* using log directory ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/GPArotation.Rcheck’ * using R Under development (unstable) (2026-07-19 r90278) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-07-19 13:22:04 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘GPArotation/DESCRIPTION’ ... OK * this is package ‘GPArotation’ version ‘2026.6-1’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GPArotation’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found calls to structure() using deprecated special names: GPArotation/tests/Revelle.R (.Dim: 1, .Dimnames: 1) '.Dim' should be changed to 'dim'. '.Dimnames' should be changed to 'dimnames'. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [21s/22s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Harman.R’ [51s/53s] Running ‘Jennrich2002.R’ Running ‘KaiserNormalization.R’ [47s/48s] Running ‘MASSoblimin.R’ [48s/50s] Running ‘Revelle.R’ Running ‘Thurstone.R’ [50s/52s] Running ‘WansbeekMeijer.R’ [46s/47s] Running ‘algorithmTests.R’ Running ‘errormessages.R’ [46s/47s] Running ‘legacyVsBB.R’ Running ‘legacyVsNew.R’ Running ‘lp.R’ [55s/56s] Running ‘normalizationTests.R’ Running ‘print-GPArotation.R’ [66s/68s] Running ‘rotations.R’ [72s/75s] Running ‘rotationsRS.R’ [57s/58s] Running ‘rotbbcayley.R’ Running ‘tableTests.r’ Running ‘target_vs_bb_clash.R’ Running ‘varimaxVarimax.R’ [54s/55s] Running ‘vgQOLD.R’ Running ‘vgQtestOldVsNew.R’ [10m/10m] ERROR Running the tests in ‘tests/rotations.R’ failed. Complete output: > # Tests here only compare against values computed previously with this code, > # to ensure there was no accidental change. It would be better to have > # comparisons with known correct values. > > # Test for oblimax is commented out as it appears to be unstable. > > > Sys.getenv("R_LIBS") [1] "/data/localhost/ripley/R/packages/tests-OpenBLAS/GPArotation.Rcheck:/data/localhost/ripley/R/test-dev:/data/localhost/ripley/R/test-BioCdata" > library() Packages in library '/data/localhost/ripley/R/packages/tests-OpenBLAS/GPArotation.Rcheck': GPArotation Gradient Projection Factor Rotation Packages in library '/data/localhost/ripley/R/test-dev': AATtools Reliability and Scoring Routines for the Approach-Avoidance Task ABACUS Apps Based Activities for Communicating and Understanding Statistics ABC.RAP Array Based CpG Region Analysis Pipeline ABCDscores Summary Scores of the Adolescent Brain Cognitive Development (ABCD) Study ABCanalysis Computed ABC Analysis ABCoptim Implementation of Artificial Bee Colony (ABC) Optimization ABHgenotypeR Easy Visualization of ABH Genotypes ABM Agent Based Model Simulation Framework ABPS The Abnormal Blood Profile Score to Detect Blood Doping ABRSQOL Quality-of-Life Solver for "Measuring Quality of Life under Spatial Frictions" ABSurvTDC Survival Analysis using Time Dependent Covariate for Animal Breeding ACDm Tools for Autoregressive Conditional Duration Models ACE.CoCo Analysis of Correlated High-Dimensional Expression (ACE) Data ACEP Análisis Computacional de Eventos de Protesta ACEsearch 'ACE' Search Engine API ACEsimFit ACE Kin Pair Data Simulations and Model Fitting ACEt Estimating Dynamic Heritability and Twin Model Comparison ACNE Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization ACSWR A Companion Package for the Book "A Course in Statistics with R" ACTCD Asymptotic Classification Theory for Cognitive Diagnosis ACV Optimal Out-of-Sample Forecast Evaluation and Testing under Stationarity ACWR Acute Chronic Workload Ratio Calculation ADAPTS Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells ADCT Adaptive Design in Clinical Trials ADDT Analysis of Accelerated Destructive Degradation Test Data ADER Data Analysis in Ecology ADGofTest Anderson-Darling GoF test ADLP Accident and Development Period Adjusted Linear Pools for Actuarial Stochastic Reserving ADMM Algorithms using Alternating Direction Method of Multipliers ADP Adoption Probability, Triers and Users Rate of a New Product ADPF Use Least Squares Polynomial Regression and Statistical Testing to Improve Savitzky-Golay ADSIHT Adaptive Double Sparse Iterative Hard Thresholding ADTSA Time Series Analysis ADVICE Automatic Direct Variable Selection via Interrupted Coefficient Estimation AEDForecasting Change Point Analysis in ARIMA Forecasting AEP Statistical Modelling for Asymmetric Exponential Power Distribution AER Applied Econometrics with R AEenrich Adverse Event Enrichment Tests AFFECT Accelerated Functional Failure Time Model with Error-Contaminated Survival Times AFR Toolkit for Regression Analysis of Kazakhstan Banking Sector Data AGBQR Adaptive Generalized Bayesian Quantile Regression AGCA4extremes Anchored Geodesic Component Analysis for Extremes AGD Analysis of Growth Data AGHmatrix Relationship Matrices for Diploid and Autopolyploid Species AGPRIS AGricultural PRoductivity in Space AHMbook Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology' Vols 1 and 2 AHPGaussian New Multicriteria Method: AHPGaussian AHPWR Compute Analytic Hierarchy Process AHPhybrid AHP Hybrid Method AHPtools Consistency in the Analytic Hierarchy Process AHSurv Flexible Parametric Accelerated Hazards Models AIBias Longitudinal Bias Auditing for Sequential Decision Systems AICcmodavg Model Selection and Multimodel Inference Based on (Q)AIC(c) AID Box-Cox Power Transformation AIDA Analysis of Interval DAta AIFFtools Read AIFF Files and Convert to WAVE Format AIGRA Agentic Item Generation, Review, and Analysis AIGovernance Statistical Auditing and Governance Reporting for Employment AI Systems AIPW Augmented Inverse Probability Weighting AIUQ Ab Initio Uncertainty Quantification AIscreenR AI Screening Tools in R for Systematic Reviewing ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account ALDEx3 Linear Models for Sequence Count Data ALDqr Quantile Regression Using Asymmetric Laplace Distribution ALFAM2 Dynamic Model of Ammonia Emission from Field-Applied Manure ALLSPICER ALLelic Spectrum of Pleiotropy Informed Correlated Effects ALS Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) ALSCPC Accelerated line search algorithm for simultaneous orthogonal transformation of several positive definite symmetric matrices to nearly diagonal form. 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Computation of BRINDA Adjusted Micronutrient Biomarkers for Inflammation BRISC Fast Inference for Large Spatial Datasets using BRISC BRL Beta Record Linkage BRPL Methods for Bivariate Poverty Line Calculations BRRAT Bayesian Regression Robustness Assessment Test BRcal Boldness-Recalibration of Binary Events BSCB Bayesian Simultaneous Credible Bands for Polynomial Regression BSDA Basic Statistics and Data Analysis BSET A Bayesian Surrogate Evaluation Test BSGW Bayesian Survival Model with Lasso Shrinkage Using Generalized Weibull Regression BSL Bayesian Synthetic Likelihood BSPADATA Bayesian Proposal to Fit Spatial Econometric Models BSPBSS Bayesian Spatial Blind Source Separation BSS Brownian Semistationary Processes BSSasymp Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates BSSoverSpace Blind Source Separation for Multivariate Spatial Data using Eigen Analysis BSSprep Whitening Data as Preparation for Blind Source Separation BSTFA Bayesian Spatio-Temporal 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Bayesian Vector Autoregression BWGS BreedWheat Genomic Selection Pipeline BWStest Baumgartner Weiss Schindler Test of Equal Distributions BaM Functions and Datasets for "Bayesian Methods: A Social and Behavioral Sciences Approach" BaSTA Age-Specific Bayesian Survival Trajectory Analysis from Incomplete Census or Capture-Recapture/Recovery Data BaSkePro Bayesian Model to Archaeological Faunal Skeletal Profiles BacenAPI Data Collection from the Central Bank of Brazil BagWhiskerPlot Bag-and-Whisker Plot BalanceCheck Balance Check for Multiple Covariates in Matched Observational Studies BalancedSampling Balanced and Spatially Balanced Sampling Ball Statistical Inference and Sure Independence Screening via Ball Statistics BallMapper The Ball Mapper Algorithm BarBorGradient Function Minimum Approximator BarcodingR Species Identification using DNA Barcodes Barnard Barnard's Unconditional Test BaseSet Working with Sets the Tidy Way BaseTempSeed Estimation of Seed Germination Base Temperature 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Clinical Trial Design with and Without Historical Control Data BayesCVI Bayesian Cluster Validity Index BayesChange Bayesian Methods for Change Point Analysis BayesCombo Bayesian Evidence Combination BayesDIP Bayesian Decreasingly Informative Priors for Early Termination Phase II Trials BayesDecon Density Deconvolution Using Bayesian Semiparametric Methods BayesDesign Bayesian Single-Arm Design with Survival Endpoints BayesDissolution Bayesian Models for Dissolution Testing BayesERtools Bayesian Exposure-Response Analysis Tools BayesESS Determining Effective Sample Size BayesFBHborrow Bayesian Dynamic Borrowing with Flexible Baseline Hazard Function BayesFM Bayesian Inference for Factor Modeling BayesFR Fitting Functional Responses in 1- and 2-Prey Systems BayesFactor Computation of Bayes Factors for Common Designs BayesFluxR Implementation of Bayesian Neural Networks BayesForge Bayesian Inference using 'numpyro' and 'XLA' BayesGP Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models BayesGPfit Fast Bayesian Gaussian Process Regression Fitting BayesGWQS Bayesian Grouped Weighted Quantile Sum Regression BayesGmed Bayesian Causal Mediation Analysis using 'Stan' BayesGrowth Estimate Fish Growth Using MCMC Analysis BayesLCA Bayesian Latent Class Analysis BayesLN Bayesian Inference for Log-Normal Data BayesLogit PolyaGamma Sampling BayesMFSurv Bayesian Misclassified-Failure Survival Model BayesMallows Bayesian Preference Learning with the Mallows Rank Model BayesMallowsSMC2 Nested Sequential Monte Carlo for the Bayesian Mallows Model BayesMixSurv Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification BayesMoFo Bayesian Mortality Forecasting BayesMortalityPlus Bayesian Mortality Modelling BayesMultMeta Bayesian Multivariate Meta-Analysis BayesMultiMode Bayesian Mode Inference BayesNSGP Bayesian Analysis of Non-Stationary Gaussian Process Models BayesNetBP Bayesian Network Belief Propagation BayesPET Bayesian Prediction of Event Times for Blinded Randomized Controlled Trials BayesPIM Bayesian Prevalence-Incidence Mixture Model BayesPPD Bayesian Power Prior Design BayesPPDSurv Bayesian Power Prior Design for Survival Data BayesPPR Bayesian Projection Pursuit Regression BayesPieceHazSelect Variable Selection in a Hierarchical Bayesian Model for a Hazard Function BayesPocket Bayesian Causal Inference for Periodontal Diseases in Longitudinal Studies BayesPostEst Generate Postestimation Quantities for Bayesian MCMC Estimation BayesPower Sample Size and Power Calculation for Bayesian Testing with Bayes Factor BayesProject Fast Projection Direction for Multivariate Changepoint Detection BayesRS Bayes Factors for Hierarchical Linear Models with Continuous Predictors BayesRTMB Bayesian Inference Using 'RTMB' BayesRegDTR Bayesian Regression for Dynamic Treatment Regimes BayesRep Bayesian Analysis of Replication Studies BayesRepDesign Bayesian Design of Replication Studies BayesS5 Bayesian Variable Selection Using Simplified Shotgun Stochastic Search with Screening (S5) BayesSIM Integrated Interface of Bayesian Single Index Models using 'nimble' BayesSUR Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings BayesSampling Bayes Linear Estimators for Finite Population BayesSurveillance Bayesian Surveillance Methods for Healthcare Performance Monitoring BayesSurvival Bayesian Survival Analysis for Right Censored Data BayesSurvive Bayesian Survival Models for High-Dimensional Data BayesTSM Bayesian Progressive Three State Model with Censoring Due to Intervention BayesTools Tools for Bayesian Analyses BayesTree Bayesian Additive Regression Trees BayesTreePrior Bayesian Tree Prior Simulation BayesTwin Bayesian Analysis of Item-Level Twin Data BayesVarSel Bayes Factors, Model Choice and Variable Selection in Linear Models BayesVolcano Creating Volcano Plots from Bayesian Model Posteriors BayesX R Utilities Accompanying the Software Package BayesX BayesXsrc Distribution of the 'BayesX' C++ Sources BayesfMRI Spatial Bayesian Methods for Task Functional MRI Studies BayesianDEB Bayesian Dynamic Energy Budget Modelling BayesianDisaggregation Evidence-Based Bayesian Disaggregation of Aggregate Indices BayesianFitForecast Bayesian Parameter Estimation and Forecasting for Epidemiological Models BayesianInference Bayesian Inference BayesianLasso Bayesian Lasso Regression and Tools for the Lasso Distribution BayesianLaterality Predict Brain Asymmetry Based on Handedness and Dichotic Listening BayesianMCPMod Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod BayesianMediationA Bayesian Mediation Analysis BayesianNetwork Bayesian Network Modeling and Analysis BayesianPlatformDesignTimeTrend Simulate and Analyse Bayesian Platform Trial with Time Trend BayesianPower Sample Size and Power for Comparing Inequality Constrained Hypotheses BayesianQDM Bayesian Quantitative Decision-Making Framework for Binary and Continuous Endpoints BayesianReasoning Plot Positive and Negative Predictive Values for Medical Tests BayesianTools General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics Bayesiangammareg Double Generalized Gamma Regression Models Bayesiantreg Bayesian t Regression for Modeling Mean and Scale Parameters Bayesrel Bayesian Reliability Estimation Bchron Age-Depth Radiocarbon Modelling BeQut Bayesian Estimation for Quantile Regression Mixed Models BeSS Best Subset Selection in Linear, Logistic and CoxPH Models BeastJar JAR Dependency for MCMC Using 'BEAST' BeeBDC Occurrence Data Cleaning Benchmarking Benchmark and Frontier Analysis Using DEA and SFA BenfordTests Statistical Tests for Evaluating Conformity to Benford's Law Bergm Bayesian Exponential Random Graph Models BerkeleyForestsAnalytics Compute and Summarize Core Forest Metrics from Field Data Bernadette Bayesian Inference and Model Selection for Stochastic Epidemics Bessel Computations and Approximations for Bessel Functions Bestie Bayesian Estimation of Intervention Effects BetaBit Mini Games from Adventures of Beta and Bit BetaDanish The Beta-Danish Distribution for Lifetime Data Analysis BetaPASS Calculate Power and Sample Size with Beta Regression BetterReg Better Statistics for OLS and Binomial Logistic Regression BeviMed Bayesian Evaluation of Variant Involvement in Mendelian Disease BeyondBenford Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset Bhat General Likelihood Exploration BiCausality Binary Causality Inference Framework BiDAG Bayesian Inference for Directed Acyclic Graphs BiDimRegression Calculates the Bidimensional Regression Between Two 2D Configurations BiObjClass Classification of Algorithms BiTSLS Bidirectional Two-Stage Least Squares Estimation BiTrinA Binarization and Trinarization of One-Dimensional Data BiVariAn Bivariate Automatic Analysis BiasCorrector A GUI to Correct Measurement Bias in DNA Methylation Analyses BiasedUrn Biased Urn Model Distributions BibPlots Plot Functions for Use in Bibliometrics BifactorIndicesCalculator Bifactor Indices Calculator BigDataPE Secure and Intuitive Access to 'BigDataPE' 'API' Datasets BigDataStatMeth Scalable Statistical Computing with HDF5-Backed Matrices BigVAR Dimension Reduction Methods for Multivariate Time Series BimodalIndex The Bimodality Index BinGSD Calculate Boundaries and Conditional Power for Single Arm Group Sequential Test with Binary Endpoint BinMat Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs) BinNonNor Data Generation with Binary and Continuous Non-Normal Components BinNor Simultaneous Generation of Multivariate Binary and Normal Variates BinOrdNonNor Concurrent Generation of Binary, Ordinal and Continuous Data BinSegBstrap Piecewise Smooth Regression by Bootstrapped Binary Segmentation Binarize Binarization of One-Dimensional Data BinaryDosage Creates, Merges, and Reads Binary Dosage Files BinaryEMVS Variable Selection for Binary Data Using the EM Algorithm BinaryEPPM Mean and Scale-Factor Modeling of Under- And Over-Dispersed Binary Data BinaryReplicates Dealing with Binary Replicates BinarybalancedCut Threshold Cut Point of Probability for a Binary Classifier Model BioCro Modular Crop Growth Simulations BioGSP Biological Graph Signal Processing for Spatial Data Analysis BioIndex Biological Indicators and Indices for MEDITS Survey Data BioInsight Filter and Plot RNA Biotypes BioM2 Biologically Explainable Machine Learning Framework BioMoR Bioinformatics Modeling with Recursion and Autoencoder-Based Ensemble BioMonTools Biomonitoring and Bioassessment Calculations 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 BioTIMEr Tools to Use and Explore the 'BioTIME' Database BioThermR Standardized Processing and Analysis of Thermal Imaging Data in Animal Studies BioTooltipR Add Bio Tooltips to HTML Reports BioTrajectory Image Processing Tools for Barnes Maze Experiments BioUtils Biological Data Analysis and Visualization BioVenn Create Area-Proportional Venn Diagrams from Biological Lists BioVizSeq Visualizing the Elements Within Bio-Sequences BioWorldR A Curated Collection of Biodiversity and Species Datasets and Utilities Biobase Biobase: Base functions for Bioconductor BiocBaseUtils Utility and internal functions for Bioconductor packages BiocCheck Bioconductor-specific package checks BiocFileCache Manage Files Across Sessions BiocGenerics S4 generic functions used in Bioconductor BiocIO Standard Input and Output for Bioconductor Packages BiocManager Access the Bioconductor Project Package Repository BiocNeighbors Nearest Neighbor Detection for Bioconductor Packages BiocParallel Bioconductor facilities for parallel evaluation BiocSingular Singular Value Decomposition for Bioconductor Packages BiocStyle Standard styles for vignettes and other Bioconductor documents BiocVersion Set the appropriate version of Bioconductor packages Biodem Biodemography Functions BiodiversityR Package for Community Ecology and Suitability Analysis Bioi Biological Image Analysis Bios2cor From Biological Sequences and Simulations to Correlation Analysis BiostatsUHNplus Nested Data Summary, Adverse Events and REDCap Biostrings Efficient manipulation of biological strings BipartiteModularityMaximization Partition Bipartite Network into Non-Overlapping Biclusters by Optimizing Bipartite Modularity BiplotML Logistic Biplot Estimation Using Machine Learning Algorithms BivGeo Basu-Dhar Bivariate Geometric Distribution BivLaplaceRL Bivariate Laplace Transforms, Stochastic Orders, and Entropy Measures in Reliability BivRec Bivariate 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 BlanketStatsments Build and Compare Statistical Models Blend Robust Bayesian Longitudinal Regularized Semiparametric Mixed Models 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 BlockwiseRankTest Block-Wise Rank in Similarity Graph Edge-Count Two-Sample Test (BRISE) BlueCarbon Estimation of Organic Carbon Stocks and Sequestration Rates from Soil Core Data 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 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 BoneDensityMapping Maps Bone Densities from CT Scans to Surface Models BoneProfileR Tools to Study Bone Compactness 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 BootstrapTests Bootstrap-Based Hypothesis Testing using Different Resampling Schemes Boptbd Bayesian Optimal Block Designs Boruta Wrapper Algorithm for All Relevant Feature Selection BosonSampling Classical Boson Sampling BoundEdgeworth Bound on the Error of the First-Order Edgeworth Expansion BoundIRT Fit Bounded Continuous Item Response Theory Models to Data BoundaryStats Boundary Overlap Statistics BoutrosLab.plotting.general Functions to Create Publication-Quality Plots BradleyTerry2 Bradley-Terry Models BrainCon Inference the Partial Correlations Based on Time Series Data BrainNetTest Hypothesis Testing for Populations of Brain Networks BranchGLM Efficient Best Subset Selection for GLMs via Branch and Bound Algorithms Branching Simulation and Estimation for Branching Processes BrazilCrime Accesses Brazilian Public Security Data from SINESP Since 2015 BrazilDataAPI Access Brazilian Data via APIs and Curated Datasets BrazilMet Download and Processing of Automatic Weather Stations (AWS) Data of INMET-Brazil BreakPoints Identify Breakpoints in Series of Data Brobdingnag Very Large Numbers in R BrokenAdaptiveRidge Broken Adaptive Ridge Regression with Cyclops Brq Bayesian Analysis of Quantile Regression Models BsMD Bayes Screening and Model Discrimination BsplineQuantReg 'Constrained Quantile Regression with Cubic B-Splines' Buddle A Deep Learning for Statistical Classification and Regression Analysis with Random Effects BuildSys System for Building and Debugging C/C++ Dynamic Libraries BurStFin Burns Statistics Financial BurStMisc Burns Statistics Miscellaneous BusinessDuration Calculates Business Duration Between Two Dates ButtR Download and Extract Data from the 'OzButterflies' Database BuyseTest Generalized Pairwise Comparisons Bvalue B-Value and Empirical Equivalence Bound BwQuant Bandwidth Selectors for Local Linear Quantile Regression C19dNUTS Dataset of Regional COVID-19 Deaths per 100,000 Pop (NUTS) C443 See a Forest for the Trees C50 C5.0 Decision Trees and Rule-Based Models CA3variants Three-Way Correspondence Analysis Variants CADF Customer Analytics Data Formatting CADFtest A Package to Perform Covariate Augmented Dickey-Fuller Unit Root Tests CAESAR.Suite CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation CAFT Rank-Based Compositional Analysis using Log-Linear Models for Microbiome Data with Zero Cells CAGR Compound Annual Growth Rate CAISEr Comparison of Algorithms with Iterative Sample Size Estimation CALANGO Comparative Analysis with Annotation-Based Genomic Components CALF Coarse Approximation Linear Function CALIBERrfimpute Multiple Imputation Using MICE and Random Forest CANE Comprehensive Groups of Experiments Analysis for Numerous Environments CAOP.RAA.2024 Official Administrative Map of the Azores (CAOP 2024) CARBayes Spatial Generalised Linear Mixed Models for Areal Unit Data CARBayesST Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data CARBayesdata Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages CARM Covariate-Adjusted Adaptive Randomization via Mahalanobis-Distance CARME CAR-MM Modelling in Stan CARMS Continuous Time Markov Rate Modeling for Reliability Analysis CARRoT Predicting Categorical and Continuous Outcomes Using One in Ten Rule CASCORE Covariate Assisted Spectral Clustering on Ratios of Eigenvectors CASIdata Datasets from Computer Age Statistical Inference CASMI 'CASMI'-Based Functions CAST 'caret' Applications for Spatial-Temporal Models CATAcode Explore and Code Responses to Check-All-that-Apply Survey Items CATT The Cochran-Armitage Trend Test CATTexact Computation of the p-Value for the Exact Conditional Cochran-Armitage Trend Test CAinterprTools Graphical Aid in Correspondence Analysis Interpretation and Significance Testings CAvariants Correspondence Analysis Variants CB2 CRISPR Pooled Screen Analysis using Beta-Binomial Test CBAModel Stochastic 3D Structure Model for Binder-Conductive Additive Phase CBASSED50 Process CBASS-Derived PAM Data CBCgrps Compare Baseline Characteristics Between Groups CBPE Correlation-Based Penalized Estimators CBPS Covariate Balancing Propensity Score CBRT CBRT Data on Turkish Economy CBSr Fits Cubic Bezier Spline Functions to Intertemporal and Risky Choice Data CBT Confidence Bound Target Algorithm CBTF Caught by the Fuzz! - A Minimalistic Fuzz-Test Runner CBnetworkMA Contrast-Based Bayesian Network Meta Analysis CC Control Charts CCA Canonical Correlation Analysis CCAMLRGIS Antarctic Spatial Data Manipulation CCI Computational Test for Conditional Independence CCM Correlation Classification Method CCMMR Minimization of the Convex Clustering Loss Function CCMnet Congruence Class Models for Networks CCP Significance Tests for Canonical Correlation Analysis (CCA) CCSRfind Convert ICD-10 Codes to CCSR Codes CCWeights Perform Weighted Linear Regression for Calibration Curve CCd The Cauchy-Cacoullos (Discrete Cauchy) Distribution CDCPLACES Access the 'CDC PLACES' API CDF Centroid Decision Forest for High-Dimensional Classification CDFt Downscaling and Bias Correction via Non-Parametric CDF-Transform CDGHMM Hidden Markov Models for Multivariate Panel Data CDM Cognitive Diagnosis Modeling CDMConnector Connect to an OMOP Common Data Model CDSE 'Copernicus Data Space Ecosystem' API Wrapper CDSS Course-Dependent Skill Structures CDSim Simulating Climate Data for Research and Modelling CDSimX Simulating Climate Data for Research and Modelling CDVI Cuddy-Della Valle Index for Capturing the Instability in Time Series Data CDatanet Econometrics of Network Data CDsampling Constrained Sampling in Paid Research Studies CEACT Cost-Effectiveness Analysis Toolkit for Clinical Trials CEC Cross-Entropy Clustering CEDA CRISPR Screen and Gene Expression Differential Analysis CEDMr Capability-Ecological Developmental Model (CEDM) Analysis CEEMDANML CEEMDAN Decomposition Based Hybrid Machine Learning Models CEGO Combinatorial Efficient Global Optimization CEOdata Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion Polls in Catalonia CERFIT Causal Effect Random Forest of Interaction Trees CEoptim Cross-Entropy R Package for Optimization CFAcoop Colony Formation Assay: Taking into Account Cellular Cooperation CFC Cause-Specific Framework for Competing-Risk Analysis CFF Simple Similarity for User-Based Collaborative Filtering Systems CFM Analyzing Censored Factor Models CFO CFO-Type Designs in Phase I/II Clinical Trials CFilt Collaborative Filtering Models for Recommendation Systems CFtime Using CF-Compliant Calendars with Climate Projection Data CGE Computing General Equilibrium CGGP Composite Grid Gaussian Processes CGManalyzer Continuous Glucose Monitoring Data Analyzer CGMissingDataR Impute Missing Glucose Values in CGM Data CGNM Cluster Gauss-Newton Method CGP Composite Gaussian Process Models CGR Compound Growth Rate for Capturing the Growth Rate Over the Period CHAPGWAS CHAP-GWAS: Leveraging Chromosomal Haplotypes to Improve Genome-Wide Association Studies CHEMIST Causal Inference with High-Dimensional Error-Prone Covariates and Misclassified Treatments CHMM Coupled Hidden Markov Models CHNCapitalStock Compute Chinese Capital Stocks CHNOSZ Thermodynamic Calculations and Diagrams for Geochemistry CHOIRBM Plots the CHOIR Body Map CIAAWconsensus Isotope Ratio Meta-Analysis CIARA Cluster Independent Algorithm for Rare Cell Types Identification CICA Clusterwise Independent Component Analysis CICI Causal Inference with Continuous (Multiple Time Point) Interventions CIEE Estimating and Testing Direct Effects in Directed Acyclic Graphs using Estimating Equations CIM Compositional Impact of Migration CIMEHR Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data CIMTx Causal Inference for Multiple Treatments with a Binary Outcome CINE Classification International Normalized of Education CINID Curculionidae INstar IDentification CINNA Deciphering Central Informative Nodes in Network Analysis CINmetrics Calculate Chromosomal Instability Metrics CIPerm Computationally-Efficient Confidence Intervals for Mean Shift from Permutation Methods CIS.DGLM Covariates, Interaction, and Selection for DGLM CITAN CITation ANalysis Toolpack CITMIC Estimation of Cell Infiltration Based on Cell Crosstalk CIfinder Estimate the Confidence Intervals for Predictive Values CIplot Functions to Plot Confidence Interval CIpostSelect Confidence Interval Post-Selection of Variable CJAMP Copula-Based Joint Analysis of Multiple Phenotypes CJIVE Canonical Joint and Individual Variation Explained (CJIVE) CKAT Composite Kernel Association Test for Pharmacogenetics Studies CKLRT Composite Kernel Machine Regression Based on Likelihood Ratio Test CKNNRLD Clustering-Based K-Nearest Neighbor Regression for Longitudinal Data CLA Critical Line Algorithm in Pure R CLAST Exact Confidence Limits after a Sequential Trial CLIC The LIC for Distributed Cosine Regression Analysis CLME Constrained Inference for Linear Mixed Effects Models CLONETv2 Clonality Estimates in Tumor CLRtools Diagnostic Tools for Logistic and Conditional Logistic Regression CLSIEP15 Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations CLUSTShiny Interactive Document for Working with Cluster Analysis CLVTools Tools for Customer Lifetime Value Estimation CLimd Generating Rainfall Rasters from IMD NetCDF Data CMAPSS Commercial Modular Aero-Propulsion System Simulation Data Set CMF Collective Matrix Factorization CMFsurrogate Calibrated Model Fusion Approach to Combine Surrogate Markers CMGFM Covariate-Augumented Generalized Factor Model CMHNPA Cochran-Mantel-Haenszel and Nonparametric ANOVA CMHSU Mental Health Status, Substance Use Status and their Concurrent Status in North American Healthcare Administrative Databases CMIP6VisR Visualization and Analysis of Coupled Model Intercomparison Project, Phase-6 (CMIP6) Hydroclimatic Data CMLS Constrained Multivariate Least Squares CMMs Compositional Mediation Model CMShiny Interactive Document for Working with Confusion Matrix CMapViz Representation Tool For Output Of Connectivity Map (CMap) Analysis CMatching Matching Algorithms for Causal Inference with Clustered Data CMplot Circle Manhattan Plot CNAIM Common Network Asset Indices Methodology (CNAIM) CNID Get Basic Information from Chinese ID Number CNLTreg Complex-Valued Wavelet Lifting for Signal Denoising CNLTtsa Complex-Valued Wavelet Lifting for Univariate and Bivariate Time Series Analysis CNPS Nonparametric Statistics CNSigs Analysis of Copy Number Signatures CNVScope A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization CNVreg CNV-Profile Regression for Copy Number Variants Association Analysis with Penalized Regression CNprep Pre-Process DNA Copy Number (CN) Data for Detection of CN Events COAP High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model COINT Unit Root Tests with Structural Breaks and Fully-Modified Estimators COINr Composite Indicator Construction and Analysis COLP Causal Discovery for Categorical Data with Label Permutation COMBAT A Combined Association Test for Genes using Summary Statistics COMBO Correcting Misclassified Binary Outcomes in Association Studies COMIX Coarsened Mixtures of Hierarchical Skew Kernels COMMA Correcting Misclassified Mediation Analysis COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression CONCUR Copy Number Profile Curve-Based Association Test COR The COR for Optimal Subset Selection in Distributed Estimation CORE Cores of Recurrent Events CORPlot Cumulative Odds Ratio Plot COST Copula-Based Semiparametric Models for Spatio-Temporal Data COUNT Functions, Data and Code for Count Data COVID19 R Interface to COVID-19 Data Hub COVIDIBGE Downloading, Reading and Analyzing PNAD COVID19 Microdata COveR Clustering with Overlaps CP Conditional Power Calculations CPBayes Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations CPC Implementation of Cluster-Polarization Coefficient CPCAT The Closure Principle Computational Approach Test CPE Concordance Probability Estimates in Survival Analysis CPGLIB Competing Proximal Gradients Library CPMCGLM Correction of the P-Value after Multiple Coding in Generalized Linear Models CPNCoverageAnalysis Conceptual Properties Norming Studies as Parameter Estimation CPP Composition of Probabilistic Preferences (CPP) CPoptim Convex Partition Optimisation CPsurv Nonparametric Change Point Estimation for Survival Data CR2 Compute Cluster Robust Standard Errors with Degrees of Freedom Adjustments CRABS Congruent Rate Analyses in Birth-Death Scenarios CRANsearcher RStudio Addin for Searching Packages in CRAN Database Based on Keywords CRBHSF Cyber-Resilient Bayesian Healthcare Surveillance Framework CRE Interpretable Discovery and Inference of Heterogeneous Treatment Effects CREAM Clustering of Genomic Regions Analysis Method CREDS Calibrated Ratio Estimator under Double Sampling Design CRMetrics Cell Ranger Output Filtering and Metrics Visualization CRTConjoint Conditional Randomization Testing (CRT) Approach for Conjoint Analysis CRTSize Sample Size Estimation Functions for Cluster Randomized Trials CRTgeeDR Doubly Robust Inverse Probability Weighted Augmented GEE Estimator CRTspat Workflow for Cluster Randomised Trials with Spillover CRediTas Generate CRediT Author Statements CSCNet Fitting and Tuning Regularized Cause-Specific Cox Models with Elastic-Net Penalty CSDownscale Statistical Downscaling of Climate Predictions CSESA CRISPR-Based Salmonella Enterica Serotype Analyzer CSHShydRology Canadian Hydrological Analyses CSIndicators Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions CSMES Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain Cost Conditions CSTE Covariate Specific Treatment Effect (CSTE) Curve CSTools Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales CSclone Bayesian Nonparametric Modeling in R CSeQTL Cell Type-Specific Expression Quantitative Trait Loci Mapping CSeqpat Frequent Contiguous Sequential Pattern Mining of Text CSwR Companion to the Book "Computational Statistics with R" CTD A Method for 'Connecting The Dots' in Weighted Graphs CTE Constant Temperature Equivalent CTNote CTN Outcomes, Treatments, and Endpoints CTRing Density Profiles of Wood from CT Scan Images CTShiny Interactive Document for Working with Classification Tree Analysis CTShiny2 Interactive Document for Working with Classification Tree Analysis CTT Classical Test Theory Functions CTTShiny Classical Test Theory via Shiny CTTvis Visualize Item Metrics of the Classical Test Theory Framework CTxCC Multivariate Normal Mean Monitoring Through Critical-to-X Control Chart CUB A Class of Mixture Models for Ordinal Data CUFF Charles's Utility Function using Formula CUMP Analyze Multivariate Phenotypes by Combining Univariate Results CUSUMdesign Compute Decision Interval and Average Run Length for CUSUM Charts CUtools Clinical Utility Tools to Analyze a Predictive Model CVD Color Vision Deficiencies CVST Fast Cross-Validation via Sequential Testing CVThresh Level-Dependent Cross-Validation Thresholding CVXR Disciplined Convex Optimization CVglasso Lasso Penalized Precision Matrix Estimation CVrisk Compute Risk Scores for Cardiovascular Diseases CWT Continuous Wavelet Transformation for Spectroscopy CaDENCE Conditional Density Estimation Network Construction and Evaluation CaMeA Causal Meta-Analysis for Aggregated Data CaPO4Sim A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis Cairo R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output CalSim The Calibration Simplex CalcThemAll.PRM Calculate Pesticide Risk Metric (PRM) Values from Multiple Pesticides...Calc Them All CalibratR Mapping ML Scores to Calibrated Predictions CalibrateSSB Weighting and Estimation for Panel Data with Non-Response CalibrationCurves Calibration Performance CamelRatiosIndex Multivariate-Weighted Indexing of CAMEL Ratios for Bank Performance CamelUp 'CamelUp' Board Game as a Teaching Aid for Introductory Statistics CancerEvolutionVisualization Publication Quality Phylogenetic Tree Plots CancerGram Prediction of Anticancer Peptides Canek Batch Correction of Single Cell Transcriptome Data CanonicalFamilyExtra Extra Canonical Link Family Objects for Generalized Linear Models Capsule Comprehensive Reproducibility Framework for R and Bioinformatics Analysis CardiacDP Automated Cardiac Data Processing via ACF, GA & Tracking Index CardioCurveR Nonlinear Modeling of R-R Interval Dynamics CardioDataSets A Comprehensive Collection of Cardiovascular and Heart Disease Datasets CareDensity Calculate the Care Density or Fragmented Care Density Given a Patient-Sharing Network CarletonStats Functions for Statistics Classes at Carleton College Carlson Carlson Elliptic Integrals and Incomplete Elliptic Integrals Cascade Selection, Reverse-Engineering and Prediction in Cascade Networks CascadeData Experimental Data of Cascade Experiments in Genomics CaseBasedReasoning Case Based Reasoning CaseCohortCoxSurvival Case-Cohort Cox Survival Inference CatDataAnalysis Datasets for Categorical Data Analysis by Agresti CatDyn Fishery Stock Assessment by Catch Dynamics Models CatEncoders Encoders for Categorical Variables CatPredi Optimal Categorisation of Continuous Variables in Prediction Models CatReg Solution Paths for Linear and Logistic Regression Models with Categorical Predictors, with SCOPE Penalty CatastRo Interface to the Spanish 'Catastro' Web Services Category Category Analysis CausCor Calculate Correlations and Estimate Causality CausalGPS Matching on Generalized Propensity Scores with Continuous Exposures CausalImpact Inferring Causal Effects using Bayesian Structural Time-Series Models CausalMBSTS MBSTS Models for Causal Inference and Forecasting CausalMetaR Causally Interpretable Meta-Analysis CausalMixGPD Bayesian Nonparametric Conditional Density Modeling in Causal Inference and Clustering with a Heavy-Tail Extension CausalModels Causal Inference Modeling for Estimation of Causal Effects CausalQueries Make, Update, and Query Binary Causal Models CausalSpline Nonlinear Causal Dose-Response Estimation via Splines CautiousLearning Control Charts with Guaranteed In-Control Performance and Cautious Parameters Learning CbKST Competence-Based Knowledge Space Theory CePa Centrality-Based Pathway Enrichment CeRNASeek Identification and Analysis of ceRNA Regulation CellDEEP Cell DiffErential Expression by Pooling ('CellDEEP') CellWindX Marker Gene Analysis and Visualization for Single-Cell Data CenBAR Broken Adaptive Ridge AFT Model with Censored Data CensMFM Finite Mixture of Multivariate Censored/Missing Data CensRegSMSN Censored Linear Regression Models under Heavy‑tailed Distributions CensSpatial Censored Spatial Models Census2016 Data from the Australian Census 2016 CepReg A Cepstral Model for Covariate-Dependent Time Series CepalStatR Access to the 'CEPALSTAT API' CerioliOutlierDetection Outlier Detection Using the Iterated RMCD Method of Cerioli (2010) Certara.DarwinReporter Data Visualization Utilities for 'pyDarwin' Machine Learning Pharmacometric Model Development Certara.ModelResults Generate Diagnostics for Pharmacometric Models Using 'shiny' Certara.NLME8 Utilities for Certara's Nonlinear Mixed-Effects Modeling Engine Certara.R Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara Certara.RDarwin Interface for 'pyDarwin' Machine Learning Pharmacometric Model Development Certara.RsNLME Pharmacometric Modeling Certara.RsNLME.ModelBuilder Pharmacometric Model Building Using 'shiny' Certara.RsNLME.ModelExecutor Execute Pharmacometric Models Using 'shiny' Certara.VPCResults Generate Visual Predictive Checks (VPC) Using 'shiny' Certara.Xpose.NLME Enhances 'xpose' Diagnostics for Pharmacometric Models from 'Certara.RsNLME' and Phoenix NLME ChIPseeker ChIPseeker for ChIP peak Annotation, Comparison, and Visualization ChainLadder Statistical Methods and Models for Claims Reserving in General Insurance ChangePointTaylor Identify Changes in Mean ChangepointTesting Change Point Estimation for Clustered Signals ChannelAttribution Markov Model for Online Multi-Channel Attribution ChannelAttributionApp Shiny Web Application for the Multichannel Attribution Problem Chaos01 0-1 Test for Chaos ChaosGame Chaos Game CharAnalysis Peak Detection and Fire History from Sediment-Charcoal Records Characterization Implement Descriptive Studies Using the Common Data Model ChauBoxplot Chauvenet-Type Boxplot CheckDigit Calculate and Verify Check Digits ChemmineR Cheminformatics Toolkit for R ChemoSpec Exploratory Chemometrics for Spectroscopy ChemoSpec2D Exploratory Chemometrics for 2D Spectroscopy ChemoSpecUtils Functions Supporting Packages ChemoSpec and ChemoSpec2D ChernoffDist Chernoff's Distribution ChessGmooG FIDE Chess Players Ratings for 2015 and 2020 ChestVolume Estimate the Chest Volume with Markers Data ChileDataAPI Access Chilean Data via APIs and Curated Datasets ChillModels Processing Chill and Heat Models for Temperate Fruit Trees ChinAPIs Access Chinese Data via Public APIs and Curated Datasets ChineseNames Chinese Name Database 1930-2008 ChoiceModelR Choice Modeling in R CholWishart Cholesky Decomposition of the Wishart Distribution CimpleG A Method to Identify Single CpG Sites for Classification and Deconvolution CircMLE Maximum Likelihood Analysis of Circular Data CircNNTSR Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models CircNNTSRSymmetric Circular Data using Symmetric NNTS Models CircNNTSRaxial Axial Data using NNTS Models CircNNTSRmult Multivariate Circular Data using MNNTS Models CircOutlier Detection of