso Shooting latentcor Fast Computation of Latent Correlations for Mixed Data latentgraph Graphical Models with Latent Variables 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 lazy Lazy Learning for Local Regression lazyarray Persistent Large Data Array with Lazy-Loading on Demand lazyeval Lazy (Non-Standard) Evaluation lbfgs Limited-memory BFGS Optimization lbfgsb3c Limited Memory BFGS Minimizer with Bounds on Parameters with optim() 'C' Interface lcc Longitudinal Concordance Correlation 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) ldsep Linkage Disequilibrium Shrinkage Estimation for Polyploids ldsr Linear Dynamical System Reconstruction ldt Automated Uncertainty Analysis leaderCluster Leader Clustering Algorithm leaps Regression Subset Selection 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 lfe Linear Group Fixed Effects lfl Linguistic Fuzzy Logic lfmm Latent Factor Mixed Models lgarch Simulation and Estimation of Log-GARCH Models lhs Latin Hypercube Samples libcoin Linear Test Statistics for Permutation Inference libgeos Open Source Geometry Engine ('GEOS') C API libr Libraries, Data Dictionaries, and a Data Step for R libstable4u Stable Distribution Functions...For You lidR Airborne LiDAR Data Manipulation and Visualization for Forestry Applications lifecontingencies Financial and Actuarial Mathematics for Life Contingencies lightgbm Light Gradient Boosting Machine limSolve Solving Linear Inverse Models lime Local Interpretable Model-Agnostic Explanations limma Linear Models for Microarray Data linERR Linear Excess Relative Risk Model lincom Linear Biomarker Combination: Empirical Performance Optimization linconGaussR Sampling Multivariate Normal Distribution under Linear Constraints 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 linkcomm Tools for Generating, Visualizing, and Analysing Link Communities in Networks 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 Random Forests for Multiple Imputation Based on 'ranger' ljr Logistic Joinpoint Regression 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 lme4breeding Relationship-Based Mixed-Effects Models lmm Linear Mixed Models 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 lobstr Visualize R Data Structures with Trees locStra Fast Implementation of (Local) Population Stratification Methods 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 lodr Linear Model Fitting with LOD Covariates log4r A Fast and Lightweight Logging System for R, Based on 'log4j' logKDE Computing Log-Transformed Kernel Density Estimates for Positive Data logconcens Maximum Likelihood Estimation of a Log-Concave Density Based on Censored Data loggit2 Easy-to-Use, Dependencyless Logger logicDT Identifying Interactions Between Binary Predictors logistf Firth's Bias-Reduced Logistic Regression logisticPCA Binary Dimensionality Reduction 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 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 lpme Nonparametric Estimation of Measurement Error Models 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 lsbclust Least-Squares Bilinear Clustering for Three-Way Data 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 lsm Estimation of the log Likelihood of the Saturated Model ltsa Linear Time Series Analysis ltsk Local Time Space Kriging ltsspca Sparse Principal Component Based on Least Trimmed Squares luajr 'LuaJIT' Scripting lubridate Make Dealing with Dates a Little Easier ludic Linkage Using Diagnosis Codes lulcc Land Use Change Modelling in R lutz Look Up Time Zones of Point Coordinates lvmcomp Stochastic EM Algorithms for Latent Variable Models with a High-Dimensional Latent Space 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 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' mapfit PH/MAP Parameter Estimation 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 marelac Tools for Aquatic Sciences marginaleffects Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests 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 Marker Association Studies 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 mathjaxr Using 'Mathjax' in Rd Files matricks Useful Tricks for Matrix Manipulation 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 maxnodf Approximate Maximisation of Nestedness in Bipartite Graphs 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 mbrglm Median Bias Reduction in Binomial-Response GLMs 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 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 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 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 meltr Read Non-Rectangular Text Data meltt Matching Event Data by Location, Time and Type memisc Management of Survey Data and Presentation of Analysis Results memo In-Memory Caching of Repeated Computations (Memoization) memuse Memory Estimation Utilities mergeTrees Aggregating Trees meshed Bayesian Regression with Meshed Gaussian Processes 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 metapack Bayesian Meta-Analysis and Network Meta-Analysis metapod Meta-Analyses on P-Values of Differential Analyses metarep Replicability-Analysis Tools for Meta-Analysis meteoland Landscape Meteorology Tools meteor Meteorological Data Manipulation meteorits Mixture-of-Experts Modeling for Complex Non-Normal Distributions 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 mfp2 Multivariable Fractional Polynomial Models with Extensions mgarchBEKK Simulating, Estimating and Diagnosing MGARCH (BEKK and mGJR) Processes mgc Multiscale Graph Correlation mgee2 Marginal Analysis of Misclassified Longitudinal Ordinal Data mgss A Matrix-Free Multigrid Preconditioner for Spline Smoothing mgwrsar GWR and MGWR with Spatial Autocorrelation mhazard Nonparametric and Semiparametric Methods for Multivariate Failure Time Data mhsmm Inference for Hidden Markov and Semi-Markov Models mhurdle Multiple Hurdle Tobit Models miRNAss Genome-Wide Discovery of Pre-miRNAs with few Labeled Examples 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 microclass Methods for Taxonomic Classification of Prokaryotes 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 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 mined Minimum Energy Designs minerva Maximal Information-Based Nonparametric Exploration for Variable Analysis minet Mutual Information NETworks miniPCH Survival Distributions with Piece-Wise Constant Hazards minic Minimization Methods for Ill-Conditioned Problems minimaxApprox Implementation of Remez Algorithm for Polynomial and Rational Function Approximation 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 mirtjml Joint Maximum Likelihood Estimation for High-Dimensional Item Factor Analysis miscF Miscellaneous Functions misclassGLM Computation of Generalized Linear Models with Misclassified Covariates Using Side Information miscset Miscellaneous Tools Set missDeaths Simulating and Analyzing Time to Event Data in the Presence of Population Mortality missSBM Handling Missing Data in Stochastic Block Models missSOM Self-Organizing Maps with Built-in Missing Data Imputation missoNet Missingness in Multi-Task Regression with Network Estimation 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 mixedMem Tools for Discrete Multivariate Mixed Membership Models mixexp Design and Analysis of Mixture Experiments mixl Simulated Maximum Likelihood Estimation of Mixed Logit Models for Large Datasets mixsqp Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions 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) mlbench Machine Learning Benchmark Problems mlegp Maximum Likelihood Estimates of Gaussian Processes mlogitBMA Bayesian Model Averaging for Multinomial Logit Models mlpack 'Rcpp' Integration for the 'mlpack' Library mlr Machine Learning in R mlr3mbo Flexible Bayesian Optimization mlr3misc Helper Functions for 'mlr3' mlr3oml Connector Between 'mlr3' and 'OpenML' mlrMBO Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions mlsbm Efficient Estimation of Bayesian SBMs & MLSBMs mlt Most Likely Transformations mmand Mathematical Morphology in Any Number of Dimensions mmap Map Pages of Memory mmapcharr Memory-Map Character Files mmcif Mixed Multivariate Cumulative Incidence Functions mmcm Modified Maximum Contrast Method mmconvert Mouse Map Converter mmpca Integrative Analysis of Several Related Data Matrices mmrm Mixed Models for Repeated Measures mmsample Multivariate Matched Sampling mnis Easy Downloading Capabilities for the Members' Name Information Service 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 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 monocle Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq 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 mop Mobility Oriented-Parity Metric morpheus Estimate Parameters of Mixtures of Logistic Regressions morse Modelling Reproduction and Survival Data in Ecotoxicology mosum Moving Sum Based Procedures for Changes in the Mean motif Local Pattern Analysis motifmatchr Fast Motif Matching in R 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 mpath Regularized Linear Models mpmi Mixed-Pair Mutual Information Estimators 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 mra Mark-Recapture Analysis mrbsizeR Scale Space Multiresolution Analysis of Random Signals 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 msBP Multiscale Bernstein Polynomials for Densities msa Multiple Sequence Alignment msce Hazard of Multi-Stage Clonal Expansion Models 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 FDR Correction multbxxc Auxiliary Routines for Influx Software multgee GEE Solver for Correlated Nominal or Ordinal Multinomial Responses 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) multispatialCCM Multispatial Convergent Cross Mapping multitaper Spectral Analysis Tools using the Multitaper Method multivar Penalized Estimation of Multiple-Subject Vector Autoregressive (multi-VAR) Models multivariance Measuring Multivariate Dependence Using Distance Multivariance multiview Cooperative Learning for Multi-View Analysis multtest Resampling-based multiple hypothesis testing muscle Multiple Sequence Alignment with MUSCLE musica Multiscale Climate Model Assessment 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 mxsem Specify 'OpenMx' Models with a 'lavaan'-Style Syntax myTAI Evolutionary Transcriptomics mzID An mzIdentML parser for R mzR parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) n1qn1 Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS Optimization 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 NNG (Nanomsg Next Gen) Lightweight Messaging Library nanoparquet Read and Write 'Parquet' Files nanotime Nanosecond-Resolution Time Support for R 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' natural Estimating the Error Variance in a High-Dimensional Linear Model navigation Analyze the Impact of Sensor Error Modelling on Navigation Performance nbfar Negative Binomial Factor Regression Models ('nbfar') nbpMatching Functions for Optimal Non-Bipartite Matching ncdf4 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files ncpen Unified Algorithm for Non-convex Penalized Estimation for Generalized Linear Models 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 netcmc Spatio-Network Generalised Linear Mixed Models for Areal Unit and Network Data netcontrol Control Theory Methods for Networks netcox Structural Learning in Cox Models with Time-Dependent Covariates netdiffuseR Analysis of Diffusion and Contagion Processes on Networks netgsa Network-Based Gene Set Analysis netrankr Analyzing Partial Rankings in Networks nets Network Estimation for Time Series 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 networkscaleup Network Scale-Up Models for Aggregated Relational Data neuRosim Simulate fMRI Data neuroim Data Structures and Handling for Neuroimaging Data nevada Network-Valued Data Analysis nfer Event Stream Abstraction using Interval Logic nftbart Nonparametric Failure Time Bayesian Additive Regression Trees ngram Fast n-Gram 'Tokenization' ngspatial Fitting the Centered Autologistic and Sparse Spatial Generalized Linear Mixed Models for Areal Data nhm Non-Homogeneous Markov and Hidden Markov Multistate Models nhppp Simulating Nonhomogeneous Poisson Point Processes niaidMI Markov Model Multiple Imputation for NIAID OS nice Get or Set UNIX Niceness nieve Miscellaneous Utilities for Extreme Value Analysis 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 nlmm Generalized Laplace Mixed-Effects Models nloptr R Interface to NLopt nltm Non-Linear Transformation Models 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) nodeSub Simulate DNA Alignments Using Node Substitutions noisysbmGGM Noisy Stochastic Block Model for GGM Inference 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 '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 npbr Nonparametric Boundary Regression npcopTest Non Parametric Test for Detecting Changes in the Copula npcp Some Nonparametric CUSUM Tests for Change-Point Detection in Possibly Multivariate Observations npcure Nonparametric Estimation in Mixture Cure Models npregfast Nonparametric Estimation of Regression Models with Factor-by-Curve Interactions nprobust Nonparametric Robust Estimation and Inference Methods using Local Polynomial Regression and Kernel Density Estimation npsf Nonparametric and Stochastic Efficiency and Productivity Analysis npsp Nonparametric Spatial Statistics nsRFA Non-Supervised Regional Frequency Analysis nse Numerical Standard Errors Computation in R nseval Tools for Lazy and Non-Standard Evaluation nuggets Extensible Data Pattern Searching Framework 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 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 My 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 oncomsm Bayesian Multi-State Models for Early Oncology ondisc Fast, Universal, and Intuitive Computing on Large-Scale Single-Cell Data 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 ontologySimilarity Calculating Ontological Similarities opa An Implementation of Ordinal Pattern Analysis openCR Open Population Capture-Recapture openair Tools for the Analysis of Air Pollution Data opencv Bindings to 'OpenCV' Computer Vision Library openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL openxlsx Read, Write and Edit xlsx Files openxlsx2 Read, Write and Edit 'xlsx' Files opera Online Prediction by Expert Aggregation 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 optpart Optimal Partitioning of Similarity Relations opusminer OPUS Miner Algorithm for Filtered Top-k Association Discovery orca Computation of Graphlet Orbit Counts in Sparse Graphs ordinal Regression Models for Ordinal Data ordinalForest Ordinal Forests: Prediction and Variable Ranking with Ordinal Target Variables ordinalNet Penalized Ordinal Regression 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 osc Orthodromic Spatial Clustering oscar Optimal Subset Cardinality Regression (OSCAR) Models Using the L0-Pseudonorm oskeyring Raw System Credential Store Access from R osmdata Import 'OpenStreetMap' Data as Simple Features or Spatial Objects osqp Quadratic Programming Solver using the 'OSQP' Library 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 overlap Estimates of Coefficient of Overlapping for Animal Activity Patterns pARI Permutation-Based All-Resolutions Inference Method pGPx Pseudo-Realizations for Gaussian Process Excursions 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 pak Another Approach to Package Installation palm Fitting Point Process Models via the Palm Likelihood pamr Pam: Prediction Analysis for Microarrays pan Multiple Imputation for Multivariate Panel or Clustered Data pander An R 'Pandoc' Writer 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 paropt Parameter Optimizing of ODE-Systems 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 patchDVI Package to Patch '.dvi' or '.synctex' Files patentr Access USPTO Bulk Data in Tidy Rectangular Format 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 pcIRT IRT Models for Polytomous and Continuous Item Responses 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 Randomized Singular Value Decomposition Algorithms with 'RcppEigen' pccc Pediatric Complex Chronic Conditions 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 pdmod Proximal/Distal Modeling Framework for Pavlovian Conditioning Phenomena 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 pedmod Pedigree Models pedometrics Miscellaneous Pedometric Tools pegas Population and Evolutionary Genetics Analysis System pems.utils Portable Emissions (and Other Mobile) Measurement System Utilities pemultinom L1-Penalized Multinomial Regression with Statistical Inference penAFT Fit the Regularized Gehan Estimator with Elastic Net and Sparse Group Lasso Penalties penMSM Estimating Regularized Multi-state Models Using L1 Penalties penPHcure Variable Selection in PH Cure Model with Time-Varying Covariates 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 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 pgsc Computes Powell's Generalized Synthetic Control Estimator ph2bayes Bayesian Single-Arm Phase II Designs ph2bye Phase II Clinical Trial Design Using Bayesian Methods 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 phonics Phonetic Spelling Algorithms phreeqc R Interface to Geochemical Modeling Software 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 phylter Detect and Remove Outliers in Phylogenomics Datasets phyr Model Based Phylogenetic Analysis physiology Calculate physiologic characteristics of awake and anesthetized adults, children and infants picante Integrating Phylogenies and Ecology picasso Pathwise Calibrated Sparse Shooting Algorithm pimeta Prediction Intervals for Random-Effects Meta-Analysis pingr Check if a Remote Computer is Up piqp R Interface to Proximal Interior Point Quadratic Programming Solver piton Parsing Expression Grammars in Rcpp pkgcache Cache 'CRAN'-Like Metadata and R Packages plac A Pairwise Likelihood Augmented Cox Estimator for Left-Truncated Data pleiotest Fast Sequential Pleiotropy Test plfm Probabilistic Latent Feature Analysis plgp Particle Learning of Gaussian Processes plier Implements the Affymetrix PLIER algorithm pliman Tools for Plant Image Analysis 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 plugdensity Plug-in Kernel Density Estimation 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 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 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 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 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 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 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 prclust Penalized Regression-Based Clustering Method precondition Lightweight Precondition, Postcondition, and Sanity Checks precrec Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves predictmeans Predicted Means for Linear and Semiparametric Models predkmeans Covariate Adaptive Clustering predtools Prediction Model Tools prefmod Utilities to Fit Paired Comparison Models for Preferences preprocessCore A collection of pre-processing functions 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 promises Abstractions for Promise-Based Asynchronous Programming 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 proxy Distance and Similarity Measures proxyC Computes Proximity in Large Sparse Matrices prqlr R Bindings for the 'prqlc' Rust Library pryr Tools for Computing on the Language 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 psgp Projected Spatial Gaussian Process Methods psp Parameter Space Partitioning MCMC for Global Model Evaluation pspearman Spearman's Rank Correlation Test pspline Penalized Smoothing Splines psqn Partially Separable Quasi-Newton 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 pullword R Interface to Pullword Service puniform Meta-Analysis Methods Correcting for Publication Bias 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' pvar Calculation and Application of p-Variation pwlmm PWIGLS for Two-Level Multivariate and Multilevel Linear Models pwrFDR FDR Power pyinit Pena-Yohai Initial Estimator for Robust S-Regression qGaussian The q-Gaussian Distribution qMRI Methods for Quantitative Magnetic Resonance Imaging ('qMRI') qad Quantification of Asymmetric Dependence qap Heuristics for the Quadratic Assignment Problem (QAP) qbld Quantile Regression for Binary Longitudinal Data qch Query Composite Hypotheses qfa Quantile-Frequency Analysis (QFA) of Time Series 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 qpmadr Interface to the 'qpmad' Quadratic Programming Solver qqconf Creates Simultaneous Testing Bands for QQ-Plots qrencoder Quick Response Code (QR Code) / Matrix Barcode Creator qris Quantile Regression Model for Residual Lifetime Using an Induced Smoothing Approach qrjoint Joint Estimation in Linear Quantile Regression qrmtools Tools for Quantitative Risk Management qrng (Randomized) Quasi-Random Number Generators qs Quick Serialization of R Objects qsplines Quaternions Splines qspray Multivariate Polynomials with Rational Coefficients 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 qtlhot Inference for QTL Hotspots qtlmt Tools for Mapping Multiple Complex Traits qtlpoly Random-Effect Multiple QTL Mapping in Autopolyploids quadprog Functions to Solve Quadratic Programming Problems quadrupen Sparsity by Worst-Case Quadratic Penalties quadtree Region Quadtrees for Spatial Data 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 rating large binary pairwiesd comparisons quickblock Quick Threshold Blocking quickmatch Quick Generalized Full Matching quotedargs A Way of Writing Functions that Quote their Arguments 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 rDEA Robust Data Envelopment Analysis (DEA) for R rEDM Empirical Dynamic Modeling ('EDM') rENA Epistemic Network Analysis rFerns Random Ferns Classifier 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 rMVP Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool rPBK Inference and Prediction of Generic Physiologically-Based Kinetic Models rPref Database Preferences and Skyline Computation rSPDE Rational Approximations of Fractional Stochastic Partial Differential Equations rSRD Sum of Ranking Differences Statistical Test rSpectral Spectral Modularity Clustering rTRNG Advanced and Parallel Random Number Generation via 'TRNG' raceland Pattern-Based Zoneless Method for Analysis and Visualization of Racial