Outliers in Circular-Circular Regression CircStats Circular Statistics, from "Topics in Circular Statistics" (2001) CircaCP Sleep and Circadian Metrics Estimation from Actigraphy Data CirceR Construct Cohort Inclusion and Restriction Criteria Expressions CirclesIntersections Algorithm for Computation of the Intersection Areas of N Circles CircularBoxplots Grouped Boxplots for Circular Data CircularDDM Circular Drift-Diffusion Model CircularRegression Circular Regression Models CircularSilhouette Fast Silhouette on Circular or Linear Data Clusters CiteSource Data-Driven Search Strategy Development and Evidence Synthesis Reporting Ckmeans.1d.dp Optimal, Fast, and Reproducible Univariate Clustering Claddis Measuring Morphological Diversity and Evolutionary Tempo ClaimsProblems Analysis of Conflicting Claims ClamR Time Series Modeling for Climate Change Proxies ClassComparison Classes and Methods for "Class Comparison" Problems on Microarrays ClassDiscovery Classes and Methods for "Class Discovery" with Microarrays or Proteomics ClassificationEnsembles Automatically Builds 12 Classification Models (6 Individual and 6 Ensembles of Models) from Classification Data ClassifyITS Fungal Assignment Pipeline CleanBSequences Curing of Biological Sequences Cleanet Automated Doublet Detection and Classification for Cytometry Data CleaningValidation Cleaning Validation Functions for Pharmaceutical Cleaning Process ClickClust Model-Based Clustering of Categorical Sequences ClickHouseHTTP A Simple HTTP Database Interface to 'ClickHouse' CliftLRD Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent for Irregularly Sampled Time Series ClimClass Climate Classification According to Several Indices ClimInd Climate Indices ClimMobTools API Client for the 'ClimMob' Platform ClimProjDiags Set of Tools to Compute Various Climate Indices ClimaRep Estimating Climate Analogue Areas ClinSigMeasures Clinical Significance Measures ClinTrialPredict Predicting and Simulating Clinical Trial with Time-to-Event Endpoint ClinicalTrialSummary Summary Measures for Clinical Trials with Survival Outcomes ClinicalUtilityRecal Recalibration Methods for Improved Clinical Utility of Risk Scores CliquePercolation Clique Percolation for Networks CloneSeeker Seeking and Finding Clones in Copy Number and Sequencing Data CluMP Clustering of Micro Panel Data ClueR Cluster Evaluation ClusBoot Bootstrap a Clustering Solution to Establish the Stability of the Clusters ClusPred Simultaneous Semi-Parametric Estimation of Clustering and Regression ClusROC ROC Analysis in Three-Class Classification Problems for Clustered Data ClusTCR2 Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2' ClusTorus Prediction and Clustering on the Torus by Conformal Prediction ClussCluster Simultaneous Detection of Clusters and Cluster-Specific Genes in High-Throughput Transcriptome Data ClustAssess Tools for Assessing Clustering ClustBlock Clustering of Datasets ClustGeo Hierarchical Clustering with Spatial Constraints ClustImpute K-Means Clustering with Build-in Missing Data Imputation ClustMC Cluster-Based Multiple Comparisons ClustOfVar Clustering of Variables ClustVarLV Clustering of Variables Around Latent Variables ClusterBootstrap Analyze Clustered Data using the Cluster Bootstrap ClusterR Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering ClusterRandSSAdj Small Sample Adjustment of Cluster Randomized Trial ClusterRankTest Rank Tests for Clustered Data ClusterStability Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions ClusterVAR Fitting Latent Class Vector-Autoregressive (VAR) Models ClusteredMutations Location and Visualization of Clustered Somatic Mutations Clustering Techniques for Evaluating Clustering CoClust A Copula-Based Clustering Algorithm CoDaImpact Interpreting CoDa Regression Models CoDaLoMic Compositional Models to Longitudinal Microbiome Data CoDiNA Co-Expression Differential Network Analysis CoFM Copula Factor Models CoImp Parametric and Nonparametric Copula-Based Imputation Methods CoMiRe Convex Mixture Regression CoNI Correlation Guided Network Integration (CoNI) CoRpower Power Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials CoSMoS Complete Stochastic Modelling Solution CoTiMA Continuous Time Meta-Analysis ('CoTiMA') CoalescentPhylo Phylogenetics via Root Distances Method Under the Coalescent CoastlineFD Calculation of the Fractal Dimension of a Coastline CodataGS Genomic Prediction Using SNP Codata CodeDepends Analysis of R Code for Reproducible Research and Code Comprehension CodelistGenerator Identify Relevant Clinical Codes and Evaluate Their Use CohortCharacteristics Summarise and Visualise Characteristics of Patients in the OMOP CDM CohortConstructor Build and Manipulate Study Cohorts Using a Common Data Model CohortContrast Enrichment Analysis of Clinically Relevant Concepts in Common Data Model Cohort Data CohortGenerator Cohort Generation for the OMOP Common Data Model CohortMethod Comparative Cohort Method with Large Scale Propensity and Outcome Models CohortPlat Simulation of Cohort Platform Trials for Combination Treatments CohortSurvival Estimate Survival from Common Data Model Cohorts CohortSymmetry Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model CoinMinD Simultaneous Confidence Intervals for Multinomial Proportions Coinprofile Coincident Profile ColOpenData Download Colombian Demographic, Climate and Geospatial Data CollocInfer Collocation Inference for Dynamic Systems ColombiAPI Access Colombian Data via APIs and Curated Datasets ColorNameR Give Colors a Name Colossus "Risk Model Regression and Analysis with Complex Non-Linear Models" ComBatFamQC Comprehensive Batch Effect Diagnostics and Harmonization ComICS Computational Methods for Immune Cell-Type Subsets ComRiskModel Fitting of Complementary Risk Models CombinS Construction Methods for Series of PBIB Designs via Combinatory Method S CombinePortfolio Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies CommEcol Community Ecology Analyses CommKern Network-Based Communities and Kernel Machine Methods CommonDataModel OMOP CDM DDL and Documentation Generator CommonJavaJars Useful Libraries for Building a Java Based GUI under R CommonMean.Copula Common Mean Vector under Copula Models Comp2ROC Compare Two ROC Curves that Intersect CompAREdesign Statistical Functions for the Design of Studies with Composite Endpoints CompClassMetrics Classification Measures when Subclasses are Involved CompDist Multisection Composite Distributions CompExpDes Designs for Computer Experimentations CompGR Complete Annual Growth Rate Generator CompMix A Comprehensive Toolkit for Environmental Mixtures Analysis CompModels Pseudo Computer Models for Optimization CompPareto Discrete Composite Distributions with Pareto Tails CompQuadForm Distribution Function of Quadratic Forms in Normal Variables CompR Paired Comparison Data Analysis CompareCausalNetworks Interface to Diverse Estimation Methods of Causal Networks CompareMultipleModels Finding the Best Model Using Eight Metrics Values CompareTests Correct for Verification Bias in Diagnostic Accuracy & Agreement ComparisonSurv Comparison of Survival Curves Between Two Groups Compind Composite Indicators Functions ComplexHeatmap Make Complex Heatmaps ComplexUpset Create Complex UpSet Plots Using 'ggplot2' Components CompositeReliability Determine the Composite Reliability of a Naturalistic, Unbalanced Dataset Compositional Compositional Data Analysis CompositionalClust Clustering with Compositional Data CompositionalHDDA High Dimensional Discriminant Analysis with Compositional Data CompositionalML Machine Learning with Compositional Data CompositionalNAimp Missing Value Imputation with Compositional Data CompositionalRF Multivariate Random Forest with Compositional Responses CompositionalSR Spatial Regression Models with Compositional Data CompoundDb Creating and Using (Chemical) Compound Annotation Databases CompoundEvents Statistical Modeling of Compound Events ComradesM The Comrades Marathon 1921 to 2019 ConFluxPro Soil Gas Analysis and Flux Modeling ConNEcT Contingency Measure-Based Networks for Binary Time Series ConSciR Tools for Conservation Science ConSpline Partial Linear Least-Squares Regression using Constrained Splines ConconiAnaerobicThresholdTest Conconi Estimate of Anaerobic Threshold from a TCX File ConcordanceTest An Alternative to the Kruskal-Wallis Based on the Kendall Tau Distance CondCopulas Estimation and Inference for Conditional Copula Models CondMVT Conditional Multivariate t Distribution, Expectation Maximization Algorithm, and Its Stochastic Variants CondiS Censored Data Imputation for Direct Modeling ConfMatrix Confusion Matrix ConfidenceEllipse Computation of 2D and 3D Elliptical Joint Confidence Regions ConfigParser Package to Parse an INI File, Including Variable Interpolation ConformalSmallest Efficient Tuning-Free Conformal Prediction ConfusionTableR Confusion Matrix Toolset CongressData A Functional Tool for 'CongressData' CongreveLamsdell2016 Distance Metrics for Trees Generated by Congreve and Lamsdell Conigrave Flexible Tools for Multiple Imputation ConjointChecks Implementation of a Method to Check the Cancellation Axioms of Additive Conjoint Measurement ConnMatTools Tools for Working with Connectivity Data ConnectednessApproach Connectedness Approach Connection Measures of Independence and Connection Without Linear Models ConsRank Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach ConsRankClass Classification and Clustering of Preference Rankings ConsReg Fits Regression & ARMA Models Subject to Constraints to the Coefficient ConsensusClusterPlus ConsensusClusterPlus ConsensusClustering Consensus Clustering ConsensusOPLS Consensus OPLS for Multi-Block Data Fusion ContRespPP Predictive Probability for a Continuous Response with an ANOVA Structure ContaminatedMixt Clustering and Classification with the Contaminated Normal ContourFunctions Create Contour Plots from Data or a Function ConvergenceClubs Finding Convergence Clubs ConvergenceConcepts Seeing Convergence Concepts in Action ConversationAlign Process Text and Compute Linguistic Alignment in Conversation Transcripts ConvertPar Estimating IRT Parameters via Machine Learning Algorithms Convolutioner Convolution of Data CooRTweet Coordinated Networks Detection on Social Media CooccurrenceAffinity Affinity in Co-Occurrence Data CoopGame Important Concepts of Cooperative Game Theory CoordinateCleaner Automated Cleaning of Occurrence Records from Biological Collections CopCTS Copula-Based Semiparametric Analysis for Time Series Data with Detection Limits CopernicusClimate Search Download and Handle Data from Copernicus Climate Data Service CopernicusDEM Copernicus Digital Elevation Models CopernicusDataspace Search Download and Handle Data from the Copernicus Data Space Ecosystem CopernicusMarine Search Download and Handle Data from Copernicus Marine Service Information Copula.Markov Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series Copula.Markov.survival Copula Markov Model with Dependent Censoring Copula.surv Analysis of Bivariate Survival Data Based on Copulas CopulaCenR Copula-Based Regression Models for Multivariate Censored Data CopulaGAMM Copula-Based Mixed Regression Models CopulaInference Estimation and Goodness-of-Fit of Copula-Based Models with Arbitrary Distributions CopulaREMADA Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies CopulaSCR Analysis of Semi-Competing Risks Data Using Copula-Based Models CorMID Correct Mass Isotopologue Distribution Vectors CoreMicrobiomeR Identification of Core Microbiome CorrBin Nonparametrics with Clustered Binary and Multinomial Data CorrMixed Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models CorrToolBox Modeling Correlational Magnitude Transformations in Discretization Contexts CorrectOverloadedPeaks Correct Overloaded Peaks from GC-APCI-MS Data CorrectedFDR Correcting False Discovery Rates Correlplot A Collection of Functions for Graphing Correlation Matrices CortSineScore Compute Cortisol Sine Score (CSS) for Diurnal Cortisol Analysis Counterfactual Estimation and Inference Methods for Counterfactual Analysis Counternull Randomization-Based Inference Countr Flexible Univariate Count Models Based on Renewal Processes CountsEPPM Mean and Variance Modeling of Count Data CovCorTest Statistical Tests for Covariance and Correlation Matrices and their Structures CovEsts Nonparametric Estimators for Covariance Functions CovSel Model-Free Covariate Selection CovTools Statistical Tools for Covariance Analysis CovidMutations Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019) CoxAIPW Doubly Robust Inference for Cox Marginal Structural Model with Informative Censoring CoxBcv Bias-Corrected Sandwich Variance Estimators for Marginal Cox Analysis of Cluster Randomized Trials CoxBoost Cox Models by Likelihood Based Boosting for a Single Survival Endpoint or Competing Risks CoxICPen Variable Selection for Cox's Model with Interval-Censored Data CoxLikelihood Robust Likelihood Ratio Test and Confidence Intervals for the Cox Model CoxMK A Model-X Knockoff Method for Genome-Wide Survival Association Analysis CoxPlus Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects Coxmos Cox MultiBlock Survival CpGFilter CpG Filtering Method Based on Intra-Class Correlation Coefficients CpGassoc Association Between Methylation and a Phenotype of Interest CpmERCCutoff Calculation of Log2 Counts per Million Cutoff from ERCC Controls CptNonPar Nonparametric Change Point Detection for Multivariate Time Series CreditRisk Evaluation of Credit Risk with Structural and Reduced Form Models Cronbach Cronbach's Alpha CropBreeding Stability Analysis in Crop Breeding CropScapeR Access Cropland Data Layer Data via the 'CropScape' Web Service CropWaterBalance Climate Water Balance for Irrigation Purposes CrossCarry Analysis of Data from a Crossover Design with GEE CrossClustering A Partial Clustering Algorithm CrossExpression Cross-Expression Analysis of Spatial Transcriptomics Data CrossValidate Classes and Methods for Cross Validation of "Class Prediction" Algorithms Crossover Analysis and Search of Crossover Designs Crosstabs.Loglinear Cross Tabulation and Loglinear Analyses of Categorical Data CryptRndTest Statistical Tests for Cryptographic Randomness CsChange Testing for Change in C-Statistic Cubist Rule- And Instance-Based Regression Modeling CureDepCens Dependent Censoring Regression Models with Cure Fraction CurricularAnalytics Exploring and Analyzing Academic Curricula CurricularComplexity Toolkit for Analyzing Curricular Complexity CurricularComplexityData Data for Exploring Curricular Complexity CustomDerivative Pricing Various Types of Custom Derivatives CustomerScoringMetrics Evaluation Metrics for Customer Scoring Models Depending on Binary Classifiers CustosAscensor Costs Allocation for the Installation of an Elevator CutpointsOEHR Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model CvmortalityMult Cross-Validation for Multi-Population Mortality Models Cyclops Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis CytOpT Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation CytoProfile Cytokine Profiling Analysis Tool CytoSimplex Simplex Visualization of Cell Fate Similarity in Single-Cell Data CytobankAPI Cytobank API Wrapper for R D3GB Interactive Genome Browser D3mirt Descriptive 2D and 3D Descriptive Multidimensional Item Response Theory Modeling D3partitionR Interactive Charts of Nested and Hierarchical Data with 'D3.js' D4TAlink.light GDP - Workflow Management DA Discriminant Analysis for Evolutionary Inference DAAG Data Analysis and Graphics Data and Functions DAAGbio Data Sets and Functions, for Demonstrations with Expression Arrays and Gene Sequences DACF Data Analysis with Ceiling and/or Floor Data DAGassist Test Robustness with Directed Acyclic Graphs DAIME Effects of Changing Deposition Rates DAISIE Dynamical Assembly of Islands by Speciation, Immigration and Extinction DAISIEprep Extracts Phylogenetic Island Community Data from Phylogenetic Trees DAKS Data Analysis and Knowledge Spaces DALEX moDel Agnostic Language for Exploration and eXplanation DALEXtra Extension for 'DALEX' Package DALSM Nonparametric Double Additive Location-Scale Model (DALSM) DALY The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R DAMOCLES Dynamic Assembly Model of Colonization, Local Extinction and Speciation DANDELION Discovery of Candidate Disease Genes Using Trans-Regulatory Effects DAPAR Tools for the Differential Analysis of Proteins Abundance with R DAST Spatio-Temporal Disaggregation for Maps with Changing Areal Boundaries DATAstudio The Research Data Warehouse of Miguel de Carvalho DArand Differential Analysis with Random Reference Genes DBCVindex Calculates the Density-Based Clustering Validation (DBCV) Index DBHC Sequence Clustering with Discrete-Output HMMs DBI R Database Interface DBItest Testing DBI Backends DBModelSelect Distribution-Based Model Selection DBNMFrank Rank Selection for Non-Negative Matrix Factorization DBR Discrete Beta Regression DBTC Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis DBfit A Double Bootstrap Method for Analyzing Linear Models with Autoregressive Errors DBmaps A Metadata-Driven Framework for Streamlining Database Joins DCCA Detrended Fluctuation and Detrended Cross-Correlation Analysis DCEM Clustering Big Data using Expectation Maximization Star (EM*) Algorithm DCEmgmt DCE Data Reshaping and Processing DCEtool Efficient and Accessible Discrete Choice Experiments DCG Data Cloud Geometry (DCG): Using Random Walks to Find Community Structure in Social Network Analysis DCL Claims Reserving under the Double Chain Ladder Model DCLEAR Distance Based Cell Lineage Reconstruction DCchoice Analyzing Dichotomous Choice Contingent Valuation Data DChaos Chaotic Time Series Analysis DCluster Functions for the Detection of Spatial Clusters of Diseases DClusterm Model-Based Detection of Disease Clusters DDD Diversity-Dependent Diversification DDESONN A Deep Dynamic Experimental Self-Organizing Neural Network Framework DDHFm Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays) DDIwR DDI with R DDL Doubly Debiased Lasso (DDL) DDM Death Registration Coverage Estimation DDPM Data Sets for Discrete Probability Models DDPstar Density Regression via Dirichlet Process Mixtures of Normal Structured Additive Regression Models DDRTree Learning Principal Graphs with DDRTree DEBBI Differential Evolution-Based Bayesian Inference DECIDE DEComposition of Indirect and Direct Effects DECIPHER Tools for curating, analyzing, and manipulating biological sequences DEET Differential Expression Enrichment Tool DEEVD Density Estimation by Extreme Value Distributions DEHOGT Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data DELTD Kernel Density Estimation using Lifetime Distributions DEM The Distributed EM Algorithms in Multivariate Gaussian Mixture Models DENSaftertransform Estimating Density after Logarithmic or Power Transformation of Data DEPONS2R Read, Plot and Analyse Output from the DEPONS Model DER Income Polarization Index DES Discrete Event Simulation DESA Detecting Epidemics using School Absenteeism DESNP Differentially Expressed Single Nucleotide Polymorphism DESeq2 Differential gene expression analysis based on the negative binomial distribution DET Representation of DET Curve with Confidence Intervals DEXiR 'DEXi' Library DEmixR Fit Two-Component Normal and Lognormal Mixture Models DEoptim Global Optimization by Differential Evolution DEoptimR Differential Evolution Optimization in Pure R DEploid Deconvolute Mixed Genomes with Unknown Proportions DEploid.utils 'DEploid' Data Analysis and Results Interpretation DEplotting Visualization Tools for German Regional Data DFA Detrended Fluctuation Analysis DFA.CANCOR Linear Discriminant Function and Canonical Correlation Analysis DFBA Distribution-Free Bayesian Analysis DFD Extract Drugs from Differential Expression Data from LINCS Database DFIT Differential Functioning of Items and Tests DGEAR Differential Gene Expression Analysis with R DGEobj Differential Gene Expression (DGE) Analysis Results Data Object DGEobj.utils Differential Gene Expression (DGE) Analysis Utility Toolkit DGLMExtPois Double Generalized Linear Models Extending Poisson Regression DGP4LCF Dependent Gaussian Processes for Longitudinal Correlated Factors DHARMa Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models DHBins Hexmaps for