Topography ragg Graphic Devices Based on AGG 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 randomForest Breiman and Cutler's Random Forests for Classification and Regression 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 randtoolbox Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests rangeBuilder Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons ranger A Fast Implementation of Random Forests rankdist Distance Based Ranking Models ranktreeEnsemble Ensemble Models of Rank-Based Trees with Extracted Decision Rules rapidjsonr 'Rapidjson' C++ Header Files 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 ratioOfQsprays Fractions of Multivariate Polynomials with Rational Coefficients 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 Read/Write, Transform, and Summarize 'BIOM' Data rbmi Reference Based Multiple Imputation rbridge Restricted Bridge Estimation rbscCI Blyth-Still-Casella Confidence Interval rcccd Class Cover Catch Digraph Classification rcdd Computational Geometry rcontroll Individual-Based Forest Growth Simulator 'TROLL' rcpptimer 'Rcpp' Tic-Toc Timer with 'OpenMP' Support rdist Calculate Pairwise Distances rdoxygen Create Doxygen Documentation for Source Code re2 R Interface to Google RE2 (C++) Regular Expression Library reReg Recurrent Event Regression read.dbc Read Data Stored in DBC (Compressed DBF) Files 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 readxl Read Excel Files readxlsb Read 'Excel' Binary (.xlsb) Workbooks 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 recosystem Recommender System using Matrix Factorization recurse Computes Revisitation Metrics for Trajectory Data reda Recurrent Event Data Analysis redist Simulation Methods for Legislative Redistricting redistmetrics Redistricting Metrics redland RDF Library Bindings in R redux R Bindings to 'hiredis' 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 rego Automatic Time Series Forecasting and Missing Value Imputation regsem Regularized Structural Equation Modeling rehh Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests relSim Relative Simulator relevent Relational Event Models relliptical The Truncated Elliptical Family of Distributions relsurv Relative Survival rem Relational Event Models (REM) 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 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 resemble Memory-Based Learning in Spectral Chemometrics reservr Fit Distributions and Neural Networks to Censored and Truncated Data resevol Simulate Agricultural Production and Evolution of Pesticide Resistance reshape Flexibly Reshape Data reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package restfulr R Interface to RESTful Web Services rethnicity Predicting Ethnic Group from Names reticulate Interface to 'Python' revdbayes Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis revealedPrefs Revealed Preferences and Microeconomic Rationality rexpokit R Wrappers for EXPOKIT; Other Matrix Functions rflashtext FlashText Algorithm for Finding and Replacing Words rflexscan The Flexible Spatial Scan Statistic rgenoud R Version of GENetic Optimization Using Derivatives rgeoda R Library for Spatial Data Analysis 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 rhdf5 R Interface to HDF5 rhdf5filters HDF5 Compression Filters rheroicons A Zero Dependency 'SVG' Icon Library for 'Shiny' rhoR Rho for Inter Rater Reliability rid Multiple Change-Point Detection in Multivariate Time Series ridge Ridge Regression with Automatic Selection of the Penalty Parameter ridgetorus PCA on the Torus via Density Ridges rim Interface to 'Maxima', Enabling Symbolic Computation ring Circular / Ring Buffers rioja Analysis of Quaternary Science Data 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 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' rkvo Read Key/Value Pair Observations rlang Functions for Base Types and Core R and 'Tidyverse' Features rlas Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data 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 rlme Rank-Based Estimation and Prediction in Random Effects Nested Models 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 rmi Mutual Information Estimators rminizinc R Interface to 'MiniZinc' rminqa Derivative-Free Optimization in R using C++ 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) rngSetSeed Seeding the Default RNG with a Numeric Vector 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 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 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" robustBLME Robust Bayesian Linear Mixed-Effects Models using ABC robustETM Robust Methods using Exponential Tilt Model robustHD Robust Methods for High-Dimensional Data robustbase Basic Robust Statistics robustcov Collection of Robust Covariance and (Sparse) Precision Matrix Estimators robustlmm Robust Linear Mixed Effects Models robustmatrix Robust Matrix-Variate Parameter Estimation robustrank Robust Rank-Based Tests robustreg Robust Regression Functions robustsae Robust Bayesian Small Area Estimation robustvarComp Robust Estimation of Variance Component Models rocTree Receiver Operating Characteristic (ROC)-Guided Classification and Survival Tree rococo Robust Rank Correlation Coefficient and Test rodeo A Code Generator for ODE-Based Models rofanova Robust Functional Analysis of Variance roll Rolling and Expanding Statistics rollinglda Construct Consistent Time Series from Textual Data rolog Query 'SWI'-'Prolog' from R rootSolve Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations 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 roxygen2 In-Line Documentation for R rpact Confirmatory Adaptive Clinical Trial Design and Analysis rpart.LAD Least Absolute Deviation Regression Trees rpf Response Probability Functions 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 rqubic Qualitative biclustering algorithm for expression data analysis in R 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 rrecsys Environment for Evaluating Recommender Systems rres Realized Relatedness Estimation and Simulation rrnni Manipulate with RNNI Tree Space rrpack Reduced-Rank Regression rrum Bayesian Estimation of the Reduced Reparameterized Unified Model with Gibbs Sampling rsae Robust Small Area Estimation rsbml R support for SBML, using libsbml rsdepth Ray Shooting Depth (i.e. RS Depth) Functions for Bivariate Analysis rsgeo An Interface to Rust's 'geo' Library rshift Paleoecology Functions for Regime Shift Analysis rsides SIDES-Based Subgroup Search Algorithms rspa Adapt Numerical Records to Fit (in)Equality Restrictions rsparse Statistical Learning on Sparse Matrices 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 rtk Rarefaction Tool Kit rtkore 'STK++' Core Library Integration to 'R' using 'Rcpp' rtmpt Fitting (Exponential/Diffusion) RT-MPT Models rtop Interpolation of Data with Variable Spatial Support rtpcr qPCR Data Analysis rtracklayer R interface to genome annotation files and the UCSC genome browser rtrend Trend Estimating Tools rts2 Real-Time Disease Surveillance rubias Bayesian Inference from the Conditional Genetic Stock Identification Model rucrdtw R Bindings for the UCR Suite rugarch Univariate GARCH Models ruimtehol Learn Text 'Embeddings' with 'Starspace' runjags Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS runner Running Operations for Vectors 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 rxode2 Facilities for Simulating from ODE-Based Models rxode2et Event Table Functions for 'rxode2' rxode2ll Log-Likelihood Functions for 'rxode2' rxode2parse Parsing and Code Generation Functions for 'rxode2' rxode2random Random Number Generation 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 saeMSPE Compute MSPE Estimates for the Fay Herriot Model and Nested Error Regression Model saeRobust Robust Small Area Estimation saeczi Small Area Estimation for Continuous Zero Inflated Data 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 samr SAM: Significance Analysis of Microarrays samurais Statistical Models for the Unsupervised Segmentation of Time-Series ('SaMUraiS') sanic Solving Ax = b Nimbly in C++ sanitizers C/C++ Source Code to Trigger Address and Undefined Behaviour Sanitizers santoku A Versatile Cutting Tool sarima Simulation and Prediction with Seasonal ARIMA Models sarsop Approximate POMDP Planning Software sasfunclust Sparse and Smooth Functional Clustering sass Syntactically Awesome Style Sheets ('Sass') satdad Sensitivity Analysis Tools for Dependence and Asymptotic Dependence satellite Handling and Manipulating Remote Sensing Data saturnin Spanning Trees Used for Network Inference sbde Semiparametric Bayesian Density Estimation sbfc Selective Bayesian Forest Classifier sbm Stochastic Blockmodels sbmSDP Semidefinite Programming for Fitting Block Models of Equal Block Sizes sbo Text Prediction via Stupid Back-Off N-Gram Models 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 scales Scale Functions for Visualization scalpel Processes Calcium Imaging Data 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 scistreer Maximum-Likelihood Perfect Phylogeny Inference at Scale scoper Spectral Clustering-Based Method for Identifying B Cell Clones 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 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 Single-Cell RNA-Seq Analysis Utilities sdcHierarchies Create and (Interactively) Modify Nested Hierarchies sdcMicro Statistical Disclosure Control Methods for Anonymization of Data and Risk Estimation sdcTable Methods for Statistical Disclosure Control in Tabular Data sde Simulation and Inference for Stochastic Differential Equations sdetorus Statistical Tools for Toroidal Diffusions sdmTMB Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB' sdpdth M-Estimator for Threshold Spatial Dynamic Panel Data Model sdprisk Measures of Risk for the Compound Poisson Risk Process with Diffusion sdpt3r Semi-Definite Quadratic Linear Programming Solver sdrt Estimating the Sufficient Dimension Reduction Subspaces in Time Series 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, Extendable-Output and Base64 Functions secsse Several Examined and Concealed States-Dependent Speciation and Extinction secure Sequential Co-Sparse Factor Regression 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 seismicRoll Fast Rolling Functions for Seismology using 'Rcpp' selectiveInference Tools for Post-Selection Inference sem Structural Equation Models semds Structural Equation Multidimensional Scaling 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 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 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 serrsBayes Bayesian Modelling of Raman Spectroscopy sets Sets, Generalized Sets, Customizable Sets and Intervals sf Simple Features for R sfcr Simulate Stock-Flow Consistent Models sfheaders Converts Between R Objects and Simple Feature Objects sgd Stochastic Gradient Descent for Scalable Estimation 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 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 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 sievePH Sieve Analysis Methods for Proportional Hazards Models sift Intelligently Peruse Data sigminer Extract, Analyze and Visualize Mutational Signatures for Genomic Variations signal Signal Processing signalHsmm Predict Presence of Signal Peptides signatureSearch Environment for Gene Expression Searching Combined with Functional Enrichment Analysis 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 simfam Simulate and Model Family Pedigrees with Structured Founders simmer Discrete-Event Simulation for R simmr A Stable Isotope Mixing Model simplexreg Regression Analysis of Proportional Data Using Simplex Distribution simplextree Provides Tools for Working with General Simplicial Complexes simputation Simple Imputation 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 sirus Stable and Interpretable RUle Set 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 skm Selective k-Means skpr Design of Experiments Suite: Generate and Evaluate Optimal Designs 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 slider Sliding Window Functions slopeOP Change-in-Slope OP Algorithm with a Finite Number of States slp Discrete Prolate Spheroidal (Slepian) Sequence Regression Smoothers sm Smoothing Methods for Nonparametric Regression and Density Estimation smaa Stochastic Multi-Criteria Acceptability Analysis smacof Multidimensional Scaling smam Statistical Modeling of Animal Movements smartsnp Fast Multivariate Analyses of Big Genomic Data smcryptoR ShangMi(SM) Cryptographic Algorithms(SM2/SM3/SM4) 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 smoots Nonparametric Estimation of the Trend and Its Derivatives in TS smurf Sparse Multi-Type Regularized Feature Modeling sna Tools for Social Network Analysis 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 snvecR Calculate Earth’s Obliquity and Precession in the Past socceR Evaluating Sport Tournament Predictions social Social Autocorrelation 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 spBFA Spatial Bayesian Factor Analysis spBayes Univariate and Multivariate Spatial-Temporal Modeling spBayesSurv Bayesian Modeling and Analysis of Spatially Correlated Survival Data spCP Spatially Varying Change Points spFW Hierarchical Spatial Finlay-Wilkinson Model 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 spTDyn Spatially Varying and Spatio-Temporal Dynamic Linear Models spTimer Spatio-Temporal Bayesian Modelling spaMM Mixed-Effect Models, with or without Spatial Random Effects 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 sparkwarc Load WARC Files into Apache Spark sparseDFM Estimate Dynamic Factor Models with Sparse Loadings sparseGAM Sparse Generalized Additive Models sparseHessianFD Numerical Estimation of Sparse Hessians 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 sparsegl Sparse Group Lasso sparseinv Computation of the Sparse Inverse Subset sparsenet Fit Sparse Linear Regression Models via Nonconvex Optimization sparsereg Sparse Bayesian Models for Regression, Subgroup Analysis, and Panel Data 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 spatialising Ising Model for Spatial Data spatialreg Spatial Regression Analysis spatialrisk Calculating Spatial Risk spatialsample Spatial Resampling Infrastructure spatialwarnings Spatial Early Warning Signals of Ecosystem Degradation spatialwidget Formats Spatial Data for Use in Htmlwidgets spatstat Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests 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 spc Statistical Process Control -- Calculation of ARL and Other Control Chart Performance Measures spcr Sparse Principal Component Regression spdep Spatial Dependence: Weighting Schemes, Statistics spduration Split-Population Duration (Cure) Regression specklestar Reduction of Speckle Data from BTA 6-m Telescope specs Single-Equation Penalized Error-Correction Selector (SPECS) spectralGraphTopology Learning Graphs from Data via Spectral Constraints spectre Predict Regional Community Composition sped Multi-Gene Descent Probabilities speedytax Rapidly Import Classifier Results into 'phyloseq' spef Semiparametric Estimating Functions spfa Semi-Parametric Factor Analysis spgs Statistical Patterns in Genomic Sequences spgwr Geographically Weighted Regression sphereTessellation Delaunay and Voronoï Tessellations on the Sphere 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 spinBayes Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection splancs Spatial and Space-Time Point Pattern Analysis 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 spnn Scale Invariant Probabilistic Neural Networks sport Sequential Pairwise Online Rating Techniques 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 sprintr Sparse Reluctant Interaction Modeling spt Sierpinski Pedal Triangle squat Statistics for Quaternion Temporal Data srm Structural Equation Modeling for the Social Relations Model ssdtools Species Sensitivity Distributions ssgraph Bayesian Graph Structure Learning using Spike-and-Slab Priors ssh Secure Shell (SSH) Client for R 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 stabreg Linear Regression with the Stable Distribution 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 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) steps Spatially- and Temporally-Explicit Population Simulator 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 stochvol Efficient Bayesian Inference for Stochastic Volatility (SV) Models stochvolTMB Likelihood Estimation of Stochastic Volatility Models stockR Identifying Stocks in Genetic Data stocks Stock Market Analysis storr Simple Key Value Stores stosim Stochastic Simulator for Reliability Modeling of Repairable Systems stpm Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes 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 strider Strided Iterator and Range string2path Rendering Font into 'data.frame' 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 strucchange Testing, Monitoring, and Dating Structural Changes strucchangeRcpp Testing, Monitoring, and Dating Structural Changes: C++ Version subplex Unconstrained Optimization using the Subplex Algorithm subrank Computes Copula using Ranks and Subsampling subselect Selecting Variable Subsets success Survival Control Charts Estimation Software sumFREGAT Fast Region-Based Association Tests on Summary Statistics sumR Approximate Summation of Series sumSome Permutation True Discovery Guarantee by Sum-Based Tests supc The Self-Updating Process Clustering Algorithms supclust Supervised Clustering of Predictor Variables Such as Genes supercells Superpixels of Spatial Data superml Build Machine Learning Models Like Using Python's Scikit-Learn Library in R surbayes Bayesian Analysis of Seemingly Unrelated Regression Models 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 Survival and Net Survival Models survPresmooth Presmoothed Estimation in Survival Analysis survSNP Power Calculations for SNP Studies with Censored Outcomes survcomp Performance Assessment and Comparison for Survival Analysis surveil Time Series Models for Disease Surveillance surveillance Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena 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 survival.svb Fit High-Dimensional Proportional Hazards Models 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 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 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 sylcount Syllable Counting and Readability Measurements symbolicQspray Multivariate Polynomials with Symbolic Parameters in their Coefficients symengine Interface to the 'SymEngine' Library symmetry Testing for Symmetry of Data and Model Residuals symphony Efficient and Precise Single-Cell Reference Atlas Mapping synMicrodata Synthetic Microdata Generator synchronicity Boost Mutex Functionality in R synlik Synthetic Likelihood Methods for Intractable Likelihoods synthACS Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data 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 tabularMLC Tabular Maximum Likelihood Classifier tabulate Pretty Console Output for Tables tagcloud Tag Clouds tailDepFun Minimum Distance Estimation of Tail Dependence Models tame Timing, Anatomical, Therapeutic and Chemical Based Medication Clustering 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 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 teigen Model-Based Clustering and Classification with the Multivariate t Distribution telefit Estimation and Prediction for Remote Effects Spatial Process Models templateICAr Estimate Brain Networks and Connectivity with ICA and Empirical Priors 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 terminaldigits Tests of Uniformity and Independence for Terminal Digits terra Spatial Data Analysis terrainmeshr Triangulate and Simplify 3D Terrain Meshes tessellation Delaunay and Voronoï Tessellations 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 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 this.path Get Executing Script's Path thor Interface to 'LMDB' thunder Computation and Visualisation of Atmospheric Convective Parameters thurstonianIRT Thurstonian IRT Models tibble Simple Data Frames tibbletime Time Aware Tibbles tibblify Rectangle Nested Lists tidyfast Fast Tidying of Data tidygenomics Tidy Verbs for Dealing with Genomic Data Frames tidygraph A Tidy API for Graph Manipulation tidylda Latent Dirichlet Allocation Using 'tidyverse' Conventions 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 timeless Fast General Purpose Date/Time Converter 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 tinycodet Functions to Help in your Coding Etiquette tipitaka Data and Tools for Analyzing 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 tmbstan MCMC Sampling from 'TMB' Model Object using 'Stan' tmcn A Text Mining Toolkit for Chinese 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 tokenbrowser Create Full Text Browsers from Annotated Token Lists tokenizers Fast, Consistent Tokenization of Natural Language Text tokenizers.bpe Byte Pair Encoding Text Tokenization topicmodels Topic Models topmodel Implementation of the Hydrological Model TOPMODEL in R 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 tram Transformation Models tramME Transformation Models with Mixed Effects tranSurv Transformation Model Based Estimation of Survival and Regression Under Dependent Truncation and Independent Censoring 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 treats Trees and Traits Simulations tree Classification and Regression Trees tree.interpreter Random Forest Prediction Decomposition and Feature Importance Measure treenomial Comparison of Trees using a Tree Defining Polynomial treeshap Compute SHAP Values for Your Tree-Based Models Using the 'TreeSHAP' Algorithm treesitter Bindings to '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' triangulr High-Performance Triangular Distribution Functions triebeard 'Radix' Trees in 'Rcpp' tripack Triangulation of Irregularly Spaced Data triptych Diagnostic Graphics to Evaluate Forecast Performance truncnorm Truncated Normal Distribution truncnormbayes Estimates Moments for a Truncated Normal Distribution using 'Stan' 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 TARMA Models tsfgrnn Time Series Forecasting Using GRNN tsfknn Time Series Forecasting Using Nearest Neighbors tsgarch Univariate GARCH 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 tuneR Analysis