NZ District Health Boards DHS.rates Calculates Demographic Indicators DHSr Create Large Scale Repeated Regression Summary Statistics Dataset and Visualization Seamlessly DICErClust Deep Significance Clustering for Clinical Risk Stratification DICOMread Reading and Saving DICOM Image Files DIDHAD Difference-in-Differences in Heterogeneous Adoption Designs with Quasi Untreated Groups DIDmultiplegt Estimators DID with Multiple Groups and Periods DIDmultiplegtDYN Estimation in Staggered First Switch Designs, where Groups Experience their First Treatment Change at Different Points in Time DIETCOST Calculate the Cost and Environmental Impact of a Ideal Diet DIFM Dynamic ICAR Spatiotemporal Factor Models DIFboost Detection of Differential Item Functioning (DIF) in Rasch Models by Boosting Techniques DIFlasso A Penalty Approach to Differential Item Functioning in Rasch Models DIFplus Multilevel Mantel-Haenszel Statistics for Differential Item Functioning Detection DIFshiny Differential Item Functioning via Shiny Application DIFtree Item Focussed Trees for the Identification of Items in Differential Item Functioning DIGSS Determination of Intervals Using Georeferenced Survey Simulation DIME Differential Identification using Mixture Ensemble DIMORA Diffusion Models R Analysis DIRECT Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior DIRMR Distributed Imputation for Random Effects Models with Missing Responses DIVINE Curated Datasets and Tools for Epidemiological Data Analysis DIZtools Lightweight Utilities for 'DIZ' R Package Development DIZutils Utilities for 'DIZ' R Package Development DImodels Diversity-Interactions (DI) Models DImodelsMulti Fit Multivariate Diversity-Interactions Models with Repeated Measures DImodelsVis Visualising and Interpreting Statistical Models Fit to Compositional Data DIscBIO A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics DJL Distance Measure Based Judgment and Learning DLASSO Implementation of Adaptive or Non-Adaptive Differentiable Lasso and SCAD Penalties in Linear Models DLEGFM Distributed Loading Estimation for General Factor Model DLFM Distributed Laplace Factor Model DLL Decorrelated Local Linear Estimator DLMRMV Distributed Linear Regression Models with Response Missing Variables DLMtool Data-Limited Methods Toolkit DLPCA The Distributed Local PCA Algorithm DMCfun Diffusion Model of Conflict (DMC) in Reaction Time Tasks DMMF Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model DMRnet Delete or Merge Regressors Algorithms for Linear and Logistic Model Selection and High-Dimensional Data DMtest Differential Methylation Tests (DMtest) DNAcopy DNA Copy Number Data Analysis DNAmf Diffusion Non-Additive Model with Tunable Precision DNAmixturesLite Statistical Inference for Mixed Traces of DNA (Lite-Version) DNAmotif DNA Sequence Motifs DNAseqtest Generating and Testing DNA Sequences DNAtools Tools for Analysing Forensic Genetic DNA Data DNMF Discriminant Non-Negative Matrix Factorization DNNSIM Single-Index Neural Network for Skewed Heavy-Tailed Data DNetFinder Estimating Differential Networks under Semiparametric Gaussian Graphical Models DOEM The Distributed Online Expectation Maximization Algorithms to Solve Parameters of Poisson Mixture Models DOIcreator Append DOIs to References in Word Documents DOPE Drug Ontology Parsing Engine DOS Design of Observational Studies DOS2 Design of Observational Studies, Companion to the Second Edition DOSE Disease Ontology Semantic and Enrichment analysis DOSPortfolio Dynamic Optimal Shrinkage Portfolio DOVE Durability of Vaccine Efficacy DOYPAColors Don't Overthink Your Palette of Colors DOvalidation Kernel Hazard Estimation with Best One-Sided and Double One-Sided Cross-Validation DPCD Dirichlet Process Clustering with Dissimilarities DPComb Discrete p-Value Combination Tests DPI The Directed Prediction Index for Causal Direction Inference from Observational Data DPP Inference of Parameters of Normal Distributions from a Mixture of Normals DPQ Density, Probability, Quantile ('DPQ') Computations DPQBootstrap Dirichlet Quantile Bootstrap for Time Series DPQmpfr DPQ (Density, Probability, Quantile) Distribution Computations using MPFR DPTM Dynamic Panel Multiple Threshold Model with Fixed Effects DPpack Differentially Private Statistical Analysis and Machine Learning DQA Data Quality Assessment Tools DQAgui Graphical User Interface for Data Quality Assessment DQAstats Core Functions for Data Quality Assessment DR.SC Joint Dimension Reduction and Spatial Clustering DRDID Doubly Robust Difference-in-Differences Estimators DREGAR Regularized Estimation of Dynamic Linear Regression in the Presence of Autocorrelated Residuals (DREGAR) DRHotNet Differential Risk Hotspots in a Linear Network DRIP Discontinuous Regression and Image Processing DRPT Density Ratio Permutation Test DRR Dimensionality Reduction via Regression DRaWR Discriminative Random Walk with Restart DRclass Consider Ambiguity in Probabilistic Descriptions Using Density Ratio Classes DRomics Dose Response for Omics DRquality Quality Measurements for Dimensionality Reduction DRsurvCRT Doubly-Robust Estimation for Survival Outcomes in Cluster-Randomized Trials DRviaSPCN Drug Repurposing in Cancer via a Subpathway Crosstalk Network DSAIDE Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution) DSAIRM Dynamical Systems Approach to Immune Response Modeling DSAM Data Splitting Algorithms for Model Developments DSBayes Bayesian Subgroup Analysis in Clinical Trials DSDRM Distributed Sampling for Dynamic Regression Models DSFM Distributed Skew Factor Model Estimation Methods DSGEr Transcriptional Disruption Score for Gene Sets DSI 'DataSHIELD' Interface DSIR Data Science Infrastructure for Global Health DSL Distributed Storage and List DSLite 'DataSHIELD' Implementation on Local Datasets DSMolgenisArmadillo 'DataSHIELD' Client for 'MOLGENIS Armadillo' DSOpal 'DataSHIELD' Implementation for 'Opal' DSSAT A Comprehensive R Interface for the DSSAT Cropping Systems Model DSWE Data Science for Wind Energy DSjobtracker What Skills and Qualifications are Required for Data Science Related Jobs? DSpoty Get 'Spotify' API Multiple Information DT A Wrapper of the JavaScript Library 'DataTables' DT2 'DataTables' 2.x for R DTAT Dose Titration Algorithm Tuning DTAXG Diagnostic Test Assessment in the Absence of Gold Standard DTAplots Creates Plots Accompanying Bayesian Diagnostic Test Accuracy Meta-Analyses DTComPair Comparison of Binary Diagnostic Tests in a Paired Study Design DTDA Doubly Truncated Data Analysis DTDA.cif Doubly Truncated Data Analysis, Cumulative Incidence Functions DTDA.ni Doubly Truncated Data Analysis, Non Iterative DTEAssurance Assurance Methods for Clinical Trials with a Delayed Treatment Effect DTEBOP2 Bayesian Optimal Phase II Randomized Clinical Trial Design with Delayed Outcomes DTFM Distributed Online Covariance Matrix Tests for Truncated Factor Model DTMCPack Suite of Functions Related to Discrete-Time Discrete-State Markov Chains DTRKernSmooth Estimate and Make Inference About Optimal Treatment Regimes via Smoothed Methods DTRlearn2 Statistical Learning Methods for Optimizing Dynamic Treatment Regimes DTRreg DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv) DTS Discrete Tempered Stable Distributions DTSEA Drug Target Set Enrichment Analysis DTSR Distributed Trimmed Scores Regression for Handling Missing Data DTSg A Class for Working with Time Series Data Based on 'data.table' and 'R6' with Largely Optional Reference Semantics DTWBI Imputation of Time Series Based on Dynamic Time Warping DTWUMI Imputation of Multivariate Time Series Based on Dynamic Time Warping DTwrappers Simplified Data Analysis with Wrapper Functions for the 'Data.Table' Package DTwrappers2 Extensions of 'DTwrappers' DUToolkit Visualizing and Quantifying Decision Uncertainty DVHmetrics Analyze Dose-Volume Histograms and Check Constraints DWDLargeR Fast Algorithms for Large Scale Generalized Distance Weighted Discrimination DWLS Gene Expression Deconvolution Using Dampened Weighted Least Squares DWaveNARDL Dual Wavelet Based NARDL Model DWreg Parametric Regression for Discrete Response DYM Did You Mean? DamageDetective Detecting Damaged Cells in Single-Cell RNA Sequencing Data DamiaNN Neural Network Numerai DandEFA Dandelion Plot for R-Mode Exploratory Factor Analysis DanielBiostatistics10th Functions for Wayne W. Daniel's Biostatistics, Tenth Edition Dark The Analysis of Dark Adaptation Data DarkDiv Estimating Dark Diversity and Site-Specific Species Pools DasGuptR Das Gupta Standardisation and Decomposition Dasst Tools for Reading, Processing and Writing 'DSSAT' Files DataClean Data Cleaning DataCraftR Create Datasets Interactively Using 'shiny' DataDNA Data Frame Fingerprints and Lineage Figures DataEditR An Interactive Editor for Viewing, Entering, Filtering & Editing Data DataExplorer Automate Data Exploration and Treatment DataFusionGDM Machine Learning for Integrating Partially Overlapped Genetic Datasets DataGraph Export Data from 'R' to 'DataGraph' DataLoader Import Multiple File Types DataMetProcess Meteorological Data Processing DataPackageR Construct Reproducible Analytic Data Sets as R Packages DataQualityDashboard Execute and View Data Quality Checks on OMOP CDM Database DataSetsUni A Collection of Univariate Data Sets DataSetsVerse A Metapackage for Thematic and Domain-Specific Datasets DataSimilarity Quantifying Similarity of Datasets and Multivariate Two- And k-Sample Testing DataSpaceR Interface to 'the CAVD DataSpace' DataSum Modern Data Summaries and Diagnostic Reports for Statistical Analysis DataVisualizations Visualizations of High-Dimensional Data DataViz Data Visualisation Using an HTML Page and 'D3.js' DatabaseConnector Connecting to Various Database Platforms DatabaseConnectorJars JAR Dependencies for the 'DatabaseConnector' Package DatabionicSwarm Swarm Intelligence for Self-Organized Clustering DatastreamDSWS2R Provides a Link Between the 'LSEG Datastream' System and R DatastreamR Datastream API DateTimeRangePicker A Datetime Range Picker Widget for Usage in 'Shiny' Applications Davies The Davies Quantile Function Dcurvature Discrete Curvature with 'shiny' Explorer DeBoinR Box-Plots and Outlier Detection for Probability Density Functions DeCAFS Detecting Changes in Autocorrelated and Fluctuating Signals DeRezende.Ferreira Zero Coupon Yield Curve Modelling DeSciDe Tool for Unbiased Literature Searching and Gene List Curation DebiasInfer Efficient Inference on High-Dimensional Linear Model with Missing Outcomes DecisionDrift Detecting, Decomposing, and Stress-Testing Temporal Change in Repeated Decision Systems DeclareDesign Declare and Diagnose Research Designs DecomposeR Empirical Mode Decomposition for Cyclostratigraphy DecorateR Fit and Deploy DECORATE Trees DedooseR Monitoring and Analyzing Dedoose Qualitative Data Exports Deducer A Data Analysis GUI for R DeductiveR Deductive Rational Method DeepLearningCausal Causal Inference with Super Learner and Deep Neural Networks DegreeDayCalc Degree-Day Phenology Calculator ('shiny' Application) Delaporte Statistical Functions for the Delaporte Distribution DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets DelayedEffect.Design Sample Size and Power Calculations using the APPLE, SEPPLE, APPLE+ and SEPPLE+ Methods DelayedMatrixStats Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects Delta Measure of Agreement Between Two Raters DeltaMAN Delta Measurement of Agreement for Nominal Data DemoDecomp Decompose Demographic Functions DemographicTable Create Demographic Table DendSer Dendrogram Seriation: Ordering for Visualisation DendroSync A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies DensParcorr Dens-Based Method for Partial Correlation Estimation in Large Scale Brain Networks DepCens Dependent Censoring Regression Models DepLogo Dependency Logo DepMod Decision-Analytic Modelling for Depression Prevention and Treatment DepthProc Statistical Depth Functions for Multivariate Analysis Deriv Symbolic Differentiation DescTools Tools for Descriptive Statistics DescToolsAddIns Interactive Functions to be Used as Shortcuts in 'RStudio' DescribeDF Description of a Data Frame DescribeDisplay An Interface to the 'DescribeDisplay' 'GGobi' Plugin DescriptiveRepresentationCalculator Characterizing Observed and Expected Representation DescriptiveStats.OBeu Descriptive Statistics 'OpenBudgets.eu' DescriptiveWH Descriptive Statistics Design.parameters Parameters of the Experimental Designs DesignLibrary Library of Research Designs Desimml Distributed Estimation in Single-Index Models with Multiple Links ('Desimml') DetLifeInsurance Life Insurance Premium and Reserves Valuation DetMCD Implementation of the DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter) DevTreatRules Develop Treatment Rules with Observational Data Devore7 Data sets from Devore's "Prob and Stat for Eng (7th ed)" Dforest Decision Forest DiDforBigData A Big Data Implementation of Difference-in-Differences Estimation with Staggered Treatment DiNAMIC.Duo Finding Recurrent DNA Copy Number Alterations and Differences DiPALM Differential Pattern Analysis via Linear Modeling DiPhiSeq Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data DiPs Directional Penalties for Optimal Matching in Observational Studies DiSCos Distributional Synthetic Controls Estimation DiSSMod Fitting Sample Selection Models for Discrete Response Variables DiagrammeR Graph/Network Visualization DiagrammeRsvg Export DiagrammeR Graphviz Graphs as SVG DiallelAnalysisR Diallel Analysis with R DiceDesign Designs of Computer Experiments DiceEval Construction and Evaluation of Metamodels DiceKriging Kriging Methods for Computer Experiments DiceOptim Kriging-Based Optimization for Computer Experiments DiceView Methods for Visualization of Computer Experiments Design and Surrogate Dict R6 Based Key-Value Dictionary Implementation DidacticBoost A Simple Implementation and Demonstration of Gradient Boosting DiffCorr Analyzing and Visualizing Differential Correlation Networks in Biological Data DiffNet Identifying Significant Node Scores using Network Diffusion Algorithm DiffXTables Pattern Analysis Across Contingency Tables DigestiveDataSets A Curated Collection of Digestive System and Gastrointestinal Disease Datasets Dimodal Spacing Tests for Multi-Modality DirStats Nonparametric Methods for Directional Data Dire Linear Regressions with a Latent Outcome Variable DirectEffects Estimating Controlled Direct Effects for Explaining Causal Findings DirectStandardisation Adjusted Means and Proportions by Direct Standardisation DirectedClustering Directed Weighted Clustering Coefficient Directional A Collection of Functions for Directional Data Analysis DirichletMultinomial Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data DirichletRF "Dirichlet Random Forest" DirichletReg Dirichlet Regression DisImpact Calculates Disproportionate Impact When Binary Success Data are Disaggregated by Subgroups DisaggregateTS High-Dimensional Temporal Disaggregation DisasterAlert Disaster Alert and Sentiment Analysis DiscreteDLM Bayesian Distributed Lag Model Fitting for Binary and Count Response Data DiscreteDatasets Example Data Sets for Use with Discrete Statistical Tests DiscreteDists Discrete Statistical Distributions DiscreteFDR FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteFWER FWER-Based Multiple Testing Procedures with Adaptation for Discrete Tests DiscreteInverseWeibull Discrete Inverse Weibull Distribution DiscreteLaplace Discrete Laplace Distributions DiscreteQvalue Improved q-Values for Discrete Uniform and Homogeneous Tests DiscreteTests Vectorised Computation of P-Values and Their Supports for Several Discrete Statistical Tests DiscreteWeibull Discrete Weibull Distributions (Type 1 and 3) DisimForMixed Calculate Dissimilarity Matrix for Dataset with Mixed Attributes DistPlotter A Graphical User Interface for Plotting Common Univariate Distributions Distance Distance Sampling Detection Function and Abundance Estimation DistatisR DiSTATIS Three Way Metric Multidimensional Scaling Distributacalcul Probability Distribution Functions DistributionIV Distributional Instrumental Variable (DIV) Model DistributionOptimization Distribution Optimization DistributionTest Powerful Goodness-of-Fit Tests Based on the Likelihood Ratio DistributionUtils Distribution Utilities Ditwah Ditwah Storm Data and Tools for Storm Monitoring and Early Warning November 2025, Sri Lanka DivE Diversity Estimator DiversificationR Econometric Tools to Measure Portfolio Diversification DiversityStats Diversity Indices with Statistical Inference DoE.MIParray Creation of Arrays by Mixed Integer Programming DoE.base Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages DoE.wrapper Wrapper Package for Design of Experiments Functionality DockerParallel Using the Docker Container to Create R Workers on Local or Cloud Platform Docovt Distributed Online Covariance Matrix Tests Dogoftest Distributed Online Goodness-of-Fit Tests for Distributed Datasets Domean Distributed Online Mean Tests DominoDataR 'Domino Data R SDK' DonutMap Donut Maps with 'sf', 'ggplot2', and 'leaflet' DoseFinding Planning and Analyzing Dose Finding Experiments DoubleCone Test Against Parametric Regression Function DoubleExpSeq Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter DoubleML Double Machine Learning in R Dowd Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's Book Measuring Market Risk DownBallotR Access Federal, State, and Local Election Data Dpit Distribution Pitting DrBats Data Representation: Bayesian Approach That's Sparse DrData Interactive Statistical Analysis and Machine Learning Platform DrImpute Imputing Dropout Events in Single-Cell RNA-Sequencing Data DrillR R Driver for Apache Drill DrivePlotR Linked Plot Maps for Multivariate High-Resolution Spatio-Temporal Data DropletUtils Utilities for Handling Single-Cell Droplet Data DrugExposureDiagnostics Diagnostics for OMOP Common Data Model Drug Records DrugSim2DR Predict Drug Functional Similarity to Drug Repurposing DrugUtilisation Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model DstarM Analyze Two Choice Reaction Time Data with the D*M Method Dtableone Tabular Comparison of Paired Diagnostic Tests Durga Effect Size Estimation and Visualisation DyMEP Dynamic Multi Environment Phenology-Model DySS Dynamic Screening Systems DyadRatios Dyad Ratios Algorithm for Latent Variable Estimation DyadiCarma Dyadic Matrices and their Algebra using 'Rcpp' and 'RcppArmadillo' Dykstra Quadratic Programming using Cyclic Projections DynClust Denoising and Clustering for Dynamical Image Sequence (2D or 3D)+t DynCount Bayesian Dynamic Models for Poisson and Binomial Time Series DynDoc Dynamic document tools DynForest Random Forest with Multivariate Longitudinal Predictors DynNom Visualising Statistical Models using Dynamic Nomograms DynTxRegime Methods for Estimating Optimal Dynamic Treatment Regimes DynareR Bringing the Power of 'Dynare' to 'R', 'R Markdown', and 'Quarto' DysPIA Dysregulated Pathway Identification Analysis DysPIAData Background and Pathway Data Used in 'DysPIA' E2E Ensemble Learning Framework for Diagnostic and Prognostic Modeling EATME Exponentially Weighted Moving Average with Adjustments to Measurement Error EAVA Deterministic Verbal Autopsy Coding with Expert Algorithm Verbal Autopsy EBASE Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism EBCHS An Empirical Bayes Method for Chi-Squared Data EBEN Empirical Bayesian Elastic Net EBImage Image processing and analysis toolbox for R EBMAforecast Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs Sampling or EM-Algorithms EBcoBART Co-Data Learning for Bayesian Additive Regression Trees EBrank Empirical Bayes Ranking ECDFniche Empirical Cumulative Distribution Function Niche Modeling Tools ECG Center of Gravity Methods ECGofTestDx A Goodness-of-Fit Test for Elliptical Distributions with Diagnostic Capabilities ECMLE Approximating Evidence via Bounded Harmonic Means ECOSolveR Embedded Conic Solver in R ECOTOXr Download and Extract Data from US EPA's ECOTOX Database ECTSVR Cointegration Based Support Vector Regression Model ECTTDNN Cointegration Based Timedelay Neural Network Model ECharts2Shiny Embedding Interactive Charts Generated with ECharts Library into Shiny Applications ECoL Complexity Measures for Supervised Problems EDCimport Import Data from EDC Software EDISON Network Reconstruction