of Music and Speech tvR Total Variation Regularization 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 tweenr Interpolate Data for Smooth Animations twinning Data Twinning 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 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 understandBPMN Calculator of Understandability Metrics for BPMN ungroup Penalized Composite Link Model for Efficient Estimation of Smooth Distributions from Coarsely Binned Data unifed The Unifed Distribution unigd Universal Graphics Device unine Unine Light Stemmer unitquantreg Parametric Quantile Regression Models for Bounded Data units Measurement Units for R Vectors 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 unsystation Stationarity Test Based on Unsystematic Sub-Sampling updog Flexible Genotyping for Polyploids urca Unit Root and Cointegration Tests for Time Series Data 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 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') varband Variable Banding of Large Precision Matrices varbvs Large-Scale Bayesian Variable Selection Using Variational Methods vasicekreg Regression Modeling Using Vasicek Distribution 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 vdg Variance Dispersion Graphs and Fraction of Design Space Plots vdiffr Visual Regression Testing and Graphical Diffing vectorbitops Vector Bitwise Operations vegan Community Ecology Package vegclust Fuzzy Clustering of Vegetation Data vein Vehicular Emissions Inventories vennplot Venn Diagrams in 2D and 3D versus Compare Data Frames vetr Trust, but Verify vglmer Variational Inference for Hierarchical Generalized Linear Models viewscape Viewscape Analysis vinereg D-Vine Quantile Regression vines Multivariate Dependence Modeling with Vines viscomplexr Phase Portraits of Functions in the Complex Number Plane vistla Detecting Influence Paths with Information Theory vita Variable Importance Testing Approaches vol2birdR Vertical Profiles of Biological Signals in Weather Radar Data volesti Volume Approximation and Sampling of Convex Polytopes vroom Read and Write Rectangular Text Data Quickly vsgoftest Goodness-of-Fit Tests Based on Kullback-Leibler Divergence vsn Variance stabilization and calibration for microarray data wCorr Weighted Correlations warbleR Streamline Bioacoustic Analysis warp Group Dates waspr Wasserstein Barycenters of Subset Posteriors 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 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 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 wkutils Utilities for Well-Known Geometry Vectors 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 wowa Weighted Ordered Weighted Average 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 wtest The W-Test for Genetic Interactions Testing wv Wavelet Variance x13binary Provide the 'x13ashtml' Seasonal Adjustment Binary xcms LC-MS and GC-MS Data Analysis xdcclarge Estimating a (c)DCC-GARCH Model in Large Dimensions xfun Supporting Functions for Packages Maintained by 'Yihui Xie' xgboost Extreme Gradient Boosting xml2 Parse XML xoi Tools for Analyzing Crossover Interference xplorerr Tools for Interactive Data Exploration 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 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 zcurve An Implementation of Z-Curves zebu Local Association Measures zenplots Zigzag Expanded Navigation Plots zfa Zoom-Focus Algorithm zic Bayesian Inference for Zero-Inflated Count Models zip Cross-Platform 'zip' Compression zlib Compression and Decompression zlibbioc An R packaged zlib-1.2.5 zoid Bayesian Zero-and-One Inflated Dirichlet Regression Modelling 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/gannet/ripley/R/test-dev': A3 Accurate, Adaptable, and Accessible Error Metrics for Predictive Models 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 ABCanalysis Computed ABC Analysis ABCoptim Implementation of Artificial Bee Colony (ABC) Optimization ABCp2 Approximate Bayesian Computational Model for Estimating P2 ABHgenotypeR Easy Visualization of ABH Genotypes ABM Agent Based Model Simulation Framework ABPS The Abnormal Blood Profile Score to Detect Blood Doping ABSurvTDC Survival Analysis using Time Dependent Covariate for Animal Breeding ACA Abrupt Change-Point or Aberration Detection in Point Series ACDm Tools for Autoregressive Conditional Duration Models ACE.CoCo Analysis of Correlated High-Dimensional Expression (ACE) Data ACEP Analisis 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 ADMMsigma Penalized Precision Matrix Estimation via ADMM ADMUR Ancient Demographic Modelling Using Radiocarbon ADP Adoption Probability, Triers and Users Rate of a New Product ADPF Use Least Squares Polynomial Regression and Statistical Testing to Improve Savitzky-Golay ADPclust Fast Clustering Using Adaptive Density Peak Detection 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 AF Model-Based Estimation of Confounder-Adjusted Attributable Fractions AFFECT Accelerated Functional Failure Time Model with Error-Contaminated Survival Times AFM Atomic Force Microscope Image Analysis AFR Toolkit for Regression Analysis of Kazakhstan Banking Sector Data AFheritability The Attributable Fraction (AF) Described as a Function of Disease Heritability, Prevalence and Intervention Specific Factors AGD Analysis of Growth Data AGHmatrix Relationship Matrices for Diploid and Autopolyploid Species AGPRIS AGricultural PRoductivity in Space AHM Additive Heredity Model: Method for the Mixture-of-Mixtures Experiments 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 AICcPermanova Model Selection of PERMANOVA Models Using AICc AICcmodavg Model Selection and Multimodel Inference Based on (Q)AIC(c) AID Box-Cox Power Transformation AIPW Augmented Inverse Probability Weighting AIUQ Ab Initio Uncertainty Quantification ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account ALDqr Quantile Regression Using Asymmetric Laplace Distribution ALEPlot Accumulated Local Effects (ALE) Plots and Partial Dependence (PD) Plots ALFAM2 Dynamic Model of Ammonia Emission from Field-Applied Manure 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. ALTopt Optimal Experimental Designs for Accelerated Life Testing 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) AMIM Compute the Adjusted Market Inefficiency Measure AMModels Adaptive Management Model Manager AMPLE Shiny Apps to Support Capacity Building on Harvest Control Rules AMR Antimicrobial Resistance Data Analysis ANCOMBC Microbiome differential abudance and correlation analyses with bias correction ANN2 Artificial Neural Networks for Anomaly Detection ANOFA Analyses of Frequency Data ANOM Analysis of Means 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 AOV1R Inference in the Balanced One-Way ANOVA Model with Random Factor 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 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 APPEstimation Adjusted Prediction Model Performance Estimation APackOfTheClones Visualization of Clonal Expansion for Single Cell Immune Profiles APtools Average Positive Predictive Values (AP) for Binary Outcomes and Censored Event Times AQEval Air Quality Evaluation AQLSchemes Retrieving Acceptance Sampling Schemes AQuadtree Confidentiality of Spatial Point Data AQuality Water and Measurements Quality AR Another Look at the Acceptance-Rejection Method 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 AROC Covariate-Adjusted Receiver Operating Characteristic Curve Inference 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 ART Aligned Rank Transform for Nonparametric Factorial Analysis ARTofR To Insert Title, Divider, and Block of Comments ARTool Aligned Rank Transform ARUtools Management and Processing of Autonomous Recording Unit (ARU) Data ARpLMEC Censored Mixed-Effects Models with Different Correlation Structures ASGS.foyer Interface to the Australian Statistical Geography Standard ASMap Linkage Map Construction using the MSTmap Algorithm 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 ATNr Run Allometric Trophic Networks Models ATR Alternative Tree Representation ATbounds Bounding Treatment Effects by Limited Information Pooling AUC Threshold Independent Performance Measures for Probabilistic Classifiers AUCell AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures) AUtests Approximate Unconditional and Permutation Tests 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 Ac3net Inferring Directional Conservative Causal Core Gene Networks AcademicThemes Colour Plots with Palettes from Academic Institutions 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 AcousticNDLCodeR Coding Sound Files for Use with NDL AcrossTic A Cost-Minimal Regular Spanning Subgraph with TreeClust ActCR Extract Circadian Rhythms Metrics from Actigraphy Data ActFrag Activity Fragmentation Metrics Extracted from Minute Level Activity Data ActiSleep Sleep Duration Estimate Algorithm ActiveDriver Finding Cancer Driver Proteins with Enriched Mutations in Post-Translational Modification Sites 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 AdMit Adaptive Mixture of Student-t Distributions AdaSampling Adaptive Sampling for Positive Unlabeled and Label Noise Learning AdapSamp Adaptive Sampling Algorithms AdaptGauss Gaussian Mixture Models (GMM) AdequacyModel Adequacy of Probabilistic Models and General Purpose Optimization AdhereR Adherence to Medications AdhereRViz Adherence to Medications 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 AeRobiology A Computational Tool for Aerobiological Data AeroSampleR Estimate Aerosol Particle Collection Through Sample Lines AggregateR Aggregate Numeric, Date and Categorical Variables AgreementInterval Agreement Interval of Two Measurement Methods 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 AirMonitor Air Quality Data Analysis Ake Associated Kernel Estimations AlgDesign Algorithmic Experimental Design AlgebraicHaploPackage Haplotype Two Snips Out of a Paired Group of Patients 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 AnaCoDa Analysis of Codon Data under Stationarity using a Bayesian Framework Anaconda Targeted Differential and Global Enrichment Analysis of Taxonomic Rank by Shared Asvs AnalysisLin Exploratory Data Analysis AnanseSeurat Construct ANANSE GRN-Analysis Seurat AncestryMapper Assigning Ancestry Based on Population References AnchorRegression Perform AnchorRegression Andromeda Asynchronous Disk-Based Representation of Massive Data AnglerCreelSurveySimulation Simulate a Bus Route Creel Survey of Anglers AnimalHabitatNetwork Networks Characterising the Physical Configurations of Animal Habitats 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 AnnuityRIR Annuity Random Interest Rates AntAngioCOOL Anti-Angiogenic Peptide Prediction AntMAN Anthology of Mixture Analysis Tools AnthropMMD An R Package for the Mean Measure of Divergence (MMD) Anthropometry Statistical Methods for Anthropometric Data AntibodyTiters Antibody Titer Analysis of Vaccinated Patients 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 Apoderoides Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree Apollonius 2D Apollonius Graphs AppliedPredictiveModeling Functions and Data Sets for 'Applied Predictive Modeling' AquaBEHER Estimation of Rainy 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 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 AsioHeaders 'Asio' C++ Header Files AssetAllocation Backtesting Simple Asset Allocation Strategies AssetCorr Estimating Asset Correlations from Default Data AssetPricing Optimal Pricing of Assets with Fixed Expiry Date AssocAFC Allele Frequency Comparison AssocBin Measuring Association with Recursive Binning AssocTests Genetic Association Studies 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 AtlasMaker Make Multiple 'leaflet' Maps in 'Shiny' AtmChile Download Air Quality and Meteorological Information of Chile 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 AutoPipe Automated Transcriptome Classifier Pipeline: Comprehensive Transcriptome Analysis 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 AutoTransQF A Novel Automatic Shifted Log Transformation AutoWeatherIndices Calculating Weather Indices Autoplotprotein Development of Visualization Tools for Protein Sequence AutoregressionMDE Minimum Distance Estimation in Autoregressive Model Autoseed Retrieve Disease-Related Genes from Public Sources 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) BACCT Bayesian Augmented Control for Clinical Trials 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 BANOVA Hierarchical Bayesian ANOVA Models BAR Bayesian Adaptive Randomization BART Bayesian Additive Regression Trees BAS Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling BASS Bayesian Adaptive Spline Surfaces BASiNET Classification of RNA Sequences using Complex Network Theory BASiNETEntropy Classification of RNA Sequences using Complex Network and Information Theory BAT Biodiversity Assessment Tools BAYSTAR On Bayesian Analysis of Threshold Autoregressive Models BAwiR Analysis of Basketball Data BB Solving and Optimizing Large-Scale Nonlinear Systems BBEST Bayesian Estimation of Incoherent Neutron Scattering Backgrounds BBI Benthic Biotic Indices Calculation from Composition Data BBSSL Bayesian Bootstrap Spike-and-Slab LASSO BBmisc Miscellaneous Helper Functions for B. Bischl BCA1SG Block Coordinate Ascent with One-Step Generalized Rosen Algorithm BCBCSF Bias-Corrected Bayesian Classification with Selected Features BCC1997 Calculation of Option Prices Based on a Universal Solution BCClong Bayesian Consensus Clustering for Multiple Longitudinal Features BCDAG Bayesian Structure and Causal Learning of Gaussian Directed Graphs BCDating Business Cycle Dating and Plotting Tools BCEA Bayesian Cost Effectiveness Analysis BCEE The Bayesian Causal Effect Estimation Algorithm BCHM Clinical Trial Calculation Based on BCHM Design BCRA Breast Cancer Risk Assessment BCSub A Bayesian Semiparametric Factor Analysis Model for Subtype Identification (Clustering) BCT Bayesian Context Trees for Discrete Time Series BCgee Bias-Corrected Estimates for Generalized Linear Models for Dependent Data BClustLonG A Dirichlet Process Mixture Model for Clustering Longitudinal Gene Expression Data BDAlgo Bloom Detecting Algorithm BDEsize Efficient Determination of Sample Size in Balanced Design of Experiments BDP2 Bayesian Adaptive Designs for Phase II Trials with Binary Endpoint BDWreg Bayesian Inference for Discrete Weibull Regression BDgraph Bayesian Structure Learning in Graphical Models using Birth-Death MCMC BE Bioequivalence Study Data Analysis 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 BEND Bayesian Estimation of Nonlinear Data (BEND) BENMMI Benthic Multi-Metric Index BESTree Branch-Exclusive Splits Trees BET Binary Expansion Testing BETS Brazilian Economic Time Series BElikelihood Likelihood Method for Evaluating Bioequivalence BFF Bayes Factor Functions BFI Bayesian Federated Inference 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 BHH2 Useful Functions for Box, Hunter and Hunter II 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 BIEN Tools for Accessing the Botanical Information and Ecology Network Database BIFIEsurvey Tools for Survey Statistics in Educational Assessment BIGDAWG Case-Control Analysis of Multi-Allelic Loci BIGL Biochemically Intuitive Generalized Loewe Model BINCOR Estimate the Correlation Between Two Irregular Time Series BIOMASS Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests BIOdry Multilevel Modeling of Dendroclimatical Fluctuations BISdata Download Data from the Bank for International Settlements (BIS) BKTR Bayesian Kernelized Tensor Regression BLA Boundary Line Analysis BLCOP Black-Litterman and Copula Opinion Pooling Frameworks BLModel Black-Litterman Posterior Distribution BLOQ Impute and Analyze Data with BLOQ Observations BLPestimatoR Performs a BLP Demand Estimation BLR Bayesian Linear Regression BLRPM Stochastic Rainfall Generator Bartlett-Lewis Rectangular Pulse Model BLRShiny Interactive Document for Working with Binary Logistic Regression Analysis BLRShiny2 Interactive Document for Working with Binary Logistic Regression Analysis BLSM Bayesian Latent Space Model BMA Bayesian Model Averaging BMAmevt Multivariate Extremes: Bayesian Estimation of the Spectral Measure BMRBr 'BMRB' File Downloader BMRMM An Implementation of the Bayesian Markov (Renewal) Mixed Models BMS Bayesian Model Averaging Library BMT The BMT Distribution BMTAR Bayesian Approach for MTAR Models with Missing Data BMconcor CONCOR for Structural- And Regular-Equivalence Blockmodeling BMisc Miscellaneous Functions for Panel Data, Quantiles, and Printing Results BNPTSclust A Bayesian Nonparametric Algorithm for Time Series Clustering BNPdensity Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures BNPmix Bayesian Nonparametric Mixture Models BNSL Bayesian Network Structure Learning BNSP Bayesian Non- And Semi-Parametric Model Fitting BNrich Pathway Enrichment Analysis Based on Bayesian Network BOIN Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials BOJ Interface to Bank of Japan Statistics BOSO Bilevel Optimization Selector Operator BOSSreg Best Orthogonalized Subset Selection (BOSS) 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 BRBVS Variable Ranking in Copula Survival Models Affected by General Censoring Scheme BRDT Binomial Reliability Demonstration Tests 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 BRVM Retrieve Historical Data of Companies Listed on the 'BRVM' Stock Exchange BRcal Boldness-Recalibration of Binary Events BRugs Interface to the 'OpenBUGS' MCMC Software BSDA Basic Statistics and Data Analysis 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 BSW Fitting a Log-Binomial Model using the Bekhit-Schöpe-Wagenpfeil (BSW) Algorithm BSagri Safety Assessment in Agricultural Field Trials BSgenome Software infrastructure for efficient representation of full genomes and their SNPs BT (Adaptive) Boosting Trees Algorithm BTLLasso Modelling Heterogeneity in Paired Comparison Data BTM Biterm Topic Models for Short Text BTSPAS Bayesian Time-Stratified Population Analysis BTSR Bounded Time Series Regression BTYD Implementing BTYD Models with the Log Sum Exp Patch BTYDplus Probabilistic Models for Assessing and Predicting your Customer Base BTdecayLasso Bradley-Terry Model with Exponential Time Decayed Log-Likelihood and Adaptive Lasso BTtest Estimate the Number of Factors in Large Nonstationary Datasets BUCSS Bias and Uncertainty Corrected Sample Size BVAR Hierarchical Bayesian Vector Autoregression BVARverse Tidy Bayesian Vector Autoregression BVSNLP Bayesian Variable Selection in High Dimensional Settings using Nonlocal Priors 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" BaSkePro Bayesian Model to Archaeological Faunal Skeletal Profiles 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 in Thermal Modelling BasketballAnalyzeR Analysis and Visualization of Basketball Data BatchExperiments Statistical Experiments on Batch Computing Clusters BatchGetSymbols Downloads and Organizes Financial Data for Multiple Tickers BatchJobs Batch Computing with R BayLum Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating Bayenet Bayesian Quantile Elastic Net for Genetic Study BayesARIMAX Bayesian Estimation of ARIMAX Model BayesBEKK Bayesian Estimation of Bivariate Volatility Model BayesBP Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix BayesBinMix Bayesian Estimation of Mixtures of Multivariate Bernoulli Distributions BayesCACE Bayesian Model for CACE Analysis BayesCR Bayesian Analysis of Censored Regression Models Under Scale Mixture of Skew Normal Distributions BayesCTDesign Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data BayesCVI Bayesian Cluster Validity Index BayesCombo Bayesian Evidence Combination BayesComm Bayesian Community Ecology Analysis BayesDA Functions and Datasets for the book "Bayesian Data Analysis" BayesDIP Bayesian Decreasingly Informative Priors for Early Termination Phase II Trials BayesDLMfMRI Statistical Analysis for Task-Based Fmri Data BayesDesign Bayesian Single-Arm Design with Survival Endpoints BayesDissolution Bayesian Models for Dissolution Testing BayesESS Determining Effective Sample Size BayesFBHborrow Bayesian Dynamic Borrowing with Flexible Baseline Hazard Function BayesFM Bayesian Inference for Factor Modeling BayesFactor Computation of Bayes Factors for Common Designs BayesFluxR Implementation of Bayesian Neural Networks BayesGOF Bayesian Modeling via Frequentist Goodness-of-Fit 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 BayesMassBal Bayesian Data Reconciliation of Separation Processes BayesMixSurv Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification 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 BayesOrdDesign Bayesian Group Sequential Design for Ordinal Data BayesPPD Bayesian Power Prior Design BayesPPDSurv Bayesian Power Prior Design for Survival Data BayesPieceHazSelect Variable Selection in a Hierarchical Bayesian Model for a Hazard Function BayesPostEst Generate Postestimation Quantities for Bayesian MCMC Estimation BayesProject Fast Projection Direction for Multivariate Changepoint Detection BayesRGMM Bayesian Robust Generalized Mixed Models for Longitudinal Data BayesRS Bayes Factors for Hierarchical Linear Models with Continuous Predictors BayesRep Bayesian Analysis of Replication Studies BayesRepDesign Bayesian Design of Replication Studies BayesReversePLLH Fits the Bayesian Piecewise Linear Log-Hazard Model BayesS5 Bayesian Variable Selection Using Simplified Shotgun Stochastic Search with Screening (S5) BayesSUR Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings BayesSampling Bayes Linear Estimators for Finite Population BayesSurvival Bayesian Survival Analysis for Right Censored Data BayesSurvive Bayesian Survival Models for High-Dimensional Data 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 BayesX R Utilities Accompanying the Software Package BayesX BayesXsrc Distribution of the 'BayesX' C++ Sources BayesfMRI Spatial Bayesian Methods for Task Functional MRI Studies BayesianFactorZoo Bayesian Solutions for the Factor Zoo: We Just Ran Two Quadrillion Models BayesianGLasso Bayesian Graphical Lasso 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 BayesianReasoning Plot Positive and Negative Predictive Values for Medical Tests BayesianTools General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics Bayesiangammareg Bayesian Gamma Regression: Joint Mean and Shape Modeling Bayesiantreg Bayesian t Regression for Modeling