and Changepoint Detection EDIutils An API Client for the Environmental Data Initiative Repository EDNE.EQ Implements the EDNE-Test for Equivalence EDOIF Empirical Distribution Ordering Inference Framework (EDOIF) EDOtrans Euclidean Distance-Optimized Data Transformation EE.Data Objects for Predicting Energy Expenditure EEAaq Handle Air Quality Data from the European Environment Agency Data Portal EEEA Explicit Exploration Strategy for Evolutionary Algorithms EEM Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data EEMDSVR Ensemble Empirical Mode Decomposition and Its Variant Based Support Vector Regression Model EEMDelm Ensemble Empirical Mode Decomposition and Its Variant Based ELM Model EEMDlstm EEMD Based LSTM Model for Time Series Forecasting EEML Ensemble Explainable Machine Learning Models EFA.MRFA Dimensionality Assessment Using Minimum Rank Factor Analysis EFA.dimensions Exploratory Factor Analysis Functions for Assessing Dimensionality EFAfactors Determining the Number of Factors in Exploratory Factor Analysis EFAtools Fast and Flexible Implementations of Exploratory Factor Analysis Tools EFAutilities Utility Functions for Exploratory Factor Analysis EFDR Wavelet-Based Enhanced FDR for Detecting Signals from Complete or Incomplete Spatially Aggregated Data EFM Elliptical Factor Models EFSATools EFSA Ensemble of Data Collections Tools EGAnet Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics EGM Intracardiac Electrograms EGRET Exploration and Graphics for RivEr Trends EGRETci Exploration and Graphics for RivEr Trends Confidence Intervals EGRNi Ensemble Gene Regulatory Network Inference EHR Electronic Health Record (EHR) Data Processing and Analysis Tool EHRmuse Multi-Cohort Selection Bias Correction using IPW and AIPW Methods EHRtemporalVariability Delineating Temporal Dataset Shifts in Electronic Health Records EIAapi Query Data from the 'EIA' API EIEntropy Ecological Inference Applying Entropy EIX Explain Interactions in 'XGBoost' EKMCMC MCMC Procedures for Estimating Enzyme Kinetics Constants EL Two-Sample Empirical Likelihood EL2Surv Empirical Likelihood (EL) for Comparing Two Survival Functions ELAplus Energy Landscape Analysis for Ecological Communities ELIC LIC for Distributed Elliptical Model ELISAtools ELISA Data Analysis with Batch Correction ELT Experience Life Tables ELYP Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model ELmethodVar Empirical Likelihood Inference of Variance Components in Linear Mixed-Effects Models EMAR Empirical Model Assessment EMAS Epigenome-Wide Mediation Analysis Study EMAtools Data Management Tools for Real-Time Monitoring/Ecological Momentary Assessment Data EMC2 Bayesian Hierarchical Analysis of Cognitive Models of Choice EMCluster EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution EMD Empirical Mode Decomposition and Hilbert Spectral Analysis EMDANNhybrid Empirical Mode Decomposition Based Artificial Neural Network Model EMDSVRhybrid Empirical Mode Decomposition Based Support Vector Regression Model EMGCR Fit a Mixture Cure Rate Model with Custom Link Function EMJMCMC Evolutionary Mode Jumping Markov Chain Monte Carlo Expert Toolbox EML Read and Write Ecological Metadata Language Files EMLI Computationally Efficient Maximum Likelihood Identification of Linear Dynamical Systems EMMAgeo End-Member Modelling of Grain-Size Data EMMIXSSL Semi-Supervised Gaussian Mixture Model with a Missing-Data Mechanism EMMIXgene A Mixture Model-Based Approach to the Clustering of Microarray Expression Data EMMIXmfa Mixture Models with Component-Wise Factor Analyzers EMMLi A Maximum Likelihood Approach to the Analysis of Modularity EMMREML Fitting Mixed Models with Known Covariance Structures EMOTIONS Ensemble Models for Lactation Curves EMP Expected Maximum Profit Classification Performance Measure EMSC Extended Multiplicative Signal Correction EMSNM EM Algorithm for Sigmoid Normal Model EMSS Some EM-Type Estimation Methods for the Heckman Selection Model EMSaov The Analysis of Variance with EMS EMT Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data EMbC Expectation-Maximization Binary Clustering EMgaussian Expectation-Maximization Algorithm for Multivariate Normal (Gaussian) with Missing Data EMpeaksR Conducting the Peak Fitting Based on the EM Algorithm ENMTools Analysis of Niche Evolution using Niche and Distribution Models ENMeval Automated Tuning and Evaluations of Ecological Niche Models EPLSIM Partial Linear Single Index Models for Environmental Mixture Analysis EPT Ensemble Patch Transform, Visualization and Decomposition EPX Ensemble of Phalanxes EQL Extended-Quasi-Likelihood-Function (EQL) EQRN Extreme Quantile Regression Neural Networks for Risk Forecasting EQUALCompareImages Comparison of Images for Researchers Without Coding Skills EQUALPrognosis Analysing Prognostic Studies EQUALSTATS Algorithm Driven Statistical Analysis for Researchers without Coding Skills EQUALencrypt Encryption and Decryption of Files and Data for Researchers Without Coding Skills EQUALrepeat Algorithm Driven Time Series Analysis for Researchers without Coding Skills EQUIVNONINF Testing for Equivalence and Noninferiority ER Effect + Residual Modelling ERDbuilder Entity Relationship Diagrams Builder ERP Significance Analysis of Event-Related Potentials Data ERPM Exponential Random Partition Models ERPeq Probabilistic Hazard Assessment ERSA Exploratory Regression 'Shiny' App ES Edge Selection ESG A Package for Asset Projection ETAS Modeling Earthquake Data Using 'ETAS' Model ETASbootstrap Bootstrap Confidence Interval Estimation for 'ETAS' Model Parameters ETC Equivalence to Control ETDQualitizer Automated Eye Tracking Data Quality Determination for Screen-Based Eye Trackers ETLUtils Utility Functions to Execute Standard Extract/Transform/Load Operations (using Package 'ff') on Large Data ETRep Analysis of Elliptical Tubes Under the Relative Curvature Condition EUfootball Football Match Data of European Leagues EVI Epidemic Volatility Index as an Early-Warning Tool EValue Sensitivity Analyses for Unmeasured Confounding and Other Biases in Observational Studies and Meta-Analyses EVchargcost Computes and Plot the Optimal Charging Strategy for Electric Vehicles EWGoF Goodness-of-Fit Tests for the Exponential and Two-Parameter Weibull Distributions EWOC.Comb Escalation with Overdose Control using 2 Drug Combinations EWS Early Warning System EWSmethods Forecasting Tipping Points at the Community Level EXPAR Fitting of Exponential Autoregressive (EXPAR) Model EXPARMA Fitting of Exponential Autoregressive Moving Average (EXPARMA) Model EXRQ Extreme Regression of Quantiles EZFragility Compute Neural Fragility for Ictal iEEG Time Series EZbakR Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data EZtune Tunes AdaBoost, Elastic Net, Support Vector Machines, and Gradient Boosting Machines Eagle Multiple Locus Association Mapping on a Genome-Wide Scale Ease Simulating Explicit Population Genetics Models EasyABC Efficient Approximate Bayesian Computation Sampling Schemes EasyDescribe A Convenient Way of Descriptive Statistics EasyMx Easy Model-Builder Functions for 'OpenMx' EasyStat Automated Statistical Analysis, Visualization and Multi-Format Narrative Reporting EbayesThresh Empirical Bayes Thresholding and Related Methods Ecdat Data Sets for Econometrics Ecfun Functions for 'Ecdat' EcoCleanR Enhancing Data Quality of Biogeographic Ranges with Application for Marine Invertebrates EcoDiet Estimating a Diet Matrix from Biotracer and Stomach Content Data EcoEnsemble A General Framework for Combining Ecosystem Models EcoMetrics Econometrics Model Building EcoNetGen Simulate and Sample from Ecological Interaction Networks EcoNiche Community Niche Position and Width Estimation Tools EcoTroph An Implementation of the EcoTroph Ecosystem Modelling Approach Ecohydmod Ecohydrological Modelling EconAndProdEfficiency Economic and Production Efficiency EconCausal Causal Analysis for Macroeconomic Time Series (ECM-MARS, BSTS, Bayesian GLM-AR(1)) EconGeo Computing Key Indicators of the Spatial Distribution of Economic Activities EcotoneFinder Characterising and Locating Ecotones and Communities Ecume Equality of 2 (or k) Continuous Univariate and Multivariate Distributions EdSurvey Analysis of NCES Education Survey and Assessment Data EffectLiteR Average and Conditional Effects EffectStars Visualization of Categorical Response Models EffectStars2 Effect Stars EffectTreat Prediction of Therapeutic Success EfficientMaxEigenpair Efficient Initials for Computing the Maximal Eigenpair EgoCor Simple Presentation of Estimated Exponential Semi-Variograms EleChemr Electrochemical Reactions Simulation ElectDecomp Decomposition of Seats-to-Votes Distortions ElicitationWizard LLM-Based Bayesian Prior Elicitation Wizard Elja Linear, Logistic and Generalized Linear Models Regressions for the EnvWAS/EWAS Approach ElliptCopulas Inference of Elliptical Distributions and Copulas EloChoice Preference Rating for Visual Stimuli Based on Elo Ratings EloOptimized Optimized Elo Rating Method for Obtaining Dominance Ranks EloRating Animal Dominance Hierarchies by Elo Rating EmbedSOM Fast Embedding Guided by Self-Organizing Map EmiR Evolutionary Minimizer for R EmissV Tools for Create Emissions for Air Quality Models EmpiricalBrownsMethod Uses Brown's method to combine p-values from dependent tests EmpiricalCalibration Routines for Performing Empirical Calibration of Observational Study Estimates EmpiricalDynamics Empirical Discovery of Differential Equations from Time Series Data EnTraineR Enhanced Teaching Assistant (AI) for Statistical Analysis EncompassTest Direct Multi-Step Forecast Based Comparison of Nested Models via an Encompassing Test EnergyOnlineCPM Distribution Free Multivariate Control Chart Based on Energy Test EngrEcon Engineering Economics Analysis for Engineering Projects Cost Analysis EngrExpt Data sets from "Introductory Statistics for Engineering Experimentation" EnhancedVolcano Publication-ready volcano plots with enhanced colouring and labeling EnrichIntersect Enrichment Analysis and Intersecting Sankey Diagram EnsCat Clustering of Categorical Data EntropicStatistics Functions Based on Entropic Statistics EntropyEstimation Estimation of Entropy and Related Quantities EnvCpt Detection of Structural Changes in Climate and Environment Time Series EnvNJ Whole Genome Phylogenies Using Sequence Environments EnvNicheR Niche Estimation EnvStats Package for Environmental Statistics, Including US EPA Guidance EnviroPRA2 Environmental Probabilistic Risk Assessment Tools Epi Statistical Analysis in Epidemiology EpiContactTrace Epidemiological Tool for Contact Tracing EpiCurve Plot an Epidemic Curve EpiDISH Epigenetic Dissection of Intra-Sample-Heterogeneity EpiDynamics Dynamic Models in Epidemiology EpiEstim Estimate Time Varying Reproduction Numbers from Epidemic Curves EpiForsk Code Sharing at the Department of Epidemiology Research at Statens Serum Institut EpiILM Spatial and Network Based Individual Level Models for Epidemics EpiInvert Variational Techniques in Epidemiology EpiLPS A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters EpiModel Mathematical Modeling of Infectious Disease Dynamics EpiNova Flexible Extended State-Space Epidemiological Models with Modern Inference EpiPvr Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays EpiReport Epidemiological Report EpiScopeK Comprehensive Epidemiological Analysis Toolkit EpiSemble Ensemble Based Machine Learning Approach for Predicting Methylation States EpiSignalDetection Signal Detection Analysis EpiSimR A 'Shiny' App to Simulate the Dynamics of Epidemic and Endemic Diseases Spread EpiStandard Directly Standardise Rates by Age EpiStats Tools for Epidemiologists EpiTest Test for Gene x Gene Interactions in Bi-Parental Populations EpidigiR Digital Epidemiological Analysis and Visualization Tools EpistemicGameTheory Constructing an Epistemic Model for the Games with Two Players Epoch IEEG (Intracranial Electroencephalography) Epoch Data Tools Equalden.HD Testing the Equality of a High Dimensional Set of Densities EquiSurv Modeling, Confidence Intervals and Equivalence of Survival Curves EquiTrends Equivalence Testing for Pre-Trends in Difference-in-Differences Designs EraBrewer Color Palettes from the Album Covers of Each Taylor Swift Era ErlangC Solve Erlang-C Model ErrorTracer Bayesian Error Propagation and Forecast Uncertainty Decomposition EstCRM Calibrating Parameters for the Samejima's Continuous IRT Model EstHTSeed Hydro Time Analysis of Seed Germination EstemPMM Polynomial Maximization Method for Non-Gaussian Regression EstimDiagnostics Diagnostic Tools and Unit Tests for Statistical Estimators EstimateBreed Estimation of Environmental Variables and Genetic Parameters EstimateGroupNetwork Perform the Joint Graphical Lasso and Selects Tuning Parameters EstimationTools Maximum Likelihood Estimation for Probability Functions from Data Sets EthSEQ Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data EuclideanSD An Euclidean View of Center and Spread Euclimatch Euclidean Climatch Algorithm Eunomia Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets EvCombR Evidence Combination in R Evacluster Evaluation Clustering Methods for Disease Subtypes Diagnosis EvalTest Tools for Evaluating Diagnostic Test Performance EvaluateCore Quality Evaluation of Core Collections EvaluationMeasures Collection of Model Evaluation Measure Functions Evapotranspiration Modelling Actual, Potential and Reference Crop Evapotranspiration EventPredInCure Event Prediction Including Cured Population EventWinRatios Event-Specific Win Ratios for Terminal and Non-Terminal Events EvidenceSynthesis Synthesizing Causal Evidence in a Distributed Research Network EviewsR A Seamless Integration of 'EViews' and R EvoPhylo Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics EvolutionaryGames Important Concepts of Evolutionary Game Theory Evomorph Evolutionary Morphometric Simulation EwR Econometrics with R ExGaussEstim Quantile Maximization Likelihood Estimation and Bayesian Ex-Gaussian Estimation ExNRuleEnsemble A k Nearest Neibour Ensemble Based on Extended Neighbourhood Rule ExPanDaR Explore Your Data Interactively ExPosition Exploratory Analysis with the Singular Value Decomposition Exact Unconditional Exact Test ExactCIdiff Inductive Confidence Intervals for the Difference Between Two Proportions ExactCIone Admissible Exact Intervals for One-Dimensional Discrete Distributions ExactCox Exact Test and Exact Confidence Interval for the Cox Model ExactMed Exact Mediation Analysis for Binary Outcomes ExactMultinom Multinomial Goodness-of-Fit Tests ExactVaRTest Exact Finite-Sample Value-at-Risk Back-Testing ExamPAData Data Sets for Predictive Analytics Exam ExceedanceTools Confidence/Credible Regions for Exceedance Sets and Contour Lines ExcelFunctionsR Imports Excel Functions to R ExcessMass Excess Mass Calculation and Plots ExclusionTable Creating Tables of Excluded Observations ExhaustiveSearch A Fast and Scalable Exhaustive Feature Selection Framework ExpAnalysis3d Pacote Para Analise De Experimentos Com Graficos De Superficie Resposta ExpBites Analyzing Human Exposure to Mosquito Biting ExpDE Modular Differential Evolution for Experimenting with Operators ExpDes Experimental Designs Package ExpGenetic Non-Additive Expression Analysis of Hybrid Offspring ExpRep Experiment Repetitions ExperimentHub Client to access ExperimentHub resources ExpertChoice Design of Discrete Choice and Conjoint Analysis ExplodeLayout Calculate Exploded Coordinates Based on Original Node Coordinates and Node Clustering Membership ExploreTheData A Set of Tools for Exploratory Data Analysis ExposR Models Topographic Exposure to Hurricane Winds ExpressionCellNet Network-Based Analysis of Gene Expression Perturbations ExtDist Extending the Range of Functions for Probability Distributions ExtMallows An Extended Mallows Model and Its Hierarchical Version for Ranked Data Aggregation ExtendedABSurvTDC Survival Analysis using Indicators under Time Dependent Covariates ExtendedLaplace The Extended Laplace Distribution ExtrPatt Spatial Dependencies and Indices for Extremes ExtractTrainData Extract Values from Raster ExtremalDep Extremal Dependence Models ExtremeBounds Extreme Bounds Analysis (EBA) ExtremeCI Realistic Confidence Intervals for Non-Stationary Extreme Value Statistics ExtremeConformal Extreme Conformal Prediction Intervals ExtremeRisks Extreme Risk Measures EzGP Easy-to-Interpret Gaussian Process Models for Computer Experiments FABInference FAB p-Values and Confidence Intervals FACTMLE Maximum Likelihood Factor Analysis FADA Variable Selection for Supervised Classification in High Dimension FADPclust Functional Data Clustering Using Adaptive Density Peak Detection FAIRmaterials Ontology Tools with Data FAIRification in Development FAMetA Fatty Acid Metabolic Analysis FAMoS A Flexible Algorithm for Model Selection FAO56 Evapotranspiration Based on FAO Penman-Monteith Equation FAOSTAT Download Data from the FAOSTAT Database FAPA Factor Analytic Profile Analysis of Ipsatized Data FARDEEP Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte from Expression Profiles using Least Trimmed Squares FARS Factor-Augmented Regression Scenarios FAS Factor-Augmented Sparse Regression Tuning-Free Testing FAST.R Analyze and Visualize FAST-Generated Data FAVA Quantify Compositional Variability Across Relative Abundance Vectors FAVAR Bayesian Analysis of a FAVAR Model FAdist Distributions that are Sometimes Used in Hydrology FAfA Factor Analysis for All FAmle Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions FAwR Functions and Datasets for "Forest Analytics with R" FBFsearch Algorithm for Searching the Space of Gaussian Directed Acyclic Graph Models Through Moment Fractional Bayes Factors FBMS Flexible Bayesian Model Selection and Model Averaging FBN FISH Based Normalization and Copy Number Inference of SNP Microarray Data FCO Flexible Cutoffs for Model Fit Evaluation in Covariance-Based Structural Models FCPS Fundamental Clustering Problems Suite FCUSUM Fourier CUSUM Cointegration Test FCVAR Estimation and Inference for the Fractionally Cointegrated VAR FD Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology FDOTT Optimal Transport Based Testing in Factorial Design FDRestimation Estimate, Plot, and Summarize False Discovery Rates FDRsamplesize2 Computing Power and Sample Size for the False Discovery Rate in Multiple Applications FDRsampsize Compute Sample Size that Meets Requirements for Average Power and FDR FDX False Discovery Exceedance Controlling Multiple Testing Procedures FDboost Boosting Functional Regression Models FEA Finite Element Modeling for R FENmlm Fixed Effects Nonlinear Maximum Likelihood Models FER Financial Engineering in R FESta Fishing Effort Standardisation FEprovideR Fixed Effects Logistic Model with High-Dimensional Parameters FFD Freedom from Disease FFTrees Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees FFdownload Download Data from Kenneth French's Website FGLMtrunc Truncated Functional Generalized Linear Models FGRepo Functional Genomics Repository for POST-GWAS Analysis FGalgorithm Flury and Gautschi algorithms FHDI Fractional Hot Deck and Fully Efficient Fractional Imputation FHtest Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class FI Provide Functions for Forest Inventory Calculations FIESTA Forest Inventory Estimation and Analysis FIESTAutils Utility Functions for Forest Inventory Estimation and Analysis FILEST Fine-Level Structure Simulator FIND Objective Comparison of Phase I Dose-Finding Designs FIRM Flexible Integration of Single-Cell RNA-Seq Data FITSio FITS (Flexible Image Transport System) Utilities FKF Fast Kalman Filter FKSUM Fast Kernel Sums FKmL Fréchet Distance-Based K-Means and Extensions for Longitudinal Data FLAG Flexible and Accurate Gaussian Graphical Models FLAME Interpretable Matching for Causal Inference FLASHMM Fast and Scalable Single Cell Differential Expression Analysis using Mixed-Effects Models FLOPART Functional Labeled Optimal Partitioning FLORAL Fit Log-Ratio Lasso Regression for Compositional Data FLR Fuzzy Logic Rule Classifier FLSSS Mining Rigs for Problems in the Subset Sum Family FLightR Reconstruct Animal Paths from Solar Geolocation Loggers Data FMAT The Fill-Mask Association Test FMAdist Frequentist Model Averaging Distribution FMC Factorial Experiments with Minimum Level Changes FMCensSkewReg