Mean and Scale Parameters Bayesrel Bayesian Reliability Estimation BcDiag Diagnostics Plots for Bicluster Data Bchron Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling BeQut Bayesian Estimation for Quantile Regression Mixed Models BeSS Best Subset Selection in Linear, Logistic and CoxPH Models BeadDataPackR Compression of Illumina BeadArray data 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 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 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 BiBitR R Wrapper for Java Implementation of BiBit 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 BiSEp Toolkit to Identify Candidate Synthetic Lethality BiTrinA Binarization and Trinarization of One-Dimensional Data BiasCorrector A GUI to Correct Measurement Bias in DNA Methylation Analyses BiasedUrn Biased Urn Model Distributions BibPlots Plot Functions for Use in Bibliometrics BicARE Biclustering Analysis and Results Exploration BifactorIndicesCalculator Bifactor Indices Calculator BigQuic Big Quadratic Inverse Covariance Estimation BigVAR Dimension Reduction Methods for Multivariate Time Series BimodalIndex The Bimodality Index BinGSD Calculation 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 BinaryEMVS Variable Selection for Binary Data Using the EM Algorithm BinaryEPPM Mean and Scale-Factor Modeling of Under- And Over-Dispersed Binary Data BinarybalancedCut Threshold Cut Point of Probability for a Binary Classifier Model BioCircos Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js' BioCro Modular Crop Growth Simulations BioInsight Filter and Plot RNA Biotypes BioM2 Biologically Explainable Machine Learning Framework BioMark Find Biomarkers in Two-Class Discrimination Problems BioNet Routines for the functional analysis of biological networks BioPET Biomarker Prognostic Enrichment Tool BioPETsurv Biomarker Prognostic Enrichment Tool for Time-to-Event Trial BioPred An R Package for Biomarkers Analysis in Precision Medicine BioProbability Probability in Biostatistics BioRssay Analyze Bioassays and Probit Graphs BioStatR Initiation à La Statistique Avec R BioVenn Create Area-Proportional Venn Diagrams from Biological Lists Biobase Biobase: Base functions for Bioconductor BiocBaseUtils General utility functions for developing Bioconductor packages 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 BiocPkgTools Collection of simple tools for learning about Bioconductor Packages 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 Biostatistics Statistics Tutorials for Biologists 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 BisRNA Analysis of RNA Cytosine-5 Methylation BisqueRNA Decomposition of Bulk Expression with Single-Cell Sequencing BivGeo Basu-Dhar Bivariate Geometric Distribution BivRec Bivariate Alternating Recurrent Event Data Analysis BivRegBLS Tolerance Interval and EIV Regression - Method Comparison Studies BivUnifBin Generation of Bivariate Uniform Data and Its Relation to Bivariate Binary Data Bivariate.Pareto Bivariate Pareto Models BlakerCI Blaker's Binomial and Poisson Confidence Limits BlandAltmanLeh Plots (Slightly Extended) Bland-Altman Plots Blendstat Joint Analysis of Experiments with Mixtures and Random Effects BlockCov Estimation of Large Block Covariance Matrices BlockMissingData Integrating Multi-Source Block-Wise Missing Data in Model Selection BlockmodelingGUI GUI for the Generalised Blockmodeling of Valued Networks BlythStillCasellaCI Blyth-Still-Casella Exact Binomial Confidence Intervals BoSSA A Bunch of Structure and Sequence Analysis BoardGames Board Games and Tools for Building Board Games Bodi Boosting Diversity in Regression Ensembles Bolstad Functions for Elementary Bayesian Inference Bolstad2 Bolstad Functions BoltzMM Boltzmann Machines with MM Algorithms BonEV An Improved Multiple Testing Procedure for Controlling False Discovery Rates BondValuation Fixed Coupon Bond Valuation Allowing for Odd Coupon Periods and Various Day Count Conventions BoneProfileR Tools to Study Bone Compactness BoolFilter Optimal Estimation of Partially Observed Boolean Dynamical Systems 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 BootMRMR Bootstrap-MRMR Technique for Informative Gene Selection BootPR Bootstrap Prediction Intervals and Bias-Corrected Forecasting BootWPTOS Test Stationarity using Bootstrap Wavelet Packet Tests BootstrapQTL Bootstrap cis-QTL Method that Corrects for the Winner's Curse 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 BoundaryStats Boundary Overlap Statistics BoutrosLab.plotting.general Functions to Create Publication-Quality Plots BradleyTerry2 Bradley-Terry Models BrailleR Improved Access for Blind Users BrainCon Inference the Partial Correlations Based on Time Series Data 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 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 BrownDog Brown Dog R Interface Brq Bayesian Analysis of Quantile Regression Models BsMD Bayes Screening and Model Discrimination 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 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 CACIMAR Cross-Species Analysis of Cell Identities, Markers and Regulations CADFtest A Package to Perform Covariate Augmented Dickey-Fuller Unit Root Tests 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 CAMAN Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN CAMML Cell-Typing using Variance Adjusted Mahalanobis Distances with Multi-Labeling CANSIM2R Directly Extracts Complete CANSIM Data Tables 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 CASMAP Detection of Statistically Significant Combinations of SNPs in Association Mapping CASMI 'CASMI'-Based Functions CAST 'caret' Applications for Spatial-Temporal Models 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 CBCgrps Compare Baseline Characteristics Between Groups CBPS Covariate Balancing Propensity Score CBSr Fits Cubic Bezier Spline Functions to Intertemporal and Risky Choice Data CBT Confidence Bound Target Algorithm CBnetworkMA Contrast-Based Bayesian Network Meta Analysis CC Control Charts CCA Canonical Correlation Analysis CCAMLRGIS Antarctic Spatial Data Manipulation CCM Correlation Classification Method CCMMR Minimization of the Convex Clustering Loss Function CCP Significance Tests for Canonical Correlation Analysis (CCA) CCTpack Consensus Analysis, Model-Based Clustering, and Cultural Consensus Theory Applications CCWeights Perform Weighted Linear Regression for Calibration Curve CDCPLACES Access the 'CDC PLACES' API 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 CDVI Cuddy-Della Valle Index for Capturing the Instability in Time Series Data CDVineCopulaConditional Sampling from Conditional C- and D-Vine Copulas CDatanet Econometrics of Network Data CEC Cross-Entropy Clustering CEDA CRISPR Screen and Gene Expression Differential 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 Tress 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 CFO CFO-Type Designs in Phase I Clinical Trials CFilt Collaborative Filtering by Reference Classes CFtime Using CF-Compliant Calendars with Climate Projection Data CGE Computing General Equilibrium CGGP Composite Grid Gaussian Processes CGManalyzer Continuous Glucose Monitoring Data Analyzer CGNM Cluster Gauss-Newton Method CGP Composite Gaussian Process Models CGPfunctions Powell Miscellaneous Functions for Teaching and Learning Statistics CGR Compound Growth Rate for Capturing the Growth Rate Over the Period CHEMIST Causal Inference with High-Dimensional Error-Prone Covariates and Misclassified Treatments CHFF Closest History Flow Field Forecasting for Bivariate Time Series 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 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 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 CKMRpop Forward-in-Time Simulation and Tallying of Pairwise Relationships CLA Critical Line Algorithm in Pure R CLAST Exact Confidence Limits after a Sequential Trial CLME Constrained Inference for Linear Mixed Effects Models CLONETv2 Clonality Estimates in Tumor 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 CMHNPA Cochran-Mantel-Haenszel and Nonparametric ANOVA CMLS Constrained Multivariate Least Squares CMMs Compositional Mediation Model CMShiny Interactive Document for Working with Confusion Matrix CMapViz Representation Tool For Output Of Connectivity Map (CMap) Analysis CMplot Circle Manhattan Plot CNAIM Common Network Asset Indices Methodology (CNAIM) CNEr CNE Detection and Visualization 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 CNVScope A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization CNprep Pre-Process DNA Copy Number (CN) Data for Detection of CN Events COAP High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model COCONUT COmbat CO-Normalization Using conTrols (COCONUT) 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 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 CORElearn Classification, Regression and Feature Evaluation 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 CP Conditional Power Calculations CPAT Change Point Analysis Tests CPBayes Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations CPC Implementation of Cluster-Polarization Coefficient 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) 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 CRE Interpretable Discovery and Inference of Heterogeneous Treatment Effects CREAM Clustering of Genomic Regions Analysis Method CREDS Calibrated Ratio Estimator under Double Sampling Design CRF Conditional Random Fields CRM Continual Reassessment Method (CRM) for Phase I Clinical Trials 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 CRWRM Changing the Reference Group without Re-Running the Model CRediTas Generate CRediT Author Statements CSCNet Fitting and Tuning Regularized Cause-Specific Cox Models with Elastic-Net Penalty CSESA CRISPR-Based Salmonella Enterica Serotype Analyzer CSGo Collecting Counter Strike Global Offensive Data 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 CSTools Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales CSclone Bayesian Nonparametric Modeling in R CSeqpat Frequent Contiguous Sequential Pattern Mining of Text CTAShiny Interactive Application for Working with Contingency Tables CTD A Method for 'Connecting The Dots' in Weighted Graphs CTM A Text Mining Toolkit for Chinese Document CTNote CTN Outcomes, Treatments, and Endpoints 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 CTTinShiny Shiny Interface for the CTT Package 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 CVD Color Vision Deficiencies CVR Canonical Variate Regression 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 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 Calculator.LR.FNs Calculator for LR Fuzzy Numbers CalibratR Mapping ML Scores to Calibrated Predictions CalibrateSSB Weighting and Estimation for Panel Data with Non-Response CalibrationCurves Calibration 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 Canopy Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing 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 API 'Sede Electronica Del Catastro' Category Category Analysis CauchyCP Powerful Test for Survival Data under Non-Proportional Hazards CausCor Calculate Correlations and Estimate Causality CausalGAM Estimation of Causal Effects with Generalized Additive Models 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 CausalModels Causal Inference Modeling for Estimation of Causal Effects CausalQueries Make, Update, and Query Binary Causal Models CautiousLearning Control Charts with Guaranteed In-Control Performance and Cautious Parameters Learning CePa Centrality-Based Pathway Enrichment CeRNASeek Identification and Analysis of ceRNA Regulation CenBAR Broken Adaptive Ridge AFT Model with Censored Data CensMFM Finite Mixture of Multivariate Censored/Missing Data CensSpatial Censored Spatial Models Census2016 Data from the Australian Census 2016 CerioliOutlierDetection Outlier Detection Using the Iterated RMCD Method of Cerioli (2010) Certara.NLME8 Utilities for Certara's Nonlinear Mixed-Effects Modeling Engine Certara.R Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and Visualization ChainLadder Statistical Methods and Models for Claims Reserving in General Insurance 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 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 ChillModels Processing Chill and Heat Models for Temperate Fruit Trees ChineseNames Chinese Name Database 1930-2008 ChoR Chordalysis R Package ChoiceModelR Choice Modeling in R CholWishart Cholesky Decomposition of the Wishart Distribution CircMLE Maximum Likelihood Analysis of Circular Data CircNNTSR Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models CircNNTSRmult Multivariate Circular Data using MNNTS Models CircOutlier Detection of Outliers in Circular-Circular Regression CircSpaceTime Spatial and Spatio-Temporal Bayesian Model for Circular Data CircStats Circular Statistics, from "Topics in Circular Statistics" (2001) CirceR Construct Cohort Inclusion and Restriction Criteria Expressions CirclesIntersections Algorithm for Computation of the Intersection Areas of N Circles CircularDDM Circular Drift-Diffusion Model CircularSilhouette Fast Silhouette on Circular or Linear Data Clusters 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 CleanBSequences Curing of Biological Sequences CleaningValidation Cleaning Validation Functions for Pharmaceutical Cleaning Process ClickClust Model-Based Clustering of Categorical Sequences ClickClustCont Mixtures of Continuous Time Markov Models 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 ClinSigMeasures Clinical Significance Measures 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 ClusVis Gaussian-Based Visualization of Gaussian and Non-Gaussian Model-Based Clustering 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 ClustOfVar Clustering of Variables ClustVarLV Clustering of Variables Around Latent Variables Cluster.OBeu Cluster Analysis 'OpenBudgets.eu' ClusterBootstrap Analyze Clustered Data with Generalized Linear Models using the Cluster Bootstrap ClusterR Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering 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 Copula Based Cluster Analysis CoDaImpact Interpreting CoDa Regression Models CoDiNA Co-Expression Differential Network Analysis CoFRA Complete Functional Regulation Analysis CoImp Parametric and Non-Parametric Copula-Based Imputation Methods CoMiRe Convex Mixture Regression CoNI Correlation Guided Network Integration (CoNI) CoOL Causes of Outcome Learning CoRpower Power Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials CoSMoS Complete Stochastic Modelling Solution 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 CohensdpLibrary Cohen's D_p Computation with Confidence Intervals CohortAlgebra Use of Interval Algebra to Create New Cohort(s) from Existing Cohorts CohortCharacteristics Summarise and Visualise Characteristics of Patients in the OMOP CDM CohortConstructor Build and Manipulate Study Cohorts Using a Common Data Model CohortExplorer Explorer of Profiles of Patients in a Cohort CohortPlat Simulation of Cohort Platform Trials for Combination Treatments CohortSymmetry Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model Coinprofile Coincident Profile CollapseLevels Collapses Levels, Computes Information Value and WoE CollocInfer Collocation Inference for Dynamic Systems ColorNameR Give Colors a Name Colossus "Risk Model Regression and Analysis with Complex Non-Linear Models" ComICS Computational Methods for Immune Cell-Type Subsets ComRiskModel Fitting of Complementary Risk Models CombinS Construction Methods of some Series of PBIB Designs CombinePortfolio Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies 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 CompDist Multisection Composite Distributions CompExpDes Computer Experiment Designs CompGR Complete Annual Growth Rate Generator CompMix A Comprehensive Toolkit for Environmental Mixtures Analysis ('CompMix') 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 CompositionalML Machine Learning with Compositional Data CompoundEvents Statistical Modeling of Compound Events ConConPiWiFun Optimisation with Continuous Convex Piecewise (Linear and Quadratic) Functions ConNEcT Contingency Measure-Based Networks for Binary Time Series ConSpline Partial Linear Least-Squares Regression using Constrained Splines Conake Continuous Associated Kernel Estimation 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 CondIndTests Nonlinear Conditional Independence Tests CondMVT Conditional Multivariate t Distribution, Expectation Maximization Algorithm, and Its Stochastic Variants CondiS Censored Data Imputation for Direct Modeling ConfIntVariance Confidence Interval for the Univariate Population Variance without Normality Assumption ConfZIC Confidence Envelopes for Model Selection Criteria Based on Minimum ZIC 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 CongreveLamsdell2016 Distance Metrics for Trees Generated by Congreve and Lamsdell Conigrave Flexible Tools for Multiple Imputation ConnMatTools Tools for Working with Connectivity Data ConnectednessApproach Connectedness Approach 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 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 CopSens Copula-Based Sensitivity Analysis for Observational Causal Inference CopernicusDEM Copernicus Digital Elevation Models 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 CorBin Generate High-Dimensional Binary Data with Correlation Structures CorMID Correct Mass Isotopologue Distribution Vectors Corbi Collection of Rudimentary Bioinformatics Tools CoreMicrobiomeR Identification of Core Microbiome CornerstoneR Collection of Scripts for Interface Between 'Cornerstone' and 'R' CoronaNetR API Access to 'CoronaNet' Data 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 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 CovCombR Combine Partial Covariance / Relationship Matrices CovRegRF Covariance Regression with Random Forests 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 CoxICPen Variable Selection for Cox's Model with Interval-Censored Data CoxPlus Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects CoxR2 R-Squared Measure Based on Partial LR Statistic, for the Cox PH Regression Model 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 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 CrossVA Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms 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 CruzPlot Plot Shipboard DAS Data CryptRndTest Statistical Tests for Cryptographic Randomness CsChange Testing for Change in C-Statistic Cubist Rule- And Instance-Based Regression Modeling CureAuxSP Mixture Cure Models with Auxiliary Subgroup Survival Probabilities CureDepCens Dependent Censoring Regression Models with Cure Fraction CurricularAnalytics Exploring and Analyzing Academic Curricula 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 CytoSimplex Simplex Visualization of Cell Fate Similarity in Single-Cell Data CytobankAPI Cytobank API Wrapper for R D2MCS Data Driving Multiple Classifier System D3GB Interactive Genome Browser D3mirt Descriptive 3D Multidimensional Item Response Theory Modelling D3partitionR Interactive Charts of Nested and Hierarchical Data with 'D3.js' D4TAlink.light FAIR Data - 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 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 DAPAR Tools for the Differential Analysis of Proteins Abundance with R DAPARdata Data accompanying the DAPAR and Prostar packages DATAstudio The Research Data Warehouse of Miguel de Carvalho DArand Differential Analysis with Random Reference Genes DBEST Detecting Breakpoints and Estimating Segments in Trend 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 DBTCShiny Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis 'shiny' Application DBfit A Double Bootstrap Method for Analyzing Linear Models with Autoregressive Errors DBpower Finite Sample Power Calculations for Detection Boundary Tests 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 DCODE List Linear n-Peptide Constraints for Overlapping Protein Regions DCSmooth Nonparametric Regression and Bandwidth Selection for Spatial Models 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 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 DDPNA Disease-Drived Differential Proteins Co-Expression Network Analysis DDRTree Learning Principal Graphs with DDRTree DDoutlier Distance & Density-Based Outlier Detection 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 DEGRE Inferring Differentially Expressed Genes using Generalized Linear Mixed Models DELTD Kernel Density Estimation using Lifetime Distributions DEM The Distributed EM Algorithms in Multivariate Gaussian Mixture Models DEMOVA DEvelopment (of Multi-Linear QSPR/QSAR) MOdels VAlidated using Test Set DEPONS2R Read, Plot and Analyse Output from the DEPONS Model DES Discrete Event Simulation DESeq2 Differential gene expression analysis based on the negative binomial distribution DEoptim Global Optimization by Differential Evolution DEoptimR Differential Evolution Optimization in Pure R 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 DGM Dynamic Graphical Models 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 DICOMread Reading and Saving DICOM Image Files DIDHAD Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Stayers DIDmultiplegt Estimation in DID with Multiple Groups and Periods DIDmultiplegtDYN Estimation in Difference-in-Difference Designs with Multiple Groups and Periods 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 DISTRIB Four Essential Functions for Statistical Distributions Analysis: A New Functional Approach DIZtools Lightweight Utilities for 'DIZ' R Package Development DIZutils Utilities for 'DIZ' R Package Development DIconvex Finding Patterns of Monotonicity and Convexity in Data 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 DLL Decorrelated Local Linear Estimator 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 DMQ Dynamic Multiple Quantile (DMQ) Model DMRnet Delete or Merge Regressors Algorithms for Linear and Logistic Model Selection and High-Dimensional Data DMTL Tools for Applying Distribution Mapping Based Transfer Learning DMtest Differential Methylation Tests (DMtest) DMwR2 Functions and Data for the Second Edition of "Data Mining with R" DNAcopy DNA Copy Number Data Analysis 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 DNH4 Crawling for Daum News Text DNLC Differential Network Local Consistency Analysis DNMF Discriminant Non-Negative Matrix Factorization DNetFinder Estimating Differential Networks under Semiparametric Gaussian Graphical Models DOEM The Distributed Online Expectation Maximization Algorithms to Solve Parameters of Poisson Mixture Models 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 DOT Render and Export DOT Graphs in R 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 DPBBM Dirichlet Process Beta-Binomial Mixture DPP Inference of Parameters of Normal Distributions from a Mixture of Normals DPQ Density, Probability, Quantile ('DPQ') Computations 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 DPtree Dirichlet-Based Polya Tree DQAgui Graphical User Interface for Data Quality Assessment DQAstats Core Functions for Data Quality Assessment DR.SC Joint Dimension Reduction and Spatial Clustering DRAYL Computation of Rayleigh Densities of Arbitrary Dimension DRDID Doubly Robust Difference-in-Differences Estimators DRDRtest A Nonparametric Doubly Robust Test for Continuous Treatment Effect 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 DRR Dimensionality Reduction via Regression DRaWR Discriminative Random Walk with Restart DRomics Dose Response for Omics DRquality Quality Measurements for Dimensionality Reduction 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 DSI 'DataSHIELD' Interface 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 DSSP Implementation of the Direct Sampling Spatial Prior 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' 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 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) DTSEA Drug Target Set Enrichment Analysis 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' 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 DWLasso Degree Weighted Lasso DWreg Parametric Regression for Discrete Response DYM Did You Mean? DYNATE Dynamic Aggregation Testing 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 Dasst Tools for Reading, Processing and Writing 'DSSAT' Files DatAssim Data Assimilation DataClean Data Cleaning DataCombine Tools for Easily Combining and Cleaning Data Sets DataEditR An Interactive Editor for Viewing, Entering, Filtering & Editing Data DataExplorer Automate Data Exploration and Treatment DataFakeR Generate Fake Data for Relational Databases 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 DataSetsUni A Collection of Univariate Data Sets DataSpaceR Interface to 'the CAVD DataSpace' 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 'Refinitiv Datastream' System and R DatastreamR Datastream API DateTimeRangePicker A Datetime Range Picker Widget for Usage in 'Shiny' Applications Davies The Davies Quantile Function 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 DebiasInfer Efficient Inference on High-Dimensional Linear Model with Missing Outcomes DeclareDesign Declare and Diagnose Research Designs DecomposeR Empirical Mode Decomposition for Cyclostratigraphy DeconRNASeq Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data DecorateR Fit and Deploy DECORATE Trees Deducer A Data Analysis GUI for R DeductiveR Deductive Rational Method DeepLearningCausal Causal Inference with Super Learner and Deep Neural Networks 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 DemoKin Estimate Population Kin Distribution DemografixeR Extrapolate Gender, Age and Nationality of a Name DemographicTable Creating 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 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' DescrTab2 Publication Quality Descriptive Statistics Tables DescribeDF Description of a Data Frame DescribeDisplay An Interface to the 'DescribeDisplay' 'GGobi' Plugin DescriptiveRepresentationCalculator Descriptive Representation Calculator: Characterizing Observed and Expected Representation DescriptiveStats.OBeu Descriptive Statistics 'OpenBudgets.eu' DescriptiveWH Descriptive Statistics Design.parameters Parameters of the Experimental Designs DesignCTPB Design Clinical Trials with Potential Biomarker Effect DesignLibrary Library of Research Designs DetLifeInsurance Life Insurance Premium and Reserves Valuation DetMCD Implementation of the DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter) DetR Suite of Deterministic and Robust Algorithms for Linear Regression 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 Diderot Bibliographic Network Analysis 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 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 DirichletReg Dirichlet Regression DisHet Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples DisImpact Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups DisaggregateTS High-Dimensional Temporal Disaggregation DiscreteDatasets Example Data Sets for Use with Discrete Statistical Tests DiscreteFDR 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 DistributionOptimization Distribution Optimization DistributionTest Powerful Goodness-of-Fit Tests Based on the Likelihood Ratio DistributionUtils Distribution Utilities DivE Diversity Estimator DiversificationR Econometric Tools to Measure Portfolio Diversification 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 DoEstRare Rare Variant Association Test Based on Position Density Estimation DockerParallel Using the Docker Container to Create R Workers on Local or Cloud Platform Dodge Acceptance Sampling Ideas Originated by H.F. Dodge DominoDataR 'Domino Data R SDK' 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 Dpit Distribution Pitting DrBats Data Representation: Bayesian Approach That's Sparse DrDimont Drug Response Prediction from Differential Multi-Omics Networks DrImpute Imputing Dropout Events in Single-Cell RNA-Sequencing Data DramaAnalysis Analysis of Dramatic Texts DriftBurstHypothesis Calculates the Test-Statistic for the Drift Burst Hypothesis DrillR R Driver for Apache Drill 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 DtD Distance to Default Dtableone Tabular Comparison of Paired Diagnostic Tests Durga Effect Size Estimation and Visualisation DyMEP Dynamic Multi Environment Phenology-Model DySS Dynamic Screening Systems Dykstra Quadratic Programming using Cyclic Projections DynClust Denoising and Clustering for Dynamical Image Sequence (2D or 3D)+t 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 DynaRankR Inferring Longitudinal Dominance Hierarchies DynamicGP Modelling and Analysis of Dynamic Computer Experiments 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' E4tools Management and Processing Tools for Data Produced by the Empatica E4 EATME Exponentially Weighted Moving Average with Adjustments to Measurement Error EAinference Estimator Augmentation and Simulation-Based Inference 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 EBPRS Derive Polygenic Risk Score Based on Emprical Bayes Theory EBglmnet Empirical Bayesian Lasso and Elastic Net Methods for Generalized Linear Models EBrank Empirical Bayes Ranking ECGofTestDx A Goodness-of-Fit Test for Elliptical Distributions with Diagnostic Capabilities ECLRMC Ensemble Correlation-Based Low-Rank Matrix Completion 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 EDA Energy Decomposition Analysis EDCimport Import Data from EDC Software EDFtest Goodness of Fit Based on Empirical Distribution Function EDISON Network Reconstruction and Changepoint Detection EDIutils An API Client for the Environmental Data Initiative Repository EDMeasure Energy-Based Dependence Measures EDNE.EQ Implements the EDNE-Test for Equivalence EDOIF Empirical Distribution Ordering Inference Framework (EDOIF) EDOtrans Euclidean Distance-Optimized Data Transformation EEAaq Handle Air Quality Data from the European Environment Agency Data Portal 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 EESPCA Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA) EFA.MRFA Dimensionality Assessment Using Minimum Rank Factor Analysis EFA.dimensions Exploratory Factor Analysis Functions for Assessing Dimensionality 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 EFS Tool for Ensemble Feature Selection EGAnet Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics EGM Evaluating Cardiac Electrophysiology Signals 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 EHRtemporalVariability Delineating Temporal Dataset Shifts in Electronic Health Records EIAapi Query Data from the 'EIA' API 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 ELISAtools ELISA Data Analysis with Batch Correction ELMR Extreme Machine Learning (ELM) ELMSO Implementation of the Efficient Large-Scale Online Display Advertising Algorithm ELT Experience Life Tables ELYP Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model EM.Fuzzy EM Algorithm for Maximum Likelihood Estimation by Non-Precise Information EMAR Empirical Model Assessment EMAS Epigenome-Wide Mediation Analysis Study 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 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 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) 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 ESG A Package for Asset Projection ESTER Efficient Sequential Testing with Evidence Ratios EScvtmle Experiment-Selector CV-TMLE for Integration of Observational and RCT Data ETAS Modeling Earthquake Data Using 'ETAS' Model ETASbootstrap Bootstrap Confidence Interval Estimation for 'ETAS' Model Parameters ETC Equivalence to Control ETLUtils Utility Functions to Execute Standard Extract/Transform/Load Operations (using Package 'ff') on Large Data 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 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 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' EbayesThresh Empirical Bayes Thresholding and Related Methods Ecdat Data Sets for Econometrics Ecfun Functions for 'Ecdat' EcoDiet Estimating a Diet Matrix from Biotracer and Stomach Content Data EcoEnsemble A General Framework for Combining Ecosystem Models EcoIndR Ecological Indicators EcoNetGen Simulate and Sample from Ecological Interaction Networks EcoTroph An Implementation of the EcoTroph Ecosystem Modelling Approach EcoVirtual Simulation of Ecological Models Ecohydmod Ecohydrological Modelling EconAndProdEfficiency Economic and Production Efficiency EconDemand General Analysis of Various Economics Demand Systems 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 EigenR Complex Matrix Algebra with 'Eigen' EleChemr Electrochemical Reactions Simulation ElevDistr Calculate the Distance to the Nearest Local Treeline 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 EmiStatR Emissions and Statistics in R for Wastewater and Pollutants in Combined Sewer Systems 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 EncDNA Encoding of Nucleotide Sequences into Numeric Feature Vectors 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 EnsembleBase Extensible Package for Parallel, Batch Training of Base Learners for Ensemble Modeling EnsembleCV Extensible Package for Cross-Validation-Based Integration of Base Learners EnsemblePCReg Extensible Package for Principal-Component-Regression-Based Heterogeneous Ensemble Meta-Learning EnsemblePenReg Extensible Classes and Methods for Penalized-Regression-Based Integration of Base Learners EntropicStatistics Functions Based on Entropic Statistics EntropyEstimation Estimation of Entropy and Related Quantities EntropyMCMC MCMC Simulation and Convergence Evaluation using Entropy and Kullback-Leibler Divergence Estimation 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 EpiDynamics Dynamic Models in Epidemiology EpiEstim Estimate Time Varying Reproduction Numbers from Epidemic Curves EpiForsk Code Sharing at the Department of Epidemiological Research at Statens Serum Institut EpiILM Spatial and Network Based Individual Level Models for Epidemics EpiILMCT Continuous Time Distance-Based 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 EpiReport Epidemiological Report EpiSemble Ensemble Based Machine Learning Approach for Predicting Methylation States EpiSignalDetection Signal Detection Analysis EpiStats Tools for Epidemiologists EpiTest Test for Gene x Gene Interactions in Bi-Parental Populations EpistemicGameTheory Constructing an Epistemic Model for the Games with Two Players Equalden.HD Testing the Equality of a High Dimensional Set of Densities EquiSurv Modeling, Confidence Intervals and Equivalence of Survival Curves EstCRM Calibrating Parameters for the Samejima's Continuous IRT Model EstMix Tumor Clones Percentage Estimations EstimDiagnostics Diagnostic Tools and Unit Tests for Statistical Estimators 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 EurosarcBayes Bayesian Single Arm Sample Size Calculation Software EvCombR Evidence Combination in R Evacluster Evaluation Clustering Methods for Disease Subtypes Diagnosis EvaluateCore Quality Evaluation of Core Collections EvaluationMeasures Collection of Model Evaluation Measure Functions Evapotranspiration Modelling Actual, Potential and Reference Crop Evapotranspiration EventDetectGUI Graphical User Interface for the 'EventDetectR' Package EventDetectR Event Detection Framework 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 ExactMed Exact Mediation Analysis for Binary Outcomes ExactMultinom Multinomial Goodness-of-Fit Tests 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 ExpDE Modular Differential Evolution for Experimenting with Operators ExpDes Experimental Designs Package ExpDes.pt Pacote Experimental Designs (Portugues) ExpGenetic Non-Additive Expression Analysis of Hybrid Offspring ExpImage Analysis of Images in Experiments ExpRep Experiment Repetitions ExperimentHub Client to access ExperimentHub resources ExpertChoice Design of Discrete Choice and Conjoint Analysis ExplainPrediction Explanation of Predictions for Classification and Regression Models ExplodeLayout Calculate Exploded Coordinates Based on Original Node Coordinates and Node Clustering Membership ExposR Models Topographic Exposure to Hurricane Winds ExtDist Extending the Range of Functions for Probability Distributions ExtMallows An Extended Mallows Model and Its Hierarchical Version for Ranked Data Aggregation ExtrPatt Spatial Dependencies and Indices for Extremes ExtractTrainData Extract Values from Raster ExtremalDep Extremal Dependence Models ExtremeBounds Extreme Bounds Analysis (EBA) ExtremeRisks Extreme Risk Measures EzGP Easy-to-Interpret Gaussian Process Models for Computer Experiments FABInference FAB p-Values and Confidence Intervals FACT Feature Attributions for ClusTering 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 FAMT Factor Analysis for Multiple Testing (FAMT) : Simultaneous Tests under Dependence in High-Dimensional Data 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 FARDEEP Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte from Expression Profiles using Least Trimmed Squares FAS Factor-Augmented Sparse Regression Tuning-Free Testing FAST.R Analyze and Visualize FAST-Generated Data FASeg Joint Segmentation of Correlated Time Series FAVAR Bayesian Analysis of a FAVAR Model FAdist Distributions that are Sometimes Used in Hydrology FAmle Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions FAwR Functions and Datasets for "Forest Analytics with R" FBCRM Phase I Optimal Dose Assignment using the FBCRM and MFBCRM Methods 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 FCMapper Fuzzy Cognitive Mapping FCO Flexible Cutoffs for Model Fit Evaluation in Covariance-Based Structural Models FCPS Fundamental Clustering Problems Suite FCSlib A Collection of Fluorescence Fluctuation Spectroscopy Analysis Methods FCVAR Estimation and Inference for the Fractionally Cointegrated VAR FD Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology 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 FDb.InfiniumMethylation.hg19 Annotation package for Illumina Infinium DNA methylation probes 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 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 FIT Transcriptomic Dynamics Models in Field Conditions FITSio FITS (Flexible Image Transport System) Utilities FKF Fast Kalman Filter FKF.SP Fast Kalman Filtering Through Sequential Processing FKSUM Fast Kernel Sums FLAME Interpretable Matching for Causal Inference FLLat Fused Lasso Latent Feature Model 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 FMAT The Fill-Mask Association Test FMAdist Frequentist Model Averaging Distribution FMC Factorial Experiments with Minimum Level Changes FMCCSD Efficient Estimation of Clustered Current Status Data 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 FORTLS Automatic Processing of Terrestrial-Based Technologies Point Cloud Data for Forestry Purposes 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 FPV Testing Hypotheses via Fuzzy P-Value in Fuzzy Environment FRACTION Numeric Number into Fraction FRAPO Financial Risk Modelling and Portfolio Optimisation with R FRCC Fast Regularized Canonical Correlation Analysis 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 FRESHD Fast Robust Estimation of Signals in Heterogeneous Data 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 FSInteract Fast Searches for Interactions 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 FUNTA Functional Tangential Angle Pseudo-Depth FWDselect Selecting Variables in Regression Models FWRGB Fresh Weight Determination from Visual Image of the Plant FaaSr FaaS (Function as a Service) Package 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 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 FairMclus Clustering for Data with Sensitive Attribute 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 FamilyRank Algorithm for Ranking Predictors Using Graphical Domain Knowledge FarmSelect Factor Adjusted Robust Model Selection FarmTest Factor-Adjusted Robust Multiple Testing 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 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 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 FastSF Fast Structural Filtering FastStepGraph A Fast Algorithm for Sparse Precision Matrix Estimation FatTailsR Kiener Distributions and Fat Tails in Finance 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 FeatureHashing Creates a Model Matrix via Feature Hashing with a Formula Interface FeatureImpCluster Feature Importance for Partitional Clustering FeatureTerminatoR Feature Selection Engine to Remove Features with Minimal Predictive Power FedData Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources FedIRT Federated Item Response Theory Models FeedbackTS Analysis of Feedback in Time Series FertBoot Fertilizer Response Curve Analysis by Bootstrapping Residuals 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 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 FinancialInstrument Financial Instrument Model Infrastructure and Meta-Data 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 FishPhyloMaker Phylogenies for a List of Finned-Ray Fishes FishResp Analytical Tool for Aquatic Respirometry 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 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 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 FluMoDL Influenza-Attributable Mortality with Distributed-Lag Models Fluidigm Handling Fluidigm Data FlyingR Simulation of Bird Flight Range FnR Inbreeding and Numerator Relationship Coefficients FoReco Forecast Reconciliation ForIT Functions to Estimate Tree Volume and Phytomass in the Italian Forest Inventory 2005 ForagingOrg Organization Measures for Visual Foraging ForeCA Forecastable Component Analysis ForeComp Size-Power Tradeoff Visualization for Equal Predictive Ability of Two Forecasts ForecastComb Forecast Combination Methods ForecastCombinations Forecast Combinations ForecastTB Test Bench for the Comparison of Forecast Methods ForestDisc Forest Discretization 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 of 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 FracKrigingR Spatial Multivariate Data Modeling FractalParameterEstimation Simulation and Parameter Estimation of Randomized Sierpinski Carpets using the p-p-p-q-Model Fragman Fragment Analysis in R Frames2 Estimation in Dual Frame Surveys FreeSortR Free Sorting Data Analysis FreqProf Frequency Profiles Computing and Plotting Fstability Calculate Feature Stability FunCC Functional Cheng and Church Bi-Clustering FunChisq Model-Free Functional Chi-Squared and Exact Tests FunWithNumbers Fun with Fractions and Number Sequences FuncDiv Compute Contributional Diversity Metrics FuncMap Hive Plots of R Package Function Calls FuncNN Functional Neural Networks FunctanSNP Functional Analysis (with Interactions) for Dense SNP Data FunnelPlotR Funnel Plots for Comparing Institutional Performance FusionLearn Fusion Learning Fuzzy.p.value Computing Fuzzy p-Value FuzzyAHP (Fuzzy) AHP Calculation FuzzyClass Fuzzy and Non-Fuzzy Classifiers FuzzyDBScan Run and Predict a Fuzzy DBScan FuzzyLP Fuzzy Linear Programming FuzzyM Fuzzy Cognitive Maps Operations FuzzyNumbers Tools to Deal with Fuzzy Numbers FuzzyNumbers.Ext.2 Apply Two Fuzzy Numbers on a Monotone Function 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 FuzzyStatProb Fuzzy Stationary Probabilities from a Sequence of Observations of an Unknown Markov Chain FuzzyStatTra Statistical Methods for Trapezoidal Fuzzy Numbers FuzzyStatTraEOO Package 'FuzzyStatTra' in Encapsulated Object Oriented Programming G2Sd Grain-Size Statistics and Description of Sediment GA Genetic Algorithms GABB Facilitation of Data Preparation and Plotting Procedures for RDA and PCA Analyses 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) 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 GARCHIto Class of GARCH-Ito Models GARCHSK Estimating a GARCHSK Model and GJRSK Model GARCOM Gene and Region Counting of Mutations ("GARCOM") GAS Generalized Autoregressive Score Models 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 GBJ Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies GCCfactor GCC Estimation of the Multilevel Factor Model GCD Global Charcoal Database GCPBayes Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure GCPM Generalized Credit Portfolio Model GCSM Implements Generic Composite Similarity Measure GCalcium A Data Manipulation and Analysis Package for Calcium Indicator Data GCalignR Simple Peak Alignment for Gas-Chromatography Data GD Geographical Detectors for Assessing Spatial Factors GDAdata Datasets for the Book Graphical Data Analysis with R GDAtools Geometric Data Analysis GDELTtools Download, Slice, and