Finite Mixture of Censored Regression Models with Skewed Distributions FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis FMM Rhythmic Patterns Modeling by FMM Models FMP Filtered Monotonic Polynomial IRT Models FMStable Finite Moment Stable Distributions FMradio Factor Modeling for Radiomics Data FMsmsnReg Regression Models with Finite Mixtures of Skew Heavy-Tailed Errors FNN Fast Nearest Neighbor Search Algorithms and Applications FOCI Feature Ordering by Conditional Independence FORD Feature Ordering by Integrated R Square Dependence FPCA3D Three Dimensional Functional Component Analysis FPCdpca The FPCdpca Criterion on Distributed Principal Component Analysis FPDclustering PD-Clustering and Related Methods FPLdata Read in Fantasy Premier League Data FRACTION Numeric Number into Fraction FRAPO Financial Risk Modelling and Portfolio Optimisation with R FRApp FRAP Data Analysis Using Nonlinear Mixed Effect Models with 'shiny' FRB Fast and Robust Bootstrap FRCC Fast Regularized Canonical Correlation Analysis FRCI Fuzzy & Randomized Confidence Intervals FREEtree Tree Method for High Dimensional Longitudinal Data FREQ FREQ: Estimate population size from capture frequencies FRESA.CAD Feature Selection Algorithms for Computer Aided Diagnosis FRI Relative Importance of Main and Interaction Effects FRK Fixed Rank Kriging FSA Simple Fisheries Stock Assessment Methods FSAdata Data to Support Fish Stock Assessment ('FSA') Package FSDAM Forward Stepwise Deep Autoencoder-Based Monotone NLDR FSK2R An Interface Between the 'FSKX' Standard and 'R' FSM Finite Selection Model FSSF Generate Fully-Sequential Space-Filling Designs Inside a Unit Hypercube FSTpackage Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotation Scores FSelector Selecting Attributes FSelectorRcpp 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature Selection Algorithms with a Sparse Matrix Support FSinR Feature Selection in R FTSgof White Noise and Goodness-of-Fit Tests for Functional Time Series FUNTA Functional Tangential Angle Pseudo-Depth FVDDPpkg Implement Fleming-Viot-Dependent Dirichlet Processes FWDselect Selecting Variables in Regression Models FWRGB Fresh Weight Determination from Visual Image of the Plant FaaSr 'FaaSr' Local Test Development Package FactChar Characterization and Diagnostic Tools for Factorial Block Designs FactEff Efficiencies of Block Designs for Factorial and Fractional Factorial Experiments FactoClass Combination of Factorial Methods and Cluster Analysis FactoInvestigate Automatic Description of Factorial Analysis FactoMineR Multivariate Exploratory Data Analysis and Data Mining FactorAssumptions Set of Assumptions for Factor and Principal Component Analysis FactorCopula Factor, Bi-Factor, Second-Order and Factor Tree Copula Models FactorCopulaModel Factor Copula Models FactorHet Estimate Heterogeneous Effects in Factorial Experiments Using Grouping and Sparsity Factoshiny Perform Factorial Analysis from 'FactoMineR' with a Shiny Application Fahrmeir Data from the Book "Multivariate Statistical Modelling Based on Generalized Linear Models", First Edition, by Ludwig Fahrmeir and Gerhard Tutz FakeDataR Privacy-Preserving Synthetic Data for 'LLM' Workflows FamEvent Family Age-at-Onset Data Simulation and Penetrance Estimation Familias Probabilities for Pedigrees Given DNA Data Families Kinship Ties in (Virtual) Multi-Generation Populations FastBandChol Fast Estimation of a Covariance Matrix by Banding the Cholesky Factor FastCUB Fast Estimation of CUB Models via Louis' Identity FastGP Efficiently Using Gaussian Processes with Rcpp and RcppEigen FastGaSP Fast and Exact Computation of Gaussian Stochastic Process FastHamming Fast Computation of Pairwise Hamming Distances FastImputation Learn from Training Data then Quickly Fill in Missing Data FastJM Semi-Parametric Joint Modeling of Longitudinal and Survival Data FastKM A Fast Multiple-Kernel Method Based on a Low-Rank Approximation FastKNN Fast k-Nearest Neighbors FastKRR Kernel Ridge Regression using 'RcppArmadillo' FastPCS FastPCS Robust Fit of Multivariate Location and Scatter FastRCS Fits the FastRCS Robust Multivariable Linear Regression Model FastRWeb Fast Interactive Framework for Web Scripting Using R FastRet Retention Time Prediction in Liquid Chromatography FastSegmentation Unsupervised Cell Segmentation by Fast Gaussian Processes FastStepGraph A Fast Algorithm for Sparse Precision Matrix Estimation FastSurvival Fast Kaplan-Meier, Log-Rank, and Hazard Ratio Estimation for Survival Analysis FastUtils Fast, Readable Utility Functions FatTailsR Kiener Distributions and Fat Tails in Finance and Neuroscience FateID Quantification of Fate Bias in Multipotent Progenitors FaultTree Fault Trees for Risk and Reliability Analysis FeaLect Scores Features for Feature Selection FeatureExtraction Generating Features for a Cohort FeatureImpCluster Feature Importance for Partitional Clustering FeatureTerminatoR Feature Selection Engine to Remove Features with Minimal Predictive Power FedData Download Geospatial Data Available from Several Federated Data Sources FedIRT Federated Item Response Theory Models FertNet Process Data from the Social Networks and Fertility Survey Fgmutils Forest Growth Model Utilities FiRE Finder of Rare Entities (FiRE) FiSh Fisher-Shannon Method FielDHub A Shiny App for Design of Experiments in Life Sciences FieldSimR Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials FilmsGmooG IMDb Film Ratings from the Summer of 2022 FinAna Financial Analysis and Regression Diagnostic Analysis FinCal Time Value of Money, Time Series Analysis and Computational Finance FinCovRegularization Covariance Matrix Estimation and Regularization for Finance FinNet Quickly Build and Manipulate Financial Networks FinTS Companion to Tsay (2005) Analysis of Financial Time Series FinanceGraphs Flexible Graphs for Analysis of Financial Data and Time Series FinancialMath Financial Mathematics for Actuaries FindIt Finding Heterogeneous Treatment Effects FinePop Fine-Scale Population Analysis FinePop2 Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis) FisPro Fuzzy Inference System Design and Optimization Fiscal Income Tax Calculations (UK) FishDiveR Classify Aquatic Animal Behaviours from Vertical Movement Data FishPhyloMaker Phylogenies for a List of Finned-Ray Fishes FishProxCompAnalyzer Proximate Composition Analysis of Fish and Feed Ingredients FisherEM The FisherEM Algorithm to Simultaneously Cluster and Visualize High-Dimensional Data FitDynMix Estimation of Dynamic Mixtures FitUltD Fit Univariate Mixed and Usual Distributions FixSeqMTP Fixed Sequence Multiple Testing Procedures FixedPoint Algorithms for Finding Fixed Point Vectors of Functions FjordLight Available Light Within the Water Column and on the Seafloor of Arctic Fjords FlexDir Tools to Work with the Flexible Dirichlet Distribution FlexGAM Generalized Additive Models with Flexible Response Functions FlexParamCurve Tools to Fit Flexible Parametric Curves FlexRL A Flexible Model for Record Linkage FlexReg Regression Models for Bounded Continuous and Discrete Responses FlexScan Flexible Scan Statistics FlexVarJM Estimate Joint Models with Subject-Specific Variance FlickrAPI Access to Flickr API FloodFreqPlot Flood Probability Plotting and Graphical Frequency Analysis FlowRegEnvCost The Environmental Costs of Flow Regulation FlowScreen Daily Streamflow Trend and Change Point Screening FlowerMate Reciprocity Indices for Style-Polymorphic Plants Fluidigm Handling Fluidigm Data FluxPoint Change Point Detection for Non-Stationary and Cross-Correlated Time Series FluxSeparator Separation of Diffusive and Ebullitive Fluxes FlyingR Simulation of Bird Flight Range FnR Inbreeding and Numerator Relationship Coefficients FoCo2 Coherent Forecast Combination for Linearly Constrained Multiple Time Series FoRDM Forest Many-Objective Robust Decision Making ('FoRDM') FoReco Forecast Reconciliation FoRecoML Forecast Reconciliation with Machine Learning ForCausality A Curated Collection of 'Causal Inference' Datasets and Tools ForIT Functions to Estimate Tree Volume and Phytomass in the Italian Forest Inventory 2005 ForLion 'ForLion' Algorithm to Find D-Optimal Designs for Experiments ForagingOrg Organization Measures for Visual Foraging ForeCA Forecastable Component Analysis ForeComp Size-Power Tradeoff Visualization for Equal Predictive Ability of Two Forecasts ForecastCombinations Forecast Combinations ForecastingEnsembles Time Series Forecasting Using 23 Individual Models ForestDisc Forest Discretization ForestElementsR Data Structures and Functions for Working with Forest Data ForestFit Statistical Modelling for Plant Size Distributions ForestGapR Tropical Forest Canopy Gaps Analysis ForestTools Tools for Analyzing Remote Sensing Forest Data FormShare A Simple Connection Between the 'FormShare App' and 'R' for Advanced Analytics FormulR Comprehensive Tools for Drug Formulation Analysis and Visualization Formula Extended Model Formulas FossilSim Simulation and Plots for Fossil and Taxonomy Data FossilSimShiny Shiny Application for 'FossilSim' FourScores A Game for Human vs. Human or Human vs. AI FourWayHMM Parsimonious Hidden Markov Models for Four-Way Data FourgameteP FourGamete Test FrF2 Fractional Factorial Designs with 2-Level Factors FrF2.catlg128 Catalogues of Resolution IV 128 Run 2-Level Fractional Factorials Up to 33 Factors that Do Have 5-Letter Words FracFixR Compositional Statistical Framework for RNA Fractionation Analysis FracKrigingR Spatial Multivariate Data Modeling FractalParameterEstimation Simulation and Parameter Estimation of Randomized Sierpinski Carpets using the p-p-p-q-Model FragiliTidy Tidyverse-Compatible Fragility Index Calculations Fragman Fragment Analysis in R FrailtyCompRisk Competing Risks Models for Multi-Center Survival Data with Frailty Frames2 Estimation in Dual Frame Surveys FreqProf Frequency Profiles Computing and Plotting Fstability Calculate Feature Stability FuelDeep3D 3D Fuel Segmentation Using Terrestrial Laser Scanning and Deep Learning FunChisq Model-Free Functional Chi-Squared and Exact Tests FunSurv Modeling Time-to-Event Data with Functional Predictors FunWithNumbers Fun with Fractions and Number Sequences FuncDiv Compute Contributional Diversity Metrics FunctanSNP Functional Analysis (with Interactions) for Dense SNP Data FunctionalCalibration Aggregated Functional Data Calibration using Splines and Wavelets FunnelPlotR Funnel Plots for Comparing Institutional Performance FusionLearn Fusion Learning FuzzyAHP (Fuzzy) AHP Calculation FuzzyClass Fuzzy and Non-Fuzzy Classifiers FuzzyImputationTest Imputation Procedures and Quality Tests for Fuzzy Data FuzzyM Fuzzy Cognitive Maps Operations FuzzyNumbers Tools to Deal with Fuzzy Numbers FuzzyPovertyR Estimation of Fuzzy Poverty Measures FuzzyQ Fuzzy Quantification of Common and Rare Species FuzzyR Fuzzy Logic Toolkit for R FuzzyResampling Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers FuzzySTs Fuzzy Statistical Tools FuzzySimRes Simulation and Resampling Methods for Epistemic Fuzzy Data FuzzySpec Fuzzy Spectral Clustering with Variable-Weighted Adjacency Matrices FuzzyStatTra Statistical Methods for Trapezoidal Fuzzy Numbers G2Sd Grain-Size Statistics and Description of Sediment GA Genetic Algorithms GABB Facilitation of Data Preparation and Plotting Procedures for RDA and PCA Analyses GACE Generalized Adaptive Capped Estimator for Time Series Forecasting GACFF Genetic Similarity in User-Based Collaborative Filtering GAD Analysis of Variance from General Principles GADAG A Genetic Algorithm for Learning Directed Acyclic Graphs GAGAs Global Adaptive Generative Adjustment Algorithm for Generalized Linear Models GAGBLUP Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction GAIPE Graphical Extension with Accuracy in Parameter Estimation (GAIPE) GALAHAD Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with Softplus Reparameterization and Trust-Region Control GALLO Genomic Annotation in Livestock for Positional Candidate LOci GAMens Applies GAMbag, GAMrsm and GAMens Ensemble Classifiers for Binary Classification GANPA Gene Association Network-Based Pathway Analysis (GANPA) GANPAdata The GANPA Datasets Package GAPR Generalized Association Plots GARCH.X Estimation and Exogenous Covariate Selection for ARCH-m(X), Additive ARCH-m(x), and GARCH-X Models GARCHIto Class of GARCH-Ito Models GARCHSK Estimating a GARCHSK Model and GJRSK Model GARCOM Gene and Region Counting of Mutations ("GARCOM") GAReg Genetic Algorithms in Regression GAparsimony Searching Parsimony Models with Genetic Algorithms GB2 Generalized Beta Distribution of the Second Kind: Properties, Likelihood, Estimation GB2group Estimation of the Generalised Beta Distribution of the Second Kind from Grouped Data GB5mcPred Gradient Boosting Algorithm for Predicting Methylation States GBASS Generalized Bayesian Adaptive Smoothing Splines GBJ Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies GBOP2 Generalized Bayesian Optimal Phase II Design (G-BOP2) GCCfactor GCC Estimation of the Multilevel Factor Model GCD Global Charcoal Database GCEstim Regression Coefficients Estimation Using the Generalized Cross Entropy GCPBayes Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure GCPM Generalized Credit Portfolio Model GCSM Implements Generic Composite Similarity Measure GCalignR Simple Peak Alignment for Gas-Chromatography Data GCubeR Estimation of Forest Volume, Biomass, and Carbon GD Geographical Detectors for Assessing Spatial Factors GDAdata Datasets for the Book Graphical Data Analysis with R GDAtools Geometric Data Analysis GDILM.ME Spatial Modeling of Infectious Diseases with Co-Variate Error GDILM.SIR Inference for Infectious Disease Transmission in SIR Framework GDINA The Generalized DINA Model Framework GDPuc Easily Convert GDP Data GDSARM Gauss - Dantzig Selector: Aggregation over Random Models GE General Equilibrium Modeling GEC Generalized Exponentiated Composite Distributions GECal Generalized Entropy Calibration GEEaSPU Adaptive Association Tests for Multiple Phenotypes using Generalized Estimating Equations (GEE) GEEmediate Mediation Analysis for Generalized Linear Models Using the Difference Method GEInfo Gene-Environment Interaction Analysis Incorporating Prior Information GEInter Robust Gene-Environment Interaction Analysis GEMSS Generalization Error Minimization in SubSampling for Gaussian Processes GENEAclassify Segmentation and Classification of Accelerometer Data GENEAcore Pre-Processing of 'GENEActiv' Data GENEAread Package for Reading Binary Files GENLIB Genealogical Data Analysis GENMETA Implements Generalized Meta-Analysis Using Iterated Reweighted Least Squares Algorithm GEOmap Topographic and Geologic Mapping GEOmetadb A compilation of metadata from NCBI GEO GEOquery Get data from NCBI Gene Expression Omnibus (GEO) GESE Gene-Based Segregation Test GET Global Envelopes GETdesigns Generalized Extended Triangular Designs ('GETdesigns') GEVACO Joint Test of Gene and GxE Interactions via Varying Coefficients GEVcdn GEV Conditional Density Estimation Network GEint Misspecified Models for Gene-Environment Interaction GEmetrics Best Linear Unbiased Prediction of Genotype-by-Environment Metrics GFA Group Factor Analysis GFD Tests for General Factorial Designs GFDmcv General Hypothesis Testing Problems for Multivariate Coefficients of Variation GFDrmst Multiple RMST-Based Tests in General Factorial Designs GFDrmtl Multiple RMTL-Based Tests for Competing Risks Data in General Factorial Designs GFDsurv Tests for Survival Data in General Factorial Designs GFE Gross Flows Estimation under Complex Surveys GFFStrandLoc Strand-Wise Gene and Protein Extraction from GFF3 Files GFGM.copula Generalized Farlie-Gumbel-Morgenstern Copula GFM Generalized Factor Model GFisher Generalized Fisher's Combination Tests Under Dependence GGClassification Gabriel Graph Based Large-Margin Classifiers GGEBiplots GGE Biplots with 'ggplot2' GGIR Raw Accelerometer Data Analysis GGIRread Wearable Accelerometer Data File Readers GGMncv Gaussian Graphical Models with Nonconvex Regularization GGMridge Gaussian Graphical Models Using Ridge Penalty Followed by Thresholding and Reestimation GGRidge Graphical Group Ridge GGUM Generalized Graded Unfolding Model GGally Extension to 'ggplot2' GGenemy Audit 'ggplot2' Visualizations for Accessibility and Best Practices GGoutlieR Identify Individuals with Unusual Geo-Genetic Patterns GHCNr Download Weather Station Data from GHCNd GHRexplore Exploratory Analysis of Temporal and Spatio-Temporal Health Data GHRmodel Bayesian Hierarchical Modelling of Spatio-Temporal Health Data GIC A General Iterative Clustering Algorithm GIFT Access to the Global Inventory of Floras and Traits (GIFT) GIGrvg Random Variate Generator for the GIG Distribution GIMMEgVAR Group Iterative Multiple Model Estimation with 'graphicalVAR' GINAX Performs Genome-Wide Iterative Fine-Mapping for Non-Gaussian Data using GINA-X GISINTEGRATION GIS Integration GISSB Network Analysis on the Norwegian Road Network GISTools Further Capabilities in Geographic Information Science GInSARCorW GACOS InSAR Correction Workflow GIplot Gaussian Interval Plot (GIplot) GJRM Generalised Joint Regression Modelling GJRM.data Data Sets for Copula Additive Distributional Regression Using R GK2011 Gaines and Kuklinski (2011) Estimators for Hybrid Experiments GLAD Gain and Loss Analysis of DNA GLBFP General Linear Blend Frequency Polygon Density Estimation GLCMTextures GLCM Textures of Raster Layers GLDEX Fitting Single and Mixture of Generalised Lambda Distributions GLDreg Fit GLD Regression/Quantile/AFT Model to Data GLMBasedRaschEstimation GLM-Based Estimation for Rasch Model Parameters GLMMRR Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data GLMMadaptive Generalized Linear Mixed Models using Adaptive Gaussian Quadrature GLMMcosinor Fit a Cosinor Model Using a Generalized Mixed Modeling Framework GLMMselect Bayesian Model Selection for Generalized Linear Mixed Models GLMcat Generalized Linear Models for Categorical Responses GLMpack Data and Code to Accompany Generalized Linear Models, 2nd Edition GLMsData Generalized Linear Model Data Sets GLSME Generalized Least Squares with Measurement Error GLSUP Generalised Linear Step-Up Procedure for Multiple Hypothesis Testing GLmom Generalized L-Moments Estimation for Extreme Value Distributions GMAC Genomic Mediation Analysis with Adaptive Confounding Adjustment GMC Generalized Measure of Correlation (GMC) GMCM Fast Estimation of Gaussian Mixture Copula Models GMDH Short Term Forecasting via GMDH-Type Neural Network Algorithms GMDH2 Binary Classification via GMDH-Type Neural Network Algorithms GMDHreg Regression using GMDH Algorithms GMLTM Generalized Multicomponent Latent Trait Model for Diagnosis GMMAT Generalized Linear Mixed Model Association Tests GMMBoost Likelihood-Based Boosting for Generalized Mixed Models GMMinit Optimal Initial Value for Gaussian Mixture Model GMPro Graph Matching with Degree Profiles GMSE Generalised Management Strategy Evaluation Simulator GMSimpute Generalized Mass Spectrum Missing Peaks Abundance Imputation GMX Extended Graphical Model Checks for the Rasch Family of Models GNAR Methods for Fitting Network Time Series Models GNE Computation of Generalized Nash Equilibria GNRS Access the 'Geographic Name Resolution Service' GNSSseg Homogenization of GNSS Series GOCompare Comprehensive GO Terms Comparison Between Species GOFShiny Interactive Document for Working with Goodness of Fit Analysis GOFclustering Goodness-of-Fit Testing for Model-Based Clustering GORCure Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data GOSemSim GO-terms Semantic Similarity Measures GOplot Visualization of Functional Analysis Data GOstats Tools for manipulating GO and microarrays GPAbin Unifying Multiple Biplot Visualisations into a Single Display GPArotateDF Derivative Free Gradient Projection Factor Rotation GPArotation Gradient Projection Factor Rotation GPBayes Tools for Gaussian Process Modeling in Uncertainty Quantification GPCMlasso Differential Item Functioning in Generalized Partial Credit Models GPCsign Gaussian Process Classification as Described in Bachoc et al. (2020) GPEMR Growth Parameter Estimation Method GPFDA Gaussian Process for Functional Data Analysis GPGame Solving Complex Game Problems using Gaussian Processes GPL2025 Convert Chip ID of the GPL2015 into GeneBank Accession and ENTREZID GPLTR