Normalize GDELT V1 Event and Sentiment API Data 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 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 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 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 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 GFDsurv Tests for Survival Data in General Factorial Designs GFE Gross Flows Estimation under Complex Surveys 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 GGMnonreg Non-Regularized Gaussian Graphical Models GGMridge Gaussian Graphical Models Using Ridge Penalty Followed by Thresholding and Reestimation GGMselect Gaussian Graphs Models Selection GGRidge Graphical Group Ridge GGUM Generalized Graded Unfolding Model GGally Extension to 'ggplot2' GGoutlieR Identify Individuals with Unusual Geo-Genetic Patterns GHS Graphical Horseshoe MCMC Sampler Using Data Augmented Block Gibbs Sampler GHap Genome-Wide Haplotyping GIC A General Iterative Clustering Algorithm GIFT Access to the Global Inventory of Floras and Traits (GIFT) GIFTr GIFT Questions Format Generator from Dataframes GIGrvg Random Variate Generator for the GIG Distribution GIMMEgVAR Group Iterative Multiple Model Estimation with 'graphicalVAR' GISINTEGRATION GIS Integration GISSB Network Analysis on the Norwegian Road Network GInSARCorW GACOS InSAR Correction Workflow GIplot Gaussian Interval Plot (GIplot) GJRM Generalised Joint Regression Modelling GK2011 Gaines and Kuklinski (2011) Estimators for Hybrid Experiments GLAD Gain and Loss Analysis of DNA GLCMTextures GLCM Textures of Raster Layers GLDEX Fitting Single and Mixture of Generalised Lambda Distributions GLDreg Fit GLD Regression/Quantile/AFT Model to Data GLIDE Global and Individual Tests for Direct Effects 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 Generalised Mixed Modelling Framework GLMMselect Bayesian Model Selection for Generalized Linear Mixed Models GLMaSPU An Adaptive Test on High Dimensional Parameters in Generalized Linear 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 GMAC Genomic Mediation Analysis with Adaptive Confounding Adjustment 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 GMKMcharlie Unsupervised Gaussian Mixture and Minkowski and Spherical K-Means with Constraints GMMAT Generalized Linear Mixed Model Association Tests GMMBoost Likelihood-Based Boosting for Generalized Mixed Models GMPro Graph Matching with Degree Profiles GMSE Generalised Management Strategy Evaluation Simulator GMSimpute Generalized Mass Spectrum Missing Peaks Abundance Imputation 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 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 GOxploreR Structural Exploration of the Gene Ontology (GO) Knowledge Base GPArotateDF Derivative Free Gradient Projection Factor Rotation GPArotation Gradient Projection Factor Rotation GPBayes Tools for Gaussian Process Modeling in Uncertainty Quantification GPCERF Gaussian Processes for Estimating Causal Exposure Response Curves GPCMlasso Differential Item Functioning in Generalized Partial Credit Models GPFDA Gaussian Process for Functional Data Analysis GPGame Solving Complex Game Problems using Gaussian Processes GPIC Quantifying Group Performance in Individual Competitions GPL2025 Convert Chip ID of the GPL2015 into GeneBank Accession and ENTREZID GPLTR Generalized Partially Linear Tree-Based Regression Model GPM Gaussian Process Modeling of Multi-Response and Possibly Noisy Datasets 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 GPUmatrix Basic Linear Algebra with GPU GPareto Gaussian Processes for Pareto Front Estimation and Optimization GPfit Gaussian Processes Modeling GPoM Generalized Polynomial Modelling GPvam Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling GPvecchia Scalable Gaussian-Process Approximations GRAPE Gene-Ranking Analysis of Pathway Expression GRCRegression Modified Poisson Regression of Grouped and Right-Censored Counts GRCdata Parameter Inference and Optimal Designs for Grouped and/or Right-Censored Count Data GRCdesigns Generalized Row-Column Designs GREENeR Geospatial Regression Equation for European Nutrient Losses (GREEN) GREMLINS Generalized Multipartite Networks GRIDCOPULA Bivariate Copula Functions Based on Regular Grid GRNNs General Regression Neural Networks Package GROAN Genomic Regression Workbench GRS.test GRS Test for Portfolio Efficiency, Its Statistical Power Analysis, and Optimal Significance Level Calculation GRShiny Graded Response Model GRSxE Testing Gene-Environment Interactions Through Genetic Risk Scores GRTo Tools for the Analysis of Gutenberg-Richter Distributions of Earthquake Magnitudes GRelevance Graph-Based k-Sample Comparisons and Relevance Analysis in High Dimensions GSA Gene Set Analysis GSA.UN Global Sensitivity Analysis Tool GSAQ Gene Set Analysis with QTL GSAfisherCombined Gene Set Analysis with Fisher Combined Method 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 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 GSelection Genomic Selection GSparO Group Sparse Optimization GTDL The Generalized Time-Dependent Logistic Family GUD Bayesian Modal Regression Based on the GUD Family GUEST Graphical Models in Ultrahigh-Dimensional and Error-Prone Data via Boosting Algorithm GUIDE GUI for DErivatives in R GUILDS Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure GUIProfiler Graphical User Interface for Rprof() 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 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 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 GWmodel Geographically-Weighted Models GWnnegPCA Geographically Weighted Non-Negative Principal Components Analysis GWpcor Geographically Weighted Partial Correlation Coefficient GWsignif Estimating Genome-Wide Significance for Whole Genome Sequencing Studies, Either Single SNP Tests or Region-Based Tests GaMaBioMD Diversity Analysis for Sequence Data GaSP Train and Apply a Gaussian Stochastic Process Model GameTheory Cooperative Game Theory GameTheoryAllocation Tools for Calculating Allocations in Game Theory Gammareg Classic Gamma Regression: Joint Modeling of Mean and Shape Parameters 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 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 GenMarkov Multivariate Markov Chains GenOrd Simulation of Discrete Random Variables with Given Correlation Matrix and Marginal Distributions 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 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 GeneScape Simulation of Single Cell RNA-Seq Data with Complex Structure GeneSelectR 'GeneSelectR' - Comprehensive Feature Selection Workflow for Bulk RNAseq Datasets GeneralOaxaca Blinder-Oaxaca Decomposition for Generalized Linear Model GeneralisedCovarianceMeasure Test for Conditional Independence Based on the Generalized Covariance Measure (GCM) GeneralizedHyperbolic The Generalized Hyperbolic Distribution GeneralizedUmatrix Credible Visualization for Two-Dimensional Projections of Data GeneralizedWendland Fully Parameterized Generalized Wendland Covariance Function GenericML Generic Machine Learning Inference GeneticSubsetter Identify Favorable Subsets of Germplasm Collections GenoScan A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence Data Analysis 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 GenomicFeatures Conveniently import and query gene models GenomicInteractions Utilities for handling genomic interaction data GenomicRanges Representation and manipulation of genomic intervals GenomicTools.fileHandler File Handlers for Genomic Data Analysis GeoAdjust Accounting for Random Displacements of True GPS Coordinates of Data GeoModels Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis GeoMongo Geospatial Queries Using 'PyMongo' GeoRange Calculating Geographic Range from Occurrence Data GeoWeightedModel User-Friendly Interface for Geographically-Weighted Models GeodRegr Geodesic Regression GeomArchetypal Finds the Geometrical Archetypal Analysis of a Data Frame GeomComb (Geometric) Forecast Combination Methods GerminaR Indices and Graphics for Assess Seed Germination Process GetBCBData Imports Datasets from BCB (Central Bank of Brazil) using Its Official API GetDFPData Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA System 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 and Simple Variable Interpolation Ghat Quantifying Evolution and Selection on Complex Traits Ghost Missing Data Segments Imputation in Multivariate Streams GhostKnockoff The Knockoff Inference Using Summary Statistics GiNA High Throughput Phenotyping 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 Gini Gini Coefficient GiniDecompLY Gini Decomposition by Income Sources GiniDistance A New Gini Correlation Between Quantitative and Qualitative Variables 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 GmptzCurve Gompertz Curve Fitting GoFKernel Testing Goodness-of-Fit with the Kernel Density Estimator GofCens Goodness-of-Fit Methods for Complete and Right-Censored Data GofKmt Khmaladze Martingale Transformation Goodness-of-Fit Test 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 GoogleImage2Array Create Array Data from 2D Image Thumbnails via Google Image Search GoogleKnowledgeGraphR Retrieve Information from 'Google Knowledge Graph' API GpGp Fast Gaussian Process Computation Using Vecchia's Approximation GrFA Group Factor Analysis GrabSVG Granularity-Based Spatially Variable Genes Identifications Grace Graph-Constrained Estimation and Hypothesis Tests GramQuad Gram Quadrature 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 Cluster-Preserving Multivariate Joint Grid Discretization GrimR Calculate Optical Parameters from Spindle Stage Measurements 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 Grouphmap 'Grouphmap' is an Automated One-Step Common Analysis of Batch Expression Profile GrpString Patterns and Statistical Differences Between Two Groups of Strings GseaVis Implement for 'GSEA' Enrichment Visualization 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" 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 HBSTM Hierarchical Bayesian Space-Time Models for Gaussian Space-Time Data HBV.IANIGLA Modular Hydrological Model HCD Hierarchical Community Detection by Recursive Partitioning HCR Causal Discovery from Discrete Data using Hidden Compact Representation HCT Calculates Significance Criteria and Power for a Single Arm Trial HCTDesign Group Sequential Design for Historical Control Trial with Survival Outcome HCTR Higher Criticism Tuned Regression HCmodelSets Regression with a Large Number of Potential Explanatory Variables HDBRR High Dimensional Bayesian Ridge Regression without MCMC HDCD High-Dimensional Changepoint Detection HDCI High Dimensional Confidence Interval Based on Lasso and Bootstrap HDCurves Hierarchical Derivative Curve Estimation HDDesign Sample Size Calculation for High Dimensional Classification Study HDF5Array HDF5 backend for DelayedArray objects HDGLM Tests for High Dimensional Generalized Linear Models HDInterval Highest (Posterior) Density Intervals HDJM Penalized High-Dimensional Joint Model 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 HDiR Directional Highest Density Regions HDoutliers Leland Wilkinson's Algorithm for Detecting Multidimensional Outliers HDtweedie The Lasso for Tweedie's Compound Poisson Model Using an IRLS-BMD Algorithm HEDA 'Hydropeaking Events Detection Algorithm' HEMDAG Hierarchical Ensemble Methods for Directed Acyclic Graphs HETOP MLE and Bayesian Estimation of Heteroskedastic Ordered Probit (HETOP) Model HEtools Homomorphic Encryption Polynomials 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 HIMA High-Dimensional Mediation Analysis HK80 Conversion Tools for HK80 Geographical Coordinate System HKRbook Apps and Data for the Book "Introduction to Statistics" HKprocess Hurst-Kolmogorov Process HLMdiag Diagnostic Tools for Hierarchical (Multilevel) Linear Models HMB Hierarchical Model-Based Estimation Approach HMC High Dimensional Mean Comparison with Projection and Cross-Fitting HMDHFDplus Read Human Mortality Database and Human Fertility Database Data from the Web HMM Hidden Markov Models HMMEsolver A Fast Solver for Henderson Mixed Model Equation via Row Operations HMMextra0s Hidden Markov Models with Extra Zeros HMMmlselect Determine the Number of States in Hidden Markov Models via Marginal Likelihood HMMpa Analysing Accelerometer Data Using Hidden Markov Models HMP Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP HMPTrees Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data HMR Flux Estimation with Static Chamber Data HMTL Heterogeneous Multi-Task Feature Learning HOasso Higher Order Assortativity for Complex Networks HPLB High-Probability Lower Bounds for the Total Variance Distance HQM Superefficient Estimation of Future Conditional Hazards Based on Marker Information HRW Datasets, Functions and Scripts for Semiparametric Regression Supporting Harezlak, Ruppert & Wand (2018) HS Homogenous Segmentation for Spatial Lines Data 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) HSDiC Homogeneity and Sparsity Detection Incorporating Prior Constraint Information HSEtest Homogeneity of Stratum Effects Test HSMMSingleCell Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) HSPOR Hidden Smooth Polynomial Regression for Rupture Detection 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 HTSSIP High Throughput Sequencing of Stable Isotope Probing Data Analysis HTSeed Fitting of Hydrotime Model for Seed Germination Time Course 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 HaDeX 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 HaploSim Functions to Simulate Haplotypes 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 HazardDiff Conditional Treatment Effect for Competing Risks HealthCal Health Calculator Heatplus Heatmaps with row and/or column covariates and colored clusters HeckmanEM Fit Normal, Student-t or Contaminated Normal Heckman Selection Models HellCor The Hellinger Correlation HelpersMG Tools for Environmental Analyses, Ecotoxicology and Various R Functions HeritSeq Heritability of Gene Expression for Next-Generation Sequencing HeterFunctionalData Test of No Main and/or Interaction Effects in Functional Data HeteroGGM Gaussian Graphical Model-Based Heterogeneity Analysis HextractoR Integrated Tool for Hairping Extraction of RNA Sequences HhP Hierarchical Heterogeneity Analysis via Penalization HiCDOC A/B compartment detection and differential analysis HiCcompare HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets HiClimR Hierarchical Climate Regionalization HiDimDA High Dimensional Discriminant Analysis HiResTEC Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data HiTC High Throughput Chromosome Conformation Capture analysis HiddenMarkov Hidden Markov Models HierPortfolios Hierarchical Clustering-Based Portfolio Allocation Strategies 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 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 An User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis Homeric Doughnut Plots HomomorphicEncryption BFV, BGV, CKKS Schema for Fully Homomorphic Encryption HospitalNetwork Building Networks of Hospitals Through Patients Transfers Hotelling Hotelling's T^2 Test and Variants HotellingEllipse Hotelling T-Square and Confidence 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 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 IAT Cleaning and Visualizing Implicit Association Test (IAT) Data 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 IBDsim Simulation of Chromosomal Regions Shared by Family Members IBFS Initial Basic Feasible Solution for Transportation Problem IBMPopSim Individual Based Model Population Simulation IBRtools Integrating Biomarker-Based Assessments and Radarchart Creation IBrokers R API to Interactive Brokers Trader Workstation ICAMS In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS') ICAOD Optimal Designs for Nonlinear Statistical Models by Imperialist Competitive Algorithm (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 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 ICDS Identification of Cancer Dysfunctional Subpathway with Omics Data ICED IntraClass Effect Decomposition ICEbox Individual Conditional Expectation Plot Toolbox ICEinfer Incremental Cost-Effectiveness Inference using Two Unbiased Samples 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 ICRanks Simultaneous Confidence Intervals for Ranks 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 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)' IDSA An Interactive Detector for Spatial Associations 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 IDetect Isolate-Detect Methodology 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 IFP Identifying Functional Polymorphisms IGCities Simulate Impact of Different Urban Policies Through a General Equilibrium Model IGST Informative Gene Selection Tool IGoRRR A Shiny Interface for Simple Data Management IHSEP Inhomogeneous Self-Exciting Process IHW Independent Hypothesis Weighting IIProductionUnknown Analyzing Data Through of Percentage of Importance Indice (Production Unknown) and Its Derivations IIVpredictor Modeling Within Individual Variability as Predictor ILS Interlaboratory Study ILSE Linear Regression Based on 'ILSE' for Missing Data ILSM Analyze Inter-Layer Structure of Multilayer Ecological Network IMD Index of Multiple Deprivation Data for the UK IMEC Ising Model of Explanatory Coherence 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 IMTest Information Matrix Test for Generalized Partial Credit Models IMak Item Maker IMmailgun Send Emails using 'Mailgun' INCATome Internal Control Analysis of Translatome Studies by Microarrays 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' INQC Quality Control of Climatological Daily Time Series INSPECTumours IN-vivo reSPonsE Classification of Tumours INSPIRE Inferring Shared Modules from Multiple Gene Expression Datasets with Partially Overlapping Gene Sets INTRIGUE Quantify and Control Reproducibility in High-Throughput Experiments IOHanalyzer Data Analysis Part of 'IOHprofiler' IOHexperimenter Benchmarking Part of the 'IOHprofiler' IOLS Iterated Ordinary Least Squares Regression IP Classes and Methods for 'IP' Addresses IPCAPS Iterative Pruning to Capture Population Structure IPCWK Kendall's Tau Partial Corr. for Survival Trait and Biomarkers IPDFileCheck Basic Functions to Check Readability, Consistency, and Content of an Individual Participant Data File 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 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 IRCcheck Irrepresentable Condition Check 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 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 ISAT Extract Cell Density and Nearest Distance Based on 'PerkinElmer InForm' Software Output 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) ISO11784Tools ISO11784 PIT Tag ID Format Converters ISOcodes Selected ISO Codes ISOpureR Deconvolution of Tumour Profiles ISOweek Week of the year and weekday according to ISO 8601 ISR The Iterated Score Regression-Based Estimation Algorithm 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 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 ImCluster Efficiency of Cluster Sampling for Crop Surveys ImFoR Non-Linear Height Diameter Models for Forestry ImHD Artificial Intelligence Based Machine Learning Algorithms for Height Diameter Relationships of Conifer Trees 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 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 ImputeLongiCovs Longitudinal Imputation of Categorical Variables via a Joint Transition Model ImputeRobust Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape InDisc Obtaining and Estimating Unidimensional and Multidimensional IRT Dual Models 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 IndexConstruction Index Construction for Time Series Data IndexNumR Index Number Calculation IndexNumber Index Numbers in Social Sciences IndexWizard Constructing and Analyzing Complex Selection Indices Indicator Composite 'Indicator' Construction and Imputation Data 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 InfoTrad Calculates the Probability of Informed Trading (PIN) 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 InspectChangepoint High-Dimensional Changepoint Estimation via Sparse Projection InsuSensCalc Insulin Sensitivity Indices Calculator IntCal Radiocarbon Calibration Curves IntNMF Integrative Clustering of Multiple Genomic Dataset InteRD The Integrated and Robust Deconvolution IntegrateBs Integration for B-Spline IntegratedJM Joint Modeling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature IntegratedMRF Integrated Prediction using Uni-Variate and Multivariate Random Forests 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 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 Inventorymodel Inventory Models Irescale Calculate and Rectify Moran's I 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 Iso Functions to Perform Isotonic Regression IsoCheck Isomorphism Check for Multi-Stage Factorial Designs with Randomization Restrictions 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 IsotopeR Stable Isotope Mixing Model 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 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 Interface Between the 'JDemetra+' Cruncher and R, and 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 JGL Performs the Joint Graphical Lasso for Sparse Inverse Covariance Estimation on Multiple Classes JGR Java GUI for R JICO Joint and Individual Regression JLPM Joint Latent Process Models JM Joint Modeling of Longitudinal and Survival Data 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 JMdesign Joint Modeling of Longitudinal and Survival Data - Power Calculation JNplots Visualize Outputs from the 'Johnson-Neyman' Technique JOPS Practical Smoothing with P-Splines JOUSBoost Implements Under/Oversampling for Probability Estimation JPEN Covariance and Inverse Covariance Matrix Estimation Using Joint Penalty JQL Jump Q-Learning for Individualized Interval-Valued Dose Rule 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 JacobiEigen Classical Jacobi Eigenvalue Algorithm JamendoR Access to 'Jamendo' API JavaGD Java Graphics Device Jaya Jaya, a Gradient-Free Optimization Algorithm 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 JustifyAlpha Justifying Alpha Levels for Hypothesis Tests KCSKNNShiny K-Nearest Neighbour Classifier KCSNBShiny Naive Bayes Classifier KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) KEGGdzPathwaysGEO KEGG Disease Datasets from GEO KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor KEPTED Kernel-Embedding-of-Probability Test for Elliptical Distribution KERE Expectile Regression in Reproducing Kernel Hilbert Space 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 Data sets 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 KOGMWU Functional Summary and Meta-Analysis of Gene Expression Data KONPsurv KONP Tests: Powerful K-Sample Tests for Right-Censored Data KOR.addrlink Matching Address Data to Reference Index KPC Kernel Partial Correlation Coefficient KRIS Keen and Reliable Interface Subroutines for Bioinformatic Analysis KRLS Kernel-Based Regularized Least Squares KRMM Kernel Ridge Mixed Model KSA Retained Component Criterion for Principal Component Analysis KSD Goodness-of-Fit Tests using Kernelized Stein Discrepancy KSEAapp Kinase-Substrate Enrichment Analysis 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 KappaGUI An R-Shiny Application for Calculating Cohen's and Fleiss' Kappa KaradaColor Color Palettes Inspired by Japanese Landscape and Culture 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 KenSyn Knowledge Synthesis in Agriculture - From Experimental Network to Meta-Analysis Kendall Kendall Rank Correlation and Mann-Kendall Trend Test 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 KinMixLite Inference About Relationships from DNA Mixtures KingCountyHouses Data on House Sales in King County WA Kira Machine Learning 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 KnockoffScreen Whole-Genome Sequencing Data Analysis via Knockoff Statistics KnockoffTrio Trio Data Analysis with Knockoff Statistics for FDR Control KnowBR Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases KoboconnectR Download Data from Kobotoolbox to R KoulMde Koul's Minimum Distance Estimation in Regression and Image Segmentation Problems Kpart Cubic Spline Fitting with Knot Selection 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 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) 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 LARF Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects 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 LBI Likelihood Based Inference LBPG The Length-Biased Power Garima Distribution LBSPR Length-Based Spawning Potential Ratio LCA Localised Co-Dependency Analysis LCAextend Latent Class Analysis (LCA) with Familial Dependence in Extended Pedigrees LCAvarsel Variable Selection for Latent Class Analysis LCCR Latent Class Capture-Recapture Models LCF Linear Combination Fitting LCFdata Data sets for package ``LMERConvenienceFunctions'' LCMCR Bayesian Non-Parametric Latent-Class Capture-Recapture LCMSQA Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment LDABiplots Biplot Graphical Interface for LDA Models LDAShiny User-Friendly Interface for Review of Scientific Literature LDATS Latent Dirichlet Allocation Coupled with Time Series Analyses LDATree Classification Trees with Linear Discriminant Analysis at Terminal Nodes 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 LDLcalc Calculate and Predict the Low Density Lipoprotein Values 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 LEGIT Latent Environmental & Genetic InTeraction (LEGIT) Model 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 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 LIM Linear Inverse Model Examples and Solution Methods LINselect Selection of Linear Estimators LIStest Tests of independence based on the Longest Increasing Subsequence LKT Logistic Knowledge Tracing LLM Logit Leaf Model Classifier for Binary Classification 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 Model Solver LMMstar Repeated Measurement Models for Discrete Times LMN Inference for Linear Models with Nuisance Parameters 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 LOCUS Low-Rank Decomposition of Brain Connectivity Matrices with Uniform Sparsity LOGAN Log File Analysis in International Large-Scale Assessments LOGANTree Tree-Based Models for the Analysis of Log Files from Computer-Based 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 LPGraph Nonparametric Smoothing of Laplacian Graph Spectra LPKsample LP Nonparametric High Dimensional K-Sample Comparison LPM Linear Parametric Models Applied to Hydrological Series LPRelevance Relevance-Integrated Statistical Inference Engine LPS Linear Predictor Score, for Binary Inference from Multiple Continuous Variables LPWC Lag Penalized Weighted Correlation for Time Series Clustering LPmerge Merging Linkage Maps by Linear Programming LPower Calculates Power, Sample Size, or Detectable Effect for Longitudinal Analyses LPsmooth LP Smoothed Inference and Graphics LREP Estimate and Test Exponential vs. Pareto Distributions LRMF3 Low Rank Matrix Factorization S3 Objects LRTesteR Likelihood Ratio Tests and Confidence Intervals LRcontrast Dose Response Signal Detection under Model Uncertainty LS2W Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme LS2Wstat A Multiscale Test of Spatial Stationarity for LS2W Processes 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 LSMRealOptions Value American and Real Options Through LSM Simulation 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 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 LTAR Tensor Forecasting Functions LTASR Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R LTCDM Latent Transition Cognitive Diagnosis Model with Covariates LTFHPlus Implementation of LT-FH++ LTPDvar LTPD and AOQL Plans for Acceptance Sampling Inspection by Variables LTRCforests Ensemble Methods for Survival Data with Time-Varying Covariates 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 LW1949 An Automated Approach to Evaluating Dose-Effect Experiments Following Litchfield and Wilcoxon (1949) 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 LaMa Fast Numerical Maximum Likelihood Estimation for Latent Markov Models 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 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 LaplacesDemon Complete Environment for Bayesian Inference LassoBacktracking Modelling Interactions in High-Dimensional Data with Backtracking LassoGEE High-Dimensional Lasso Generalized Estimating Equations LassoNet 3CoSE Algorithm LassoSIR Sparsed Sliced Inverse Regression via Lasso Laterality Functions to Calculate Common Laterality Statistics in Primatology LatticeDesign Lattice-Based Space-Filling Designs LatticeKrig Multi-Resolution Kriging Based on Markov Random Fields LavaCvxr Lava Estimation for the Sum of Sparse and Dense Signals(3 Methods) Lavash Lava Estimation for the Sum of Sparse and Dense Signals LeArEst Border and Area Estimation of Data Measured with Additive Error LeMaRns Length-Based Multispecies Analysis by Numerical Simulation LeafArea Rapid Digital Image Analysis of Leaf Area LearnBayes Functions for Learning Bayesian Inference LearnClust Learning Hierarchical Clustering Algorithms LearnGeom Learning Plane Geometry LearnPCA Functions, Data Sets and Vignettes to Aid in Learning Principal Components Analysis (PCA) LearnSL Learn Supervised Classification Methods Through Examples and Code LearningRlab Statistical Learning Functions LearningStats Elemental Descriptive and Inferential Statistics LexFindR Find Related Items and Lexical Dimensions in a Lexicon LexisNexisTools Working with Files from 'LexisNexis' LexisPlotR Plot Lexis Diagrams for Demographic Purposes LibOPF Design of Optimum-Path Forest Classifiers 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 LifeTables Two-Parameter HMD Model Life Table System LifemapR Data Visualisation on 'Lifemap' Tree Lifertable Life and Fertility Tables Specially for Insects LiftTest A Bootstrap Proportion Test for Brand Lift Testing LightningR Tools for Communication with Lightning-Viz Server LikertMakeR Synthesise and Correlate Rating-Scale Data 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 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 LinkageMapView Plot Linkage Group Maps with Quantitative Trait Loci 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 Lmoments L-Moments and Quantile Mixtures LncFinder LncRNA Identification and Analysis Using Heterologous Features LncPath Identifying the Pathways Regulated by LncRNA Sets of Interest LoBrA Generalized Spline Mixed Effect Models for Longitudinal Breath Data LobsterCatch Models the Capture Processes in American Lobster Trap Fishery 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 LogisticCurveFitting Logistic Curve Fitting by Rhodes Method 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 LongMemoryTS Long Memory Time Series LongituRF Random Forests for Longitudinal Data 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 LorenzRegression Lorenz and Penalized Lorenz Regressions LowRankQP Low Rank Quadratic Programming LowWAFOMNX Low WAFOM Niederreiter-Xing Sequence LowWAFOMSobol Low WAFOM Sobol Sequence 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 MAAPER Analysis of Alternative Polyadenylation Using 3' End-Linked Reads MABOUST Multi-Armed Bayesian Ordinal Utility-Based Sequential Trial MACER Molecular Acquisition, Cleaning, and Evaluation in R 'MACER' MAGEE Mixed Model Association Test for GEne-Environment Interaction MAGMA.R MAny-Group MAtching MAGNAMWAR A Pipeline for Meta-Genome Wide Association MAINT.Data Model and Analyse Interval Data 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 MANCIE Matrix Analysis and Normalization by Concordant Information Enhancement MANOVA.RM Resampling-Based Analysis of Multivariate Data and Repeated Measures Designs MAP Multimodal Automated Phenotyping MAPA Multiple Aggregation Prediction Algorithm MAPITR MArginal ePIstasis Test for Regions 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 MARVEL Revealing Splicing Dynamics at Single-Cell Resolution 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 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 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 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 MCDA Support for the Multicriteria Decision Aiding Process 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.OTU Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology MCMC.qpcr Bayesian Analysis of qRT-PCR Data MCMC4Extremes Posterior Distribution of Extreme Value Models in R MCMCglmm MCMC Generalised Linear Mixed Models MCMCpack Markov Chain Monte Carlo (MCMC) Package MCMCprecision Precision of Discrete Parameters in Transdimensional MCMC MCMCtreeR Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees 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 MCTrend Monte Carlo Trend Analysis MChtest Monte Carlo Hypothesis Tests with Sequential Stopping MDBED Moran-Downton Bivariate Exponential Distribution MDEI Implementing the Method of Direct Estimation and Inference MDFS MultiDimensional Feature Selection MDMA Mathijs Deen's Miscellaneous Auxiliaries MDMAPR Molecular Detection Mapping and Analysis Platform MDMR Multivariate Distance Matrix Regression MDOLS Inference of Quadratic Functional for Moderate-Dimensional OLS 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 MDimNormn Multi-Dimensional MA Normalization for Plate Effect MDplot Visualising Molecular Dynamics Analyses MED Mediation by Tilted Balancing MEDseq Mixtures of Exponential-Distance Models with Covariates MEFM Perform MEFM Estimation on Matrix Time Series MEGENA Multiscale Clustering of Geometrical Network MEMSS Data Sets from Mixed-Effects Models in S MEPDF Creation of Empirical Density Functions Based on Multivariate Data 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 MF.beta4 Measuring Ecosystem Multi-Functionality and Its Decomposition MFAg Multiple Factor Analysis (MFA) MFDFA MultiFractal Detrended Fluctuation Analysis MFO Maximal Fat Oxidation and Kinetics Calculation MFPCA Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains MFSIS Model-Free Sure Independent Screening Procedures MFT The Multiple Filter Test for Change Point Detection MG1StationaryProbability Computes Stationary Distribution for M/G/1 Queuing System 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 MGMS2 'MGMS2' for Polymicrobial Samples 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 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 MICsplines The Computing of Monotonic Spline Bases and Constrained Least-Squares Estimates MIDN Nearly Exact Sample Size Calculation for Exact Powerful Nonrandomized Tests for Differences Between Binomial Proportions 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 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 MLCIRTwithin Latent Class Item Response Theory (LC-IRT) Models under Within-Item Multidimensionality MLCM Maximum Likelihood Conjoint Measurement MLCOPULA Classification Models with Copula Functions MLDS Maximum Likelihood Difference Scaling MLDataR Collection of Machine Learning Datasets for Supervised Machine Learning MLEce Asymptotic Efficient Closed-Form Estimators for Multivariate Distributions MLEcens Computation of the MLE for Bivariate Interval Censored Data 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 MLModelSelection Model Selection in Multivariate Longitudinal Data Analysis MLMusingR Practical Multilevel Modeling MLPUGS Multi-Label Prediction Using Gibbs Sampling (and Classifier Chains) MLVSBM A Stochastic Block Model for Multilevel Networks MLZ Mean Length-Based Estimators of Mortality using TMB MLeval Machine Learning Model Evaluation MLmetrics Machine Learning Evaluation Metrics MLpreemption Maximum Likelihood Estimation of the Niche Preemption Model MM The Multiplicative Multinomial Distribution MM2Sdata Gene Expression Datasets for the 'MM2S' Package MM4LMM Inference of Linear Mixed Models Through MM Algorithm MMAC Data for Mathematical Modeling and Applied Calculus MMAD MM Algorithm Based on the 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 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 MMVBVS Missing Multivariate Bayesian Variable Selection 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 Model MNLR Interactive Shiny Presentation for Working with Multinomial Logistic Regression MNLpred Simulated Predicted Probabilities for Multinomial Logit Models MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks MNP Fitting the Multinomial Probit Model MNS Mixed Neighbourhood Selection MOCCA Multi-Objective Optimization for Collecting Cluster Alternatives MOCHA Modeling for Single-Cell Open Chromatin Analysis MODISTools Interface to the 'MODIS Land Products Subsets' Web Services MOEADr Component-Wise MOEA/D Implementation MOFAT Maximum One-Factor-at-a-Time Designs MOLHD Multiple Objective Latin Hypercube Design MOQA Basic Quality Data Assurance for Epidemiological Research MOSS Multi-Omic Integration via Sparse Singular Value Decomposition MOST Multiphase Optimization Strategy MOTE Effect Size and Confidence Interval Calculator MPBoost Treatment Allocation in Clinical Trials by the Maximal Procedure MPCI Multivariate Process Capability Indices (MPCI) MPCR Multi- And Mixed-Precision Computations 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 Modeling Phylogenetic Signals using Eigenvector Maps MPTinR Analyze Multinomial Processing Tree Models MPTmultiverse Multiverse Analysis of 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 Multivariate Bidirectional Mendelian Randomization Networks MRCE Multivariate Regression with Covariance Estimation MRFA Fitting and Predicting Large-Scale Nonlinear Regression Problems using Multi-Resolution Functional ANOVA (MRFA) Approach MRFcov Markov Random Fields with Additional Covariates MRHawkes Multivariate Renewal Hawkes Process MRMCaov Multi-Reader Multi-Case Analysis of Variance 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 MRS Multi-Resolution Scanning for Cross-Sample Differences MRTAnalysis Primary and Secondary Analyses 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 MRmediation A Causal Mediation Method with Methylated Region (MR) as the Mediator MSBStatsData Data Sets for Courses at the Münster School of Business 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 MSML Model Selection Based on Machine Learning (ML) MSMwRA Multivariate Statistical Methods with R Applications MSPRT A Modified Sequential Probability Ratio Test (MSPRT) MSRDT Multi-State Reliability Demonstration Tests (MSRDT) MSSQL Tools to Work with Microsoft SQL Server Databases via 'RODBC' MST Multivariate Survival Trees MSTest Hypothesis Testing for Markov Switching Models 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 MSiP 'MassSpectrometry' Interaction Prediction MSigSeg Multiple SIGnal SEGmentation MSmix Finite Mixtures of Mallows Models with Spearman Distance for Full and Partial Rankings 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 MTAFT Data-Driven Estimation for Multi-Threshold Accelerate Failure Time Model MTAR Multi-Trait Analysis of Rare-Variant Association Study MTDrh Mass Transportation Distance Rank Histogram 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 MUS Monetary Unit Sampling and Estimation Methods, Widely Used in Auditing MVA An Introduction to Applied Multivariate Analysis with R MVET Multivariate Estimates and Tests MVLM Multivariate Linear Model with Analytic p-Values MVN Multivariate Normality Tests MVNBayesian Bayesian Analysis Framework for MVN (Mixture) Distribution MVNtestchar Test for Multivariate Normal Distribution Based on a Characterization MVPBT Publication Bias Tests for Meta-Analysis of Diagnostic Accuracy Test MVQuickGraphs Quick Multivariate Graphs MVR Mean-Variance Regularization 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 MXM Feature Selection (Including Multiple Solutions) and Bayesian Networks MaOEA Many Objective Evolutionary Algorithm Maaslin2 "Multivariable Association Discovery in Population-scale Meta-omics Studies" MacBehaviour Behavioural Studies of Large Language Models MachineShop Machine Learning Models and Tools MacroZooBenthosWaterA Fresh Water Quality Analysis Based on Macrozoobenthos MadanText Persian Text Mining Tool for Frequency Analysis, Statistical Analysis, and Word Clouds MadanTextNetwork Persian Text Mining Tool for Co-Occurrence Network 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 MantaID A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs 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 MarZIC Marginal Mediation Effects with Zero-Inflated Compositional Mediator MareyMap Estimation of Meiotic Recombination Rates Using Marey Maps MargCond Joint Marginal-Conditional Model MarginalMediation Marginal Mediation 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 MatSkew Matrix Skew-T Parameter Estimation 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 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 MatrixLDA Penalized Matrix-Normal Linear Discriminant Analysis MatrixMixtures Model-Based Clustering via Matrix-Variate Mixture Models MatrixModels Modelling with Sparse and Dense Matrices MaxPro Maximum Projection Designs MaxSkew Orthogonal Data Projections with Maximal Skewness 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 Mcomp Data from the M-Competitions MeTo Meteorological Tools MedDietCalc Multi Calculator to Compute Scores of Adherence to Mediterranean Diet MedLEA Morphological and Structural Features of Medicinal Leaves MediaK Calculate MeDiA_K Distance Mediana Clinical Trial Simulations MedianaDesigner Power and Sample Size Calculations for Clinical Trials Mega2R Accessing and Processing a 'Mega2' Genetic Database 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 MetChem Chemical Structural Similarity Analysis MetGen Stochastic Weather Generator MetProc Separate Metabolites into Likely Measurement Artifacts and True Metabolites MetSizeR A Shiny App for Sample Size Estimation in Metabolomic Experiments MetaAnalyser An Interactive Visualisation of Meta-Analysis as a Physical Weighing Machine MetaComp EDGE Taxonomy Assignments Visualization MetaCycle Evaluate Periodicity in Large Scale Data MetaHD A Multivariate Meta-Analysis Model for Metabolomics Data MetaIntegration Ensemble Meta-Prediction Framework MetaIntegrator Meta-Analysis of Gene Expression Data MetaLandSim Landscape and Range Expansion Simulation MetaLonDA Metagenomics Longitudinal Differential Abundance Method MetaNLP Natural Language Processing for Meta Analysis MetaNet Network Analysis for Omics Data 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 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 MetaculR Analyze Metaculus Predictions and Questions MethComp Analysis of Agreement in Method Comparison Studies MethEvolSIM Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies MethodCompare Bias and Precision Plots 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 MfUSampler Multivariate-from-Univariate (MfU) MCMC Sampler Mfuzz Soft clustering of time series gene expression data Mhorseshoe Approximate Algorithm for Horseshoe Prior MiDA Microarray Data Analysis MiMIR Metabolomics-Based Models for Imputing Risk MiRKAT Microbiome Regression-Based Kernel Association Tests MiRNAQCD Micro-RNA Quality Control and Diagnosis MiRSEA 'MicroRNA' Set Enrichment Analysis MiSPU Microbiome Based Sum of Powered Score (MiSPU) Tests 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 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 MindOnStats Data sets included in Utts and Heckard's Mind on Statistics Minirand Minimization Randomization MisRepARMA Misreported Time Series Analysis 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 MixAll Clustering and Classification using Model-Based Mixture Models MixGHD Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions 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 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 MixtureMissing Robust and Flexible Model-Based Clustering for Data Sets with Missing Values at Random MixviR Analysis and Exploration of Mixed Microbial Genomic Samples 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 MoLE Modeling Language Evolution MoNAn Mobility Network Analysis MoTBFs Learning Hybrid Bayesian Networks using Mixtures of Truncated Basis Functions MobileTrigger Run Reports, Models, and Scripts from a Mobile Device ModEstM Mode Estimation, Even in the Multimodal Case ModStatR Statistical Modelling in Action with R ModTools Tools for Building Regression and Classification Models 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 Momocs Morphometrics using R Mondrian A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events MonetDB.R Connect MonetDB to R MonoInc Monotonic Increasing MonoPhy Explore Monophyly of Taxonomic Groups in a Phylogeny MonoPoly Functions to Fit Monotone Polynomials Monte.Carlo.se Monte Carlo Standard Errors MonteCarlo Automatic Parallelized Monte Carlo Simulations MonteCarloSEM Monte Carlo Data Simulation Package Morpho Calculations and Visualisations Related to Geometric Morphometrics MorphoTools2 Multivariate Morphometric Analysis Morphoscape Computation and Visualization of Adaptive Landscapes 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 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 MtreeRing A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images MuChPoint Multiple Change Point MuMIn Multi-Model Inference MuViCP MultiClass Visualizable Classification using Combination of Projections MullerPlot Generates Muller Plot from Population/Abundance/Frequency Dynamics Data MultAlloc Optimal Allocation in Stratified Sampling MultBiplotR Multivariate Analysis Using Biplots in R MultEq Multiple Equivalence Tests and Simultaneous Confidence Intervals MultIS Reconstruction of Clones from Integration Site Readouts and Visualization 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 MultiFit Multiscale Fisher's Independence Test for Multivariate Dependence MultiGlarmaVarSel Variable Selection in Sparse Multivariate GLARMA Models 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 MultiObjMatch Multi-Objective Matching Algorithm MultiOrd Generation of Multivariate Ordinal Variates MultiPhen A Package to Test for Multi-Trait Association MultiRNG Multivariate Pseudo-Random Number Generation MultiRR Bias, Precision, and Power for Multi-Level Random Regressions MultiRobust Multiply Robust Methods for Missing Data Problems MultiSkew Measures, Tests and Removes Multivariate Skewness MultiStatM Multivariate Statistical Methods MultiVarMI Multiple Imputation for Multivariate Data MultiVarSel Variable Selection in a Multivariate Linear Model Multiaovbay Classic, Nonparametric and Bayesian Two-Way Analysis of Variance Panel MultinomialCI Simultaneous Confidence Intervals for Multinomial Proportions According to the Method by Sison and Glaz 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 MultisiteMediation Causal Mediation Analysis in Multisite Trials MultivariateAnalysis Pacote Para Analise Multivariada MultivariateRandomForest Models Multivariate Cases Using Random Forests 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 N2H4 Handling Methods for Naver News Text Crawling 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 NADIA NA Data Imputation Algorithms NAEPirtparams IRT Parameters for the National Assessment of Education Progress NAEPprimer The NAEP Primer NAIR Network Analysis of Immune Repertoire NAM Nested Association Mapping NAP Non-Local Alternative Priors in Psychology NB.MClust Negative Binomial Model-Based Clustering NBAloveR Help Basketball Data Analysis NBBDesigns Neighbour Balanced Block Designs (NBBDesigns) NBDdirichlet NBD-Dirichlet Model of Consumer Buying Behavior for Marketing Research NBDesign Design and Monitoring of Clinical Trials with Negative Binomial Endpoint 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 NCSampling Nearest Centroid (NC) Sampling 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 NEONiso Tools to Calibrate and Work with NEON Atmospheric Isotope Data NEpiC Network Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals NFCP N-Factor Commodity Pricing Through Term Structure Estimation 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 NHSE/I 'Making Data Count' Programme 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 NLRoot searching for the root of equation NMA Network Meta-Analysis Based on Multivariate Meta-Analysis Models NMADiagT Network Meta-Analysis of Multiple Diagnostic Tests NMAoutlier Detecting Outliers in Network Meta-Analysis NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) NMFN Non-Negative Matrix Factorization NMI Normalized Mutual Information of Community Structure in Network 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 NNS Nonlinear Nonparametric Statistics NNTbiomarker Calculate Design Parameters for Biomarker Validation Studies NNbenchmark Datasets and Functions to Benchmark Neural Network Packages NO.PING.PONG Incorporating Previous Findings When Evaluating New Data NORMA Builds General Noise SVRs NPBayesImputeCat Non-Parametric Bayesian Multiple Imputation for Categorical Data NPCD Nonparametric Methods for Cognitive Diagnosis NPCirc Nonparametric Circular Methods NPCox Nonparametric and Semiparametric Proportional Hazards Model NPHMC Sample Size Calculation for the Proportional Hazards Mixture Cure Model NPHazardRate Nonparametric Hazard Rate Estimation NPIstats Nonparametric Predictive Inference NPMLEcmprsk Type-Specific Failure Rate and Hazard Rate on Competing Risks Data NPP Normalized Power Prior Bayesian Analysis NPflow Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data NRejections Metrics for Multiple Testing with Correlated Outcomes NSAE Nonstationary Small Area Estimation NSM3 Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition NSO1212 National Statistical Office of Mongolia's Open Data API Handler 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 NVAR Nonlinear Vector Autoregression Models NVCSSL Nonparametric Varying Coefficient Spike-and-Slab Lasso NameNeedle Using Needleman-Wunsch to Match Sample Names NasdaqDataLink API Wrapper for Nasdaq Data Link NatParksPalettes Color Palettes Inspired by National Parks NatureSounds Animal Sounds for Bioacustic Analysis NbClust Determining the Best Number of Clusters in a Data Set 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 NestMRMC Single Reader Between-Cases AUC Estimator in Nested Data NestedCategBayesImpute Modeling, Imputing and Generating Synthetic Versions of Nested Categorical Data in the Presence of Impossible Combinations NestedMenu A Nested Menu Widget for 'Shiny' Applications 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 NetFACS Network Applications to Facial Communication Data 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 NetSimR Actuarial Functions for Non-Life Insurance Modelling NetSwan Network Strengths and Weaknesses Analysis 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 Regression Model on Network-Linked Data with Statistical Inference NetworkRiskMeasures Risk Measures for (Financial) Networks NetworkToolbox Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis NeuralNetTools Visualization and Analysis Tools for Neural Networks NeuralSens Sensitivity Analysis of Neural Networks NeuroDecodeR Decode Information from Neural Activity 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 NicheBarcoding Niche-model-Based Species Identification 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 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 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 Nozzle.R1 Nozzle Reports 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 OCA Optimal Capital Allocations OCNet Optimal Channel Networks OCSdata Download Data from the 'Open Case Studies' Repository ODB Open Document Databases (.odb) Management ODEnetwork Network of Differential Equations ODEsensitivity Sensitivity Analysis of Ordinary Differential Equations 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 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 OHCSpackage Prepare Housing Data for Analysis OHPL Ordered Homogeneity Pursuit Lasso for Group Variable Selection OLCPM Online Change Point Detection for Matrix-Valued Time Series OLStrajr Ordinary Least Squares Trajectory Analysis ONEST Observers Needed to Evaluate Subjective Tests OOBCurve Out of Bag Learning Curve OOR Optimistic Optimization in R OOS Out-of-Sample Time Series Forecasting OPC The Online Principal Component Estimation Method OPDOE Optimal Design of Experiments OPI Open Perimetry Interface OPTS Optimization via Subsampling (OPTS) OPTtesting Optimal Testing ORCME Order Restricted Clustering for Microarray Experiments ORFID Manage and Summarize Data from Oregon RFID ORMR and ORSR Antenna Readers ORIClust Order-Restricted Information Criterion-Based Clustering Algorithm ORION Ordinal Relations ORKM The Online Regularized K-Means Clustering Algorithm ORTSC Connects to Google Cloud API for Label Detection OSAT OSAT: Optimal Sample Assignment Tool OSCV One-Sided Cross-Validation OSDR Finds an Optimal System of Distinct Representatives OSFD Output Space-Filling Design OSLdecomposition Signal Component Analysis for Optically Stimulated Luminescence OSMscale Add a Scale Bar to 'OpenStreetMap' Plots OSNMTF Orthogonal Sparse Non-Negative Matrix Tri-Factorization OSTE Optimal Survival Trees Ensemble OSsurvival Assessing Surrogacy with a Censored Outcome 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: The Binormal Approach and Alternatives OVtool Omitted Variable Tool OWEA Optimal Weight Exchange Algorithm for Optimal Designs for Three Models Oarray Arrays with Arbitrary Offsets 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 OenoKPM Modeling the Kinetics of Carbon Dioxide Production in Alcoholic Fermentation 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 OlympicRshiny 'Shiny' Application for Olympic Data OmegaG Omega-Generic: Composite Reliability of Multidimensional Measures OmicKriging Poly-Omic Prediction of Complex TRaits OmicNavigator Open-Source Software for 'Omic' Data Analysis and Visualization OmicSense Biosensor Development using Omics Data OmicsPLS Data Integration with Two-Way Orthogonal Partial Least Squares OmicsQC Nominating Quality Control Outliers in Genomic Profiling Studies Omisc Univariate Bootstrapping and Other Things OmnibusFisher A Modified Fisher’s Method to Test Overall Gene-Level Effect OnAge Test of Between-Group Differences in the Onset of Senescence OnboardClient Bindings for Onboard Data's Building Data API 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 OnomasticDiversity Onomastic Diversity Measures OpEnHiMR Optimization Based Ensemble Model for Prediction of Histone Modifications in Rice 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.org' API OpenMx Extended Structural Equation Modelling OpenRepGrid Tools to Analyze Repertory Grid Data OpenRepGrid.ic Interpretive Clustering for Repertory Grids OpenSpecy Analyze, Process, Identify, and Share Raman and (FT)IR Spectra OpenStreetMap Access to Open Street Map Raster Images OpenTreeChronograms Open Tree of Life Chronograms 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' OptSig Optimal Level of Significance for Regression and Other Statistical Tests OptiSembleForecasting Optimization Based Ensemble Forecasting Using MCS Algorithm OptimModel Perform Nonlinear Regression Using 'optim' as the Optimization Engine OptimaRegion Confidence Regions for Optima of Response Surfaces OptimalCutpoints Computing Optimal Cutpoints in Diagnostic Tests OptimalDesign A Toolbox for Computing Efficient Designs of Experiments OptimalGoldstandardDesigns Design Parameter Optimization for Gold-Standard Non-Inferiority Trials 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 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 OrgMassSpecR Organic Mass Spectrometry OrganismDbi Software to enable the smooth interfacing of different database packages 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 OutliersLearn Educational Outlier Package with Common Outlier Detection Algorithms OutliersO3 Draws Overview of Outliers (O3) Plots OwenQ Owen Q-Function OxyBS Processing of Oxy-Bisulfite Microarray Data PAC Partition-Assisted Clustering and Multiple Alignments of Networks PACLasso Penalized and Constrained Lasso Optimization PACVr Plastome Assembly Coverage Visualization PADOG Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) PAFit Generative Mechanism Estimation in Temporal Complex Networks PAGFL Joint Estimation of Latent Groups and Group-Specific Coefficients in 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 PASenseWear Summarize Daily Physical Activity from 'SenseWear' Accelerometer Data PAmeasures Prediction and Accuracy Measures for Nonlinear Models and for Right-Censored Time-to-Event Data PAsso Assessing the Partial Association Between Ordinal Variables 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 PCAmatchR Match Cases to Controls Based on Genotype Principal Components PCAmixdata Multivariate Analysis of Mixed Data PCBS Principle 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 PCICt Implementation of POSIXct Work-Alike for 365 and 360 Day Calendars 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 PCS Calculate the Probability of Correct Selection (PCS) PCSinR Parallel Constraint Satisfaction Networks in R PCovR Principal Covariates Regression PDE Extract Tables and Sentences from PDFs with User Interface PDFEstimator Multivariate Nonparametric Probability Density Estimator 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' PDtoolkit Collection of Tools for PD Rating Model Development and Validation PEACH Pareto Enrichment Analysis for Combining Heterogeneous Datasets 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 PEkit Partition Exchangeability Toolkit PEtests Power-Enhanced (PE) Tests for High-Dimensional Data PFIM Population Fisher Information Matrix PGEE Penalized Generalized Estimating Equations in High-Dimension PGM2 Nested Resolvable Designs and their Associated Uniform Designs PGRdup Discover Probable Duplicates in Plant Genetic Resources Collections 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 with a Standardized Score Process PICBayes Bayesian Models for Partly Interval-Censored Data 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 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 PKPDsim Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations 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 PLMIX Bayesian Analysis of Finite Mixtures of Plackett-Luce Models for Partial Rankings/Orderings PLNmodels Poisson Lognormal Models PLORN Prediction with Less Overfitting and Robust to Noise PLRModels Statistical Inference in Partial Linear Regression Models PLSiMCpp Methods for Partial Linear Single Index Model PLindleyROC Receiver Operating Characteristic Based on Power Lindley Distribution PLmixed Estimate (Generalized) Linear Mixed Models with Factor Structures PLordprob Multivariate Ordered Probit Model via Pairwise Likelihood PLreg Power Logit Regression for Modeling Bounded Data PMA Penalized Multivariate Analysis PMAPscore Identify Prognosis-Related Pathways Altered by Somatic Mutation 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 PMwR Portfolio Management with R PNADcIBGE Downloading, Reading and Analyzing PNADC Microdata PNAR Poisson Network Autoregressive Models 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) 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 POUMM The Phylogenetic Ornstein-Uhlenbeck Mixed Model 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 PPLasso Prognostic Predictive Lasso for Biomarker Selection 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 PPTcirc Projected Polya Tree for Circular Data PPbigdata Projection Pursuit for Big Data Based on Data Nuggets PPforest Projection Pursuit Classification Forest PPtreeViz Projection Pursuit Classification Tree Visualization PPtreeregViz Projection Pursuit Regression Tree Visualization PQLseq Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies PRDA Conduct a Prospective or Retrospective Design Analysis PRECAST Embedding and Clustering with Alignment for Spatial Datasets PREPShiny Interactive Document for Preprocessing the Dataset PRIMAL Parametric Simplex Method for Sparse Learning PRIMEplus Study Design for Immunotherapy Clinical Trials PRIMME Eigenvalues and Singular Values and Vectors from Large Matrices 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 PRISMAstatement Plot Flow Charts According to the "PRISMA" Statement PRNG A Pseudo-Random Number Generator PROBShiny Interactive Document for Working with Basic Probability 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 PRSPGx Construct PGx PRS PRSim Stochastic Simulation of Streamflow Time Series using Phase Randomization 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 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 PSPManalysis Analysis of Physiologically Structured Population Models PSS.Health Power and Sample Size for Health Researchers via Shiny PSSIM Test of Independence & Image Structural Similarity Measure PSSIM PSSMCOOL Features Extracted from Position Specific Scoring Matrix (PSSM) PST Probabilistic Suffix Trees and Variable Length Markov Chains PSW Propensity Score Weighting Methods for Dichotomous Treatments PScr Estimation for the Power Series Cure Rate Model PSinference Inference for Released Plug-in Sampling Single Synthetic Dataset 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 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 PUPAIM A Collection of Physical and Chemical Adsorption Isotherm Models 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 PVR Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve PVplr Performance Loss Rate Analysis Pipeline 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 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 PanCanVarSel Pan-Cancer Variable Selection PanJen A Semi-Parametric Test for Specifying Functional Form Pandora Retrieve Data using the API of the 'Pandora' Data Platform PanelCount Random Effects and/or Sample Selection Models for Panel Count Data PanelMatch Matching Methods for Causal Inference with Time-Series Cross-Sectional Data PanelTM Two- And Three-Way Dynamic Panel Threshold Regression Model for Change Point Detection PantaRhei Plots Sankey Diagrams ParBayesianOptimization Parallel Bayesian Optimization of Hyperparameters ParDNAcopy Parallel implementation of the "segment" function of package "DNAcopy" ParallelLogger Support for Parallel Computation, Logging, and Function Automation ParallelPC Paralellised Versions of Constraint Based Causal Discovery Algorithms 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 PartCensReg Estimation and Diagnostics for Partially Linear Censored Regression Models Based on Heavy-Tailed Distributions PartialNetwork Estimating Peer Effects Using Partial Network Data Partiallyoverlapping Partially Overlapping Samples Tests PatientProfiles Identify Characteristics of Patients in the OMOP Common Data Model Patterns Deciphering Biological Networks with Patterned Heterogeneous Measurements PdPDB Pattern Discovery in PDB Structures of Metalloproteins Peacock.test Two and Three Dimensional Kolmogorov-Smirnov Two-Sample Tests 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 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 PepSAVIms PepSAVI-MS Data Analysis Peptides Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences PerFit Person Fit PerMat Performance Metrics in Predictive Modeling 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 PermutationR Conduct Permutation Analysis of Variance in R PerseusR Perseus R Interop PersianStemmer Persian Stemmer for Text Analysis PersomicsArray Automated Persomics Array Image Extraction PesticideLoadIndicator Computes Danish Pesticide Load Indicator Petersen Estimators for Two-Sample Capture-Recapture Studies PetfindeR 'Petfinder' API Wrapper PhageCocktail Design of the Best Phage Cocktail Phase123 Simulating and Conducting Phase 123 Trials Phase12Compare Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes 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 Phenotype A Tool for Phenotypic Data Processing PhenotypeSimulator Flexible Phenotype Simulation from Different Genetic and Noise Models Phi2rho Owen's T Function and Bivariate Normal Integral PhilipsHue R Interface to the Philips Hue API PhitestR Analyzing the Heterogeneity of Single-Cell Populations 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 PhytosanitaryCalculator Phytosanitary Calculator for Inspection Plans Based on Risks PieGlyph Axis Invariant Scatter Pie Plots PieceExpIntensity Bayesian Model to Find Changepoints Based on Rates and Count Data Pijavski Global Univariate Minimization PlackettLuce Plackett-Luce Models for Rankings PlaneGeometry Plane Geometry 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 PlasmaMutationDetector2 Tumor Mutation Detection in Plasma using Barcoding Plasmidprofiler Visualization of Plasmid Profile Results 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 PlotPrjNetworks Useful Networking Tools for Project Management PlotTools Add Continuous Legends to Plots PoA Finds the Price of Anarchy for Routing Games PoDBAY Vaccine Efficacy Estimation Package PoPdesign Posterior Predictive (PoP) Design for Phase I Clinical Trials PoSI Valid Post-Selection Inference for Linear LS Regression 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 Generalized 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 PolyHaplotyper Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids PolyPatEx Paternity Exclusion in Autopolyploid Species PolyTree Estimate Causal Polytree from Data PolyTrend Trend Classification Algorithm 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 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 PopVar Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation PopulationGrowthR Linear Population Growth Scenarios PortRisk Portfolio Risk Analysis 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 PosRatioDist Quotient of Random Variables Conditioned to the Positive Quadrant PostcodesioR API Wrapper Around 'Postcodes.io' PottsUtils Utility Functions of the Potts Models Power2Stage Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies PowerNormal Power Normal Distribution PowerSDI Calculate Standardised Drought Indices Using NASA POWER Data PowerTOST Power and Sample Size for (Bio)Equivalence Studies PowerUpR Power Analysis Tools for Multilevel Randomized Experiments 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 PredCRG Computational Prediction of Proteins Encoded by Circadian Genes PredPsych Predictive Approaches in Psychology 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 PrevMap Geostatistical Modelling of Spatially Referenced Prevalence Data 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 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 ProTrackR 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 ProbSamplingI Probabilistic Sampling Design and Strategies ProbYX Inference for the Stress-Strength Model R = P(Y