Generalized Partially Linear Tree-Based Regression Model GPP Gaussian Process Projection GPRMortality Gaussian Process Regression for Mortality Rates GPSCDF Generalized Propensity Score Cumulative Distribution Function GPSeqClus Sequential Clustering Algorithm for Location Data GPTCM Generalized Promotion Time Cure Model with Bayesian Shrinkage Priors GPTreeO Dividing Local Gaussian Processes for Online Learning Regression GPUmatrix Basic Linear Algebra with GPU GPareto Gaussian Processes for Pareto Front Estimation and Optimization GPfit Gaussian Processes Modeling GPflexViz Graphical Visualizations Related to Genomic Prediction GPoM Generalized Polynomial Modelling GPpenalty Penalized Likelihood in Gaussian Processes GPvam Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling GPvecchia Scalable Gaussian-Process Approximations GRAB Genome-Wide Robust Analysis for Biobank Data (GRAB) GRANDpriv Graph Release with Assured Node Differential Privacy GRCFE Generate Optimal Row-Column Factorial Experiments GRCRegression Modified Poisson Regression of Grouped and Right-Censored Counts GRCdesigns Generalized Row-Column Designs GREENREG Tool for Statistical and Environmental Analysis GREENeR Geospatial Regression Equation for European Nutrient Losses (GREEN) GREMLINS Generalized Multipartite Networks GRIN2 Genomic Random Interval (GRIN) GRNNs General Regression Neural Networks Package GROAN Genomic Regression Workbench GRShiny Graded Response Model GRSxE Testing Gene-Environment Interactions Through Genetic Risk Scores GRelevance Graph-Based k-Sample Comparisons and Relevance Analysis in High Dimensions GSA Gene Set Analysis GSA.UN Global Sensitivity Analysis Tool GSD Graph Signal Decomposition GSDA Gene Set Distance Analysis (GSDA) GSE Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data GSEABase Gene set enrichment data structures and methods GSED Group Sequential Enrichment Design GSEMA Gene Set Enrichment Meta-Analysis GSM Gamma Shape Mixture GSMX Multivariate Genomic Selection GSODR Global Surface Summary of the Day ('GSOD') Weather Data Client GSSE Genotype-Specific Survival Estimation GSSTDA Progression Analysis of Disease with Survival using Topological Data Analysis GSVA Gene Set Variation Analysis for Microarray and RNA-Seq Data GSbench Benchmarking Genomic Selection and Machine-Learning Prediction Models GSelection Genomic Selection GSparO Group Sparse Optimization GTAPViz Automating 'GTAP' Data Processing and Visualization GTDL The Generalized Time-Dependent Logistic Family GTEs Group Technical Effects GTFSwizard Creating, Exploring and Manipulating 'GTFS' Files GTRT Graph Theoretic Randomness Tests GTbasedIM Game Theory-Based Influence Measures GUD Bayesian Modal Regression Based on the GUD Family GUEST Graphical Models in Ultrahigh-Dimensional and Error-Prone Data via Boosting Algorithm GUILDS Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure GUTS Fast Calculation of the Likelihood of a Stochastic Survival Model GUniFrac Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis GVARX Perform Global Vector Autoregression Estimation and Inference GVS 'Geocoordinate Validation Service' GWASExactHW Exact Hardy-Weinburg Testing for Genome Wide Association Studies GWASTools Tools for Genome Wide Association Studies GWASbyCluster Identifying Significant SNPs in Genome Wide Association Studies (GWAS) via Clustering GWASinlps Non-Local Prior Based Iterative Variable Selection Tool for Genome-Wide Association Studies GWASinspector Comprehensive and Easy to Use Quality Control of GWAS Results GWEX Multi-Site Stochastic Models for Daily Precipitation and Temperature GWI Count and Continuous Generalized Variability Indexes GWLelast Geographically Weighted Logistic Elastic Net Regression GWPR.light Geographically Weighted Panel Regression GWRLASSO A Hybrid Model for Spatial Prediction Through Local Regression GWRM Generalized Waring Regression Model for Count Data GWSDAT GroundWater Spatiotemporal Data Analysis Tool (GWSDAT) GWalkR Interactive Exploratory Data Analysis Tool GWlasso Geographically Weighted Lasso GWmodel Geographically-Weighted Models GWnnegPCA Geographically Weighted Non-Negative Principal Components Analysis GWnorm G-Wishart Normalising Constants for Gaussian Graphical Models GWpcor Geographically Weighted Partial Correlation Coefficient GWsignif Estimating Genome-Wide Significance for Whole Genome Sequencing Studies, Either Single SNP Tests or Region-Based Tests GaSP Train and Apply a Gaussian Stochastic Process Model GalaxyR 'Galaxy' API Implementation GameTheory Cooperative Game Theory GammaFrailty Gamma Frailty Regression Models with Multiple Baseline Distributions Gammareg Classic Gamma Regression: Joint Modeling of Mean and Shape Parameters GapAnalysis Conservation Indicators Using Spatial Information GauPro Gaussian Process Fitting GaussSuppression Tabular Data Suppression using Gaussian Elimination GaussianHMM1d Inference, Goodness-of-Fit and Forecast for Univariate Gaussian Hidden Markov Models GeDS Geometrically Designed Spline Regression GeNetIt Spatial Graph-Theoretic Genetic Gravity Modelling GeRnika Simulation, Visualization and Comparison of Tumor Evolution Data GenAI Generative Artificial Intelligence GenAlgo Classes and Methods to Use Genetic Algorithms for Feature Selection GenBinomApps Clopper-Pearson Confidence Interval and Generalized Binomial Distribution GenEst Generalized Mortality Estimator GenHMM1d Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov Models GenMarkov Multivariate Markov Chains GenOU Sequential Change-Point Tests for Generalized Ornstein-Uhlenbeck Processes GenOrd Simulation of Discrete Random Variables with Marginal Distributions and Correlation Matrix and via a Gaussian or Student's t Copula GenSA R Functions for Generalized Simulated Annealing GenTag Generate Color Tag Sequences GenTwoArmsTrialSize Generalized Two Arms Clinical Trial Sample Size Calculation GenWin Spline Based Window Boundaries for Genomic Analyses GencoDymo2 Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs GenderInfer This is a Collection of Functions to Analyse Gender Differences GeneCycle Identification of Periodically Expressed Genes GeneF Package for Generalized F-Statistics GeneNMF Non-Negative Matrix Factorization for Single-Cell Omics GeneNet Modeling and Inferring Gene Networks GenePopStats Population Genetics Statistics for Selective Sweep GeneScape Simulation of Single Cell RNA-Seq Data with Complex Structure GeneScoreR Gene Scoring from Count Tables GeneralOaxaca Blinder-Oaxaca Decomposition for Generalized Linear Model GeneralizedHyperbolic The Generalized Hyperbolic Distribution GeneralizedUmatrix Credible Visualization for Two-Dimensional Projections of Data GeneralizedUmatrixGPU Credible Visualization for Two-Dimensional Projections of Data GeneralizedWendland Fully Parameterized Generalized Wendland Covariance Function GenerateIndexPedigree Generate Pedigrees for Index Case Based on US Census Data GenericML Generic Machine Learning Inference GeneticSubsetter Identify Favorable Subsets of Germplasm Collections GenoPop Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files GenoTriplo Genotyping Triploids (or Diploids) from Luminescence Data GenomeAdmixR Simulate Admixture of Genomes GenomeInfoDb Utilities for manipulating chromosome names, including modifying them to follow a particular naming style GenomicAlignments Representation and manipulation of short genomic alignments GenomicDataCommons NIH / NCI Genomic Data Commons Access GenomicFeatures Query the gene models of a given organism/assembly GenomicInteractions Utilities for handling genomic interaction data GenomicRanges Representation and manipulation of genomic intervals GenomicSig Computation of Genomic Signatures GenomicTools.fileHandler File Handlers for Genomic Data Analysis GeoAdjust Accounting for Random Displacements of True GPS Coordinates of Data GeoDensityR Generate Density Rasters from Polygon and Census Data GeoFIS Spatial Data Processing for Decision Making GeoModels Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis GeoMongo Geospatial Queries Using 'PyMongo' GeoRange Calculating Geographic Range from Occurrence Data GeoThinneR Efficient Spatial Thinning of Species Occurrences GeoTox Spatiotemporal Mixture Risk Assessment GeoVersa Design-Based Residual-Correction Forests for Digital Soil Mapping GeoWeightedModel User-Friendly Interface for Geographically-Weighted Models GeodRegr Geodesic Regression GeomArchetypal Finds the Geometrical Archetypal Analysis of a Data Frame GeometricMorphometricsMix Heterogeneous Methods for Shape and Other Multidimensional Data GephiForR 'Gephi' Network Visualization GerminaR Indices and Graphics for Assess Seed Germination Process GetBCBData Imports Datasets from BCB (Central Bank of Brazil) using Its Official API GetDFPData2 Reading Annual and Quarterly Financial Reports from B3 GetFREData Reading FRE Corporate Data of Public Traded Companies from B3 GetLattesData Reading Bibliometric Data from Lattes Platform GetQuandlData Fast and Cached Import of Data from 'Quandl' Using the 'json API' GetTDData Get Data for Brazilian Bonds (Tesouro Direto) GetoptLong Parsing Command-Line Arguments Ghat Quantifying Evolution and Selection on Complex Traits Ghost Missing Data Segments Imputation in Multivariate Streams GiANT Gene Set Uncertainty in Enrichment Analysis GiRaF Gibbs Random Fields Analysis Gifi Multivariate Analysis with Optimal Scaling GillespieSSA Gillespie's Stochastic Simulation Algorithm (SSA) GillespieSSA2 Gillespie's Stochastic Simulation Algorithm for Impatient People GimmeMyPlot Graphical Utilities for Visualizing and Exploring Data GimmeMyStats Statistics Utilities Gini Gini Coefficient GiniDecompLY Gini Decomposition by Income Sources GiniDistance A New Gini Correlation Between Quantitative and Qualitative Variables GitAI Extracts Knowledge from 'Git' Repositories GitStats Standardized Git Repository Data GlarmaVarSel Variable Selection in Sparse GLARMA Models Glarmadillo Solve the Graphical Lasso Problem with 'Armadillo' GlmSimulatoR Creates Ideal Data for Generalized Linear Models GlobalAncova Global test for groups of variables via model comparisons GlobalOptions Generate Functions to Get or Set Global Options Gmedian Geometric Median, k-Medians Clustering and Robust Median PCA Gmisc Descriptive Statistics, Transition Plots, and More GmooG Datasets for the Book 'Getting (more out of) Graphics' GmptzCurve Gompertz Curve Fitting GoFKernel Testing Goodness-of-Fit with the Kernel Density Estimator GoMiner Automate the Mapping Between a List of Genes and Gene Ontology Categories GofCens Goodness-of-Fit Methods for Right-Censored Data GomoGomonoMi Animate Text using the 'Animate.css' Library GoodFibes Detection and Reconstruction of Muscle Fibers from diceCT Image Data GoodFitSBM Monte Carlo Goodness-of-Fit Tests for Stochastic Block Models GoodmanKruskal Association Analysis for Categorical Variables GoogleKnowledgeGraphR Retrieve Information from 'Google Knowledge Graph' API GowerSom Self-Organizing Maps for Mixed-Attribute Data Using Gower Distance GpGp Fast Gaussian Process Computation Using Vecchia's Approximation GrFA Group Factor Analysis GrabSVG Granularity-Based Spatially Variable Genes Identifications GramQuad Gram Quadrature GraphRankTest Rank in Similarity Graph Edge-Count Two-Sample Test (RISE) GrapheR A Multi-Platform GUI for Drawing Customizable Graphs in R GreedyEPL Greedy Expected Posterior Loss GreedyExperimentalDesign Greedy Experimental Design Construction GreedyExperimentalDesignJARs GreedyExperimentalDesign JARs Greg Regression Helper Functions GregoryQuadrature Gregory Weights for Function Integration GreyModel Fitting and Forecasting of Grey Model Greymodels Shiny App for Grey Forecasting Model GridOnClusters Cluster-Preserving Multivariate Joint Grid Discretization GroupBN Inferring Group Bayesian Networks using Hierarchical Feature Clustering GroupComparisons Paired/Unpaired Parametric/Non-Parametric Group Comparisons GroupSeq Group Sequential Design Probabilities - With Graphical User Interface GroupTest Multiple Testing Procedure for Grouped Hypotheses GrowthCurveME Mixed-Effects Modeling for Growth Data GrpString String Patterns and Statistical Differences Between Two Groups of Strings GsymPoint Estimation of the Generalized Symmetry Point, an Optimal Cutpoint in Continuous Diagnostic Tests Guerry Maps, Data and Methods Related to Guerry (1833) "Moral Statistics of France" GulFM General Unilateral Load Estimator for Two-Layer Latent Factor Models Gviz Plotting data and annotation information along genomic coordinates GxEScanR Run GWAS/GWEIS Scans Using Binary Dosage Files GxEprs Genotype-by-Environment Interaction in Polygenic Score Models H2x2Factorial Sample Size Calculation in Hierarchical 2x2 Factorial Trials HAC Estimation, Simulation and Visualization of Hierarchical Archimedean Copulae (HAC) HACSim Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment HAMMER High-Dimensional Factor-Analytic Representation Modeling and Metrics HARplus Enhanced R Package for 'GEMPACK' .har and .sl4 Files HARr 'HAR' ('GEMPACK') File Read/Write Utility HBSTM Hierarchical Bayesian Space-Time Models for Gaussian Space-Time Data HBV.IANIGLA Modular Hydrological Model HCD Hierarchical Community Detection by Recursive Partitioning HCPclust Hierarchical Conformal Prediction for Clustered Data with Missing Responses HCR Causal Discovery from Discrete Data using Hidden Compact Representation HCTDesign Group Sequential Design for Historical Control Trial with Survival Outcome HCUPtools Access and Work with HCUP Resources and Datasets HCmodelSets Regression with a Large Number of Potential Explanatory Variables HDANOVA High-Dimensional Analysis of Variance HDBRR High Dimensional Bayesian Ridge Regression without MCMC HDCD High-Dimensional Changepoint Detection HDCurves Hierarchical Derivative Curve Estimation HDF5Array HDF5 datasets as array-like objects in R HDGLM Tests for High Dimensional Generalized Linear Models HDInterval Highest (Posterior) Density Intervals HDLSSkST Distribution-Free Exact High Dimensional Low Sample Size k-Sample Tests HDMAADMM ADMM for High-Dimensional Mediation Models HDMFA High-Dimensional Matrix Factor Analysis HDMT A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses HDNRA High-Dimensional Location Testing with Normal-Reference Approaches HDOMDesign High-Dimensional Orthogonal Maximin Distance Designs HDRFA High-Dimensional Robust Factor Analysis HDShOP High-Dimensional Shrinkage Optimal Portfolios HDSinRdata Data for the 'Mastering Health Data Science Using R' Online Textbook HDSpatialScan Multivariate and Functional Spatial Scan Statistics HDStIM High Dimensional Stimulation Immune Mapping ('HDStIM') HDTSA High Dimensional Time Series Analysis Tools HDXBoxeR Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data HDclassif High Dimensional Supervised Classification and Clustering HDclust Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks HDcpDetect Detect Change Points in Means of High Dimensional Data HDtweedie The Lasso for Tweedie's Compound Poisson Model Using an IRLS-BMD Algorithm HEDA 'Hydropeaking Events Detection Algorithm' HEssRNA Heritability-Based Estimation of Sample Size for RNA-Seq Data HEtools Homomorphic Encryption Polynomials HGDMr Hysteretic and Gatekeeping Depressions Model HGMND Heterogeneous Graphical Model for Non-Negative Data HGNChelper Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols HGSL Heterogeneous Group Square-Root Lasso HGraph Use Graph Structure to Travel HH Statistical Analysis and Data Display: Heiberger and Holland HHBayes Bayesian Household Transmission Modeling with 'Stan' HIViz Interactive Dashboard for 'HIV' Data Visualization HK80 Conversion Tools for HK80 Geographical Coordinate System HKRbook Apps and Data for the Book "Introduction to Statistics" HLAtools Toolkit for HLA Immunogenomics HLMdiag Diagnostic Tools for Hierarchical (Multilevel) Linear Models HLSM Hierarchical Latent Space Network Model HMC High-Dimensional Mean Comparison with Projection and Cross-Fitting HMDA Holistic Multimodel Domain Analysis for Exploratory Machine Learning HMDHFDplus Read Human Mortality Database and Human Fertility Database Data from the Web HMM Hidden Markov Models HMMHSMM Inference and Estimation of Hidden Markov Models and Hidden Semi-Markov Models HMMRel Hidden Markov Models for Reliability and Maintenance HMMcopula Markov Regime Switching Copula Models Estimation and Goodness-of-Fit HMMextra0s Hidden Markov Models with Extra Zeros HMMpa Analysing Accelerometer Data Using Hidden Markov Models HMR Flux Estimation with Static Chamber Data HMTL Heterogeneous Multi-Task Feature Learning HNPclassifier Hierarchical Neyman-Pearson Classification for Ordered Classes HOIF Higher-Order Influence Function Estimators for the Average Treatment Effect HOIFCar Covariate Adjustment in RCT by Higher-Order Influence Functions HOME Harmonized Orphanhood Mortality Estimation HOasso Higher Order Assortativity for Complex Networks HPZoneAPI 'HPZone' API Interface HQM Superefficient Estimation of Future Conditional Hazards Based on Marker Information HRTnomaly Historical, Relational, and Tail Anomaly-Detection Algorithms HRW Datasets, Functions and Scripts for Semiparametric Regression Supporting Harezlak, Ruppert & Wand (2018) HSAR Hierarchical Spatial Autoregressive Model HSAUR A Handbook of Statistical Analyses Using R (1st Edition) HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition) HSAUR3 A Handbook of Statistical Analyses Using R (3rd Edition) HSEtest Homogeneity of Stratum Effects Test HSPOR Hidden Smooth Polynomial Regression for Rupture Detection HTDV Hypothesis Testing for Dependent Variables with Unbalanced Data HTGM High Throughput 'GoMiner' HTGM2D Two Dimensional High Throughput 'GoMiner' HTGM3D Three Dimensional High Throughput 'GoMiner' HTGM4D Four Dimensional High Throughput 'GoMiner' HTLR Bayesian Logistic Regression with Heavy-Tailed Priors HTMLUtils Facilitates Automated HTML Report Creation HTRX Haplotype Trend Regression with eXtra Flexibility (HTRX) HTSCluster Clustering High-Throughput Transcriptome Sequencing (HTS) Data HTSFilter Filter replicated high-throughput transcriptome sequencing data HTSeed Fitting of Hydrotime Model for Seed Germination Time Course HTSeedGLM Hydro Thermal Time Analysis of Seed Germination Using Generalised Linear Model HTT Hypothesis Testing Tree HUM Compute HUM Value and Visualize ROC Curves HVT Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis HWEintrinsic Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem HYDROCAL Hydraulic Roughness Calculator HYPEtools Tools for Processing and Analyzing Files from the Hydrological Catchment Model HYPE HZIP Likelihood-Based Inference for Joint Modeling of Correlated Count and Binary Outcomes with Extra Variability and Zeros HaDeX Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data HaDeX2 Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data HadIBDs Incomplete Block Designs using Hadamard Matrix (HadIBDs) HadamardR Hadamard Matrix Generation HanStat Package for Easy Interpretation of Statistical Methods HandTill2001 Multiple Class Area under ROC Curve Hapi Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells Haplin Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes HaploCatcher A Predictive Haplotyping Package HaploDiploidEquilibrium Calculate F Statistics Using Mixed Haploid and Diploid Organism Data HaploSim Functions to Simulate Haplotypes HaploVar Defining Local Haplotype Variants for Use in Trait Association and Trait Prediction Analyses HardyWeinberg Statistical Tests and Graphics for Hardy-Weinberg Equilibrium Harvest.Tree Harvest the Classification Tree Hassani.SACF Computing Lower Bound of Ljung-Box Test Hassani.Silva A Test for Comparing the Predictive Accuracy of Two Sets of Forecasts HausdorffGoF One- And Two-Sample Hausdorff Goodness-of-Fit Test HazardDiff Conditional Treatment Effect for Competing Risks HealthCal Health Calculator HealthMarkers Clinical and Metabolic Biomarker Calculation Toolkit HeatmapR Create Heatmaps Using Base Graphics Heatplus Heatmaps with row and/or column covariates and colored clusters HeckmanEM Fit Normal, Student-t or Contaminated Normal Heckman Selection Models HeckmanStan Heckman Selection Models Based on Bayesian Analysis HellCor The Hellinger Correlation HelloFrog A Quirky ASCII-Art Frog Alternative to 'print' HelpersMG Tools for Various R Functions Helpers HetSeq Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity HeterFunctionalData Test of No Main and/or Interaction Effects in Functional Data HextractoR Integrated Tool for Hairping Extraction of RNA Sequences HhP Hierarchical Heterogeneity Analysis via Penalization HiCDOC A/B compartment detection and differential analysis HiCParser Parser for HiC data in R HiCcompare HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets HiClimR Hierarchical Climate Regionalization HiCocietyExample Example HiC and Two 'HiCociety' Outputs for Demonstration and Testing HiDimDA High Dimensional Discriminant Analysis HiGarrote Nonnegative Garrote Method Incorporating Hierarchical Relationships HiResTEC Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data HiTC High Throughput Chromosome Conformation Capture analysis HiddenMarkov Hidden Markov Models HierPortfolios Hierarchical Risk Clustering Portfolio Allocation Strategies HighFive The 'HighFive' 'C++' Interface to 'HDF5' HighestMedianRules Implementation of Voting Rules Electing the Candidate with Highest Median Grade HistDAWass Histogram-Valued Data Analysis HistDat Summary Statistics for Histogram/Count Data HistData Data Sets from the History of Statistics and Data Visualization HistogramTools Utility Functions for R Histograms HiveR 2D and 3D Hive Plots for R Hmisc Harrell Miscellaneous Hmsc Hierarchical Model of Species Communities HoRM Supplemental Functions and Datasets for "Handbook of Regression Methods" HodgesTools Common Use Tools for Genomic Analysis Holomics A User-Friendly R 'shiny' Application for Multi-Omics Data Integration and Analysis HomeRangeR Predict Vertebrate Home-Range Sizes Using Allometric Models Homeric Doughnut Plots HomomorphicEncryption BFV, BGV, CKKS Schema for Fully Homomorphic Encryption HonestDiD Robust Inference in Difference-in-Differences and Event Study Designs Horsekicks Provide Extensions to the Prussian Army Death by Horsekick Data HospitalNetwork Building Networks of Hospitals Through Patients Transfers Hotelling Hotelling's T^2 Test and Variants HotellingEllipse Hotelling’s T-Squared Statistic and Ellipse HuraultMisc Guillem Hurault Functions' Library HurreconR Models Hurricane Wind Speed, Wind Direction, and Wind Damage HyMETT Hydrologic Model Evaluation and Time-Series Tools HyRiM Multicriteria Risk Management using Zero-Sum Games with Vector-Valued Payoffs that are Probability Distributions HybridDesign Hybrid Design for Phase I Dose-Finding Studies HybridMicrobiomes Analysis of Host-Associated Microbiomes from Hybrid Organisms HydroCode Hydrological Codes HydroMe Estimating Water Retention and Infiltration Model Parameters using Experimental Data HydroPonicsK Hydroponic Data Analysis Tools HydroPortailStats 'HydroPortail' Statistical Functions HyperG Hypergraphs in R HyperbolicDist The Hyperbolic Distribution IADT Interaction Difference Test for Prediction Models IALS Iterative Alternating Least Square Estimation for Large-Dimensional Matrix Factor Model IAPWS95 Thermophysical Properties of Water and Steam IASD Model Selection for Index of Asymmetry Distribution IATScore Scoring Algorithm for the Implicit Association Test (IAT) IATanalytics Compute Effect Sizes and Reliability for Implicit Association Test (IAT) Data IATscores Implicit Association Test Scores Using Robust Statistics IAcsSPCR Data and Functions for "An Intro. to Accept. Samp. & SPC/R" IBCF.MTME Item Based Collaborative Filtering for Multi-Trait and Multi-Environment Data IBDInfer Design-Based Causal Inference Method for Incomplete Block Designs IBFS Initial Basic Feasible Solution for Transportation Problem IBGS Iterated Block Gibbs Sampler for Ultrahigh-Dimensional Variable Selection and Model Averaging IBLM Interpretable Boosted Linear Models IBMPopSim Individual Based Model Population Simulation IBRtools Integrating Biomarker-Based Assessments and Radarchart Creation IBclust Information Bottleneck Methods for Clustering Mixed-Type Data IBrokers R API to Interactive Brokers Trader Workstation ICAOD Optimal Designs for Nonlinear Models via ICA ICBioMark Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers ICC Facilitating Estimation of the Intraclass Correlation Coefficient ICC.Sample.Size Calculation of Sample Size and Power for ICC ICCDesign Intraclass Correlation Coefficient (ICC) Design, Calculation and Interactive 'shiny' Toolkit ICCbin Facilitates Clustered Binary Data Generation, and Estimation of Intracluster Correlation Coefficient (ICC) for Binary Data ICD10gm Metadata Processing for the German Modification of the ICD-10 Coding System ICED IntraClass Effect Decomposition ICEHmeasures The Equiplot Graph and Complex Inequality Measures ICEbox Individual Conditional Expectation Plot Toolbox ICGE Estimation of Number of Clusters and Identification of Atypical Units ICGOR Fit Generalized Odds Rate Hazards Model with Interval Censored Data ICODS Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring ICS Tools for Exploring Multivariate Data via ICS/ICA ICSClust Tandem Clustering with Invariant Coordinate Selection ICSKAT Interval-Censored Sequence Kernel Association Test ICSNP Tools for Multivariate Nonparametrics ICSOutlier Outlier Detection Using Invariant Coordinate Selection ICSS ICSS Algorithm by Inclan/Tiao (1994) ICSShiny ICS via a Shiny Application ICSsmoothing Data Smoothing by Interpolating Cubic Splines ICV Indirect Cross-Validation (ICV) for Kernel Density Estimation ICcalib Cox Model with Interval-Censored Starting Time of a Covariate ICcforest An Ensemble Method for Interval-Censored Survival Data ICglm Information Criteria for Generalized Linear Regression ICompELM Independent Component Analysis Based Extreme Learning Machine ICsurv Semiparametric Regression Analysis of Interval-Censored Data ICtest Estimating and Testing the Number of Interesting Components in Linear Dimension Reduction ICvectorfields Vector Fields from Spatial Time Series of Population Abundance IDCard Update Chinese ID Card Number to Eighteen Digits IDE Integro-Difference Equation Spatio-Temporal Models IDEAFilter Agnostic, Idiomatic Data Filter Module for Shiny IDEATools Individual and Group Farm Sustainability Assessments using the IDEA4 Method IDF Estimation and Plotting of IDF Curves IDLFM Individual Dynamic Latent Factor Model IDMIR Identification of Dysregulated MiRNAs Based on MiRNA-MiRNA Interaction Network IDPSurvival Imprecise Dirichlet Process for Survival Analysis IDPmisc 'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)' IDSL.CSA Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses IDSL.FSA Fragmentation Spectra Analysis (FSA) IDSL.IPA Intrinsic Peak Analysis (IPA) for HRMS Data IDSL.MXP Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data) IDSL.NPA Nominal Peak Analysis (NPA) IDSL.SUFA Simplified UFA IDSL.UFA United Formula Annotation (UFA) for HRMS Data Processing IDSL.UFAx Exhaustive Chemical Enumeration for United Formula Annotation IDSpatialStats Estimate Global Clustering in Infectious Disease IDetect Isolate-Detect Method for Multiple Change-Point Detection IDmeasurer Assessment of Individual Identity in Animal Signals IDmining Intrinsic Dimension for Data Mining IETD Inter-Event Time Definition IFC Tools for Imaging Flow Cytometry IFMCDM Intuitionistic Fuzzy Multi-Criteria Decision Making Methods IFTPredictor Predictions Using Item-Focused Tree Models IGC.CSM Simulate Impact of Different Urban Policies Through a General Equilibrium Model IGST Informative Gene Selection Tool IHSEP Inhomogeneous Self-Exciting Process IHW Independent Hypothesis Weighting IIProductionUnknown Analyzing Data Through of Percentage of Importance Indice (Production Unknown) and Its Derivations IIS Datasets to Accompany Wolfe and Schneider - Intuitive Introductory Statistics IIVpredictor Modeling Within Individual Variability as Predictor IJSE Infinitesimal Jackknife Standard Errors for 'brms' Models ILORA Indian Alien Flora Information Database Retrieval ILRCM Convert Irregular Longitudinal Data to Regular Intervals and Perform Clustering ILS Interlaboratory Study ILSAmerge Merge and Download International Large-Scale Assessments (ILSA) Data ILSAstats Statistics for International Large-Scale Assessments (ILSA) ILSM Analyze Interconnection Structure of Tripartite Interaction Networks IMD Index of Multiple Deprivation Data for the UK IMIFA Infinite Mixtures of Infinite Factor Analysers and Related Models IMIX Gaussian Mixture Model for Multi-Omics Data Integration IMP Interactive Model Performance Evaluation IMPACT The Impact of Items IMR Incomplete Matrix Regression IMTest Information Matrix Test for Generalized Partial Credit Models IMak Item Maker IMmailgun Send Emails using 'Mailgun' INCVCommunityDetection Inductive Node-Splitting Cross-Validation for Community Detection INFOSET Computing a New Informative Distribution Set of Asset Returns INLA Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations INLABMA Bayesian Model Averaging with INLA INLAjoint Multivariate Joint Modeling for Longitudinal and Time-to-Event Outcomes with 'INLA' INLAspacetime Spatial and Spatio-Temporal Models using 'INLA' INLAtools Functionalities for the 'INLA' Package INLAvaan Approximate Bayesian Latent Variable Analysis INQC Quality Control of Climatological Daily Time Series INTRIGUE Quantify and Control Reproducibility in High-Throughput Experiments INetTool Integration Network IOBR Immune Oncology Biological Research IOLS Iterated Ordinary Least Squares Regression IPAG Tools for IPAG Courses IPCWK Kendall's Tau Partial Corr. for Survival Trait and Biomarkers IPDfromKM Map Digitized Survival Curves Back to Individual Patient Data IPEC Root Mean Square Curvature Calculation IPEDS Data from the Integrated Post-Secondary Education Data System IPEDSuploadables Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload IPLGP Identification of Parental Lines via Genomic Prediction IPMRF Intervention in Prediction Measure for Random Forests IPMbook Functions and Data for the Book 'Integrated Population Models' IPPP Inhomogeneous Poisson Point Processes IPV Item Pool Visualization IPWboxplot Adapted Boxplot to Missing Observations IQCC Improved Quality Control Charts IRISMustangMetrics Statistics and Metrics for Seismic Data IRISSeismic Classes and Methods for Seismic Data Analysis IRR2FPR Computing False Positive Rate from Inter-Rater Reliability IRTBEMM Family of Bayesian EMM Algorithm for Item Response Models IRTM Theory-Driven Item Response Theory (IRT) Models IRTShiny Item Response Theory via Shiny IRTest Parameter Estimation of Item Response Theory with Estimation of Latent Distribution IRanges Foundation of integer range manipulation in Bioconductor IRdisplay 'Jupyter' Display Machinery IRexamples Collection of Practical Institutional Research Examples and Tutorials IRkernel Native R Kernel for the 'Jupyter Notebook' IRon Solving Imbalanced Regression Tasks ISAR Introduction to Sports Analytics using R (ISAR) Data ISCA Compare Heterogeneous Social Groups ISCAM Companion to the Book "Investigating Statistical Concepts, Applications, and Methods" ISCO08ConveRsions Converts ISCO-08 to Job Prestige Scores, ISCO-88 and Job Name ISEtools Ion Selective Electrodes Analysis Methods ISLR Data for an Introduction to Statistical Learning with Applications in R ISLR2 Introduction to Statistical Learning, Second Edition ISM Interpretive Structural Modelling (ISM) ISMtools Interpretive Structural Modelling Analysis Tools ISO11784Tools ISO11784 PIT Tag ID Format Converters ISO6976.2016 Calorific Values and Properties of Natural Gas per ISO 6976:2016 ISOcodes Selected ISO Codes ISOweek Week of the year and weekday according to ISO 8601 ISPYARDSWinProbabilityGSDesign Trial Design in Respiratory Disease Based on the Win Probability ISR The Iterated Score Regression-Based Estimation ISRaD Tools and Data for the International Soil Radiocarbon Database ISS Isotonic Subgroup Selection ISwR Introductory Statistics with R ITNr Analysis of the International Trade Network IVCor A Robust Integrated Variance Correlation IVDML Double Machine Learning with Instrumental Variables and Heterogeneity IVPP Invariance Partial Pruning Test IVYplot Produces an IVY Plot (Similar to Dot Plot) with/without Frequencies IceSat2R 'ICESat-2' Altimeter Data using R Icens NPMLE for Censored and Truncated Data IgAScores Score Taxon-Level IgA Binding in IgA-Seq Experiments IgorR Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data) ImCluster Efficiency of Cluster Sampling for Crop Surveys ImFoR Non-Linear Height Diameter Models for Forestry ImML Machine Learning Algorithms Fitting and Validation for Forestry ImNN Neural Networks for Predicting Volume of Forest Trees ImVol Volume Prediction of Trees Using Linear and Nonlinear Allometric Equations Immigrate Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection ImmuneSigR Immune Cell Signature Retrieval and Single-Cell Scoring Immutables Fast and Functional Data Structures Imneuron AI Powered Neural Network Solutions for Regression Tasks ImpShrinkage Improved Shrinkage Estimations for Multiple Linear Regression ImpactEffectsize Calculation and Visualization of the Impact Effect Size Measure ImportExport Import and Export Data ImportanceIndice Analyzing Data Through of Percentage of Importance Indice and Its Derivations ImprintCapASM Allele-Specific Methylation Analysis for Imprinted DMR Diagnostics ImputeLongiCovs Longitudinal Imputation of Categorical Variables via a Joint Transition Model ImputeRobust Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape InPosition Inference Tests for ExPosition InSilicoVA Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm IncDTW Incremental Calculation of Dynamic Time Warping IncidencePrevalence Estimate Incidence and Prevalence using the OMOP Common Data Model IncomPair Comparison of Means for the Incomplete Paired Data IndGenErrors Tests of Independence Between Innovations of Generalized Error Models IndTestPP Tests of Independence and Analysis of Dependence Between Point Processes in Time IndepTest Nonparametric Independence Tests Based on Entropy Estimation IndependenceTests Non-Parametric Tests of Independence Between Random Vectors IndexConstruction Index Construction for Time Series Data IndexNumR Index Number Calculation IndexNumber Index Numbers in Social Sciences IndexNumberTools Working with Index Numbers IndexWizard Constructing and Analyzing Complex Selection Indices IndiAPIs Access Indian Data via Public APIs and Curated Datasets Indicator Composite 'Indicator' Construction and Imputation Data IndonesiAPIs Access Indonesian Data via Public APIs and Curated Datasets InferenceSMR Inference About the Standardized Mortality Ratio when Evaluating the Effect of a Screening Program on Survival InfiniumPurify Estimate and Account for Tumor Purity in Cancer Methylation Data Analysis Inflation Core Inflation InflectSSP Melt Curve Fitting and Melt Shift Analysis Inflongitudinal Detecting Influential Subjects in Longitudinal Data InfluenceBorrowing Adaptive Influence-Based Borrowing for Hybrid Control Trials Information Data Exploration with Information Theory (Weight-of-Evidence and Information Value) InformativeCensoring Multiple Imputation for Informative Censoring Infusion Inference Using Simulation InjurySeverityScore Translate ICD-9 into Injury Severity Score Inquilab Dissipation Kinetics Analysis, Half Life Period, Rate Constant, Plots InsectLabelR Create Labels for Insect in Collection InspectChangepoint High-Dimensional Changepoint Estimation via Sparse Projection InspectionPlanner Phytosanitary Inspection Sampling Planner InsuSensCalc Insulin Sensitivity Indices Calculator IntCal Radiocarbon Calibration Curves IntNMF Integrative Clustering of Multiple Genomic Dataset IntegratedJM Joint Modeling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature InterNL Time Series Intervention Model Using Non-Linear Function InterSIM Simulation of Inter-Related Genomic Datasets InterVA4 Replicate and Analyse 'InterVA4' InterVA5 Replicate and Analyse 'InterVA5' InteractionPoweR Power Analyses for Interaction Effects in Cross-Sectional Regressions InteractionSet Base Classes for Storing Genomic Interaction Data InteractiveComplexHeatmap Make Interactive Complex Heatmaps Interatrix Compute Chi-Square Measures with Corrections InterfaceqPCR GUI to Analyse qPCR Results after PMA Treatment or not InterpolateR A Comprehensive Toolkit for Fast and Efficient Spatial Interpolation InterpretMSSpectrum Interpreting High Resolution Mass Spectra IntervalQuestionStat Tools to Deal with Interval-Valued Responses in Questionnaires IntervalSurgeon Operating on Integer-Bounded Intervals InvStablePrior Inverse Stable Prior for Widely-Used Exponential Models InvariantCausalPrediction Invariant Causal Prediction InvasionCorrection Invasion Correction IrishDirectorates A Dynamic Bipartite Latent Space Model to Analyse Irish Companies' Boards from 2003 to 2013 IrregLong Analysis of Longitudinal Data with Irregular Observation Times Iscores Proper Scoring Rules for Missing Value Imputation IsingFit Fitting Ising Models Using the ELasso Method IsingSampler Sampling Methods and Distribution Functions for the Ising Model Isinglandr Landscape Construction and Simulation for Ising Networks IsletCalc Calculators for Insulin and Glucagon Release Indices Iso Functions to Perform Isotonic Regression IsoCor Analyze Isotope Ratios in a 'Shiny'-App IsoMemo Retrieve Data using the 'IsoMemo' API IsoSpecR The IsoSpec Algorithm IsoplotR Statistical Toolbox for Radiometric Geochronology IsoplotRgui Web Interface to 'IsoplotR' IsoriX Isoscape Computation and Inference of Spatial Origins using Mixed Models IssueTrackeR List Things to Do ItemRest Automated Item Removal Strategies for Exploratory Factor Analysis IterativeHardThresholding Iterative Hard Thresholding Extensions to Cyclops IxPopDyMod Framework for Tick Population and Infection Modeling JADE Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria JANE Just Another Latent Space Network Clustering Algorithm JATSdecoder A Metadata and Text Extraction and Manipulation Tool Set JBrowseR An R Interface to the JBrowse 2 Genome Browser JCRImpactFactor Journal Citation Reports ('JCR') Impact Factor by 'Clarivate' 'Analytics' JDCruncheR 'JDemetra+' Quality Report Generator JFE Tools for Analyzing Time Series Data of Just Finance and Econometrics JFM Rock Mass Structural Analysis from 3D Mesh of Point Cloud JGR Java GUI for R JICO Joint and Individual Regression JLPM Joint Latent Process Models JM Joint Modeling of Longitudinal and Survival Data JM4QTN Joint Mapping for Quantitative Trait Loci JMH Joint Model of Heterogeneous Repeated Measures and Survival Data JMI Jackknife Mutual Information JMbayes Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach JMbayes2 Extended Joint Models for Longitudinal and Time-to-Event Data JMbdirect Joint Model for Longitudinal and Multiple Time to Events Data JMdesign Joint Modeling of Longitudinal and Survival Data - Power Calculation JNplots Visualize Outputs from the 'Johnson-Neyman' Technique JOPS Practical Smoothing with P-Splines JPEN Covariance and Inverse Covariance Matrix Estimation Using Joint Penalty JPSurv Joinpoint Model for Relative and Cause-Specific Survival JSDNE Estimating the Age using Auricular Surface by DNE JSM Semiparametric Joint Modeling of Survival and Longitudinal Data JSUparameters Estimate Parameters of the Best-Fitting JohnsonSU Distribution JSconsole A 'RStudio' Addin to Send 'JavaScript' Code to the 'V8' Console JSmediation Mediation Analysis Using Joint Significance JSparO Joint Sparse Optimization via Proximal Gradient Method for Cell Fate Conversion JUMP Replicability Analysis of High-Throughput Experiments JWileymisc Miscellaneous Utilities and Functions Jacquard Estimation of Jacquard's Genetic Identity Coefficients JamendoR Access to 'Jamendo' API JapanAPIs Access Japanese Data via Public APIs and Curated Datasets JavaGD Java Graphics Device Jaya Gradient-Free Optimization Algorithm for Single and Multi-Objective Problems Jcvrisk Risk Calculator for Cardiovascular Disease in Japan Jdmbs Monte Carlo Option Pricing Algorithms for Jump Diffusion Models with Correlational Companies Jmisc Julian Miscellaneous Function JoF Modelling and Simulating Judgments of Frequency JoSAE Unit-Level and Area-Level Small Area Estimation JointAI Joint Analysis and Imputation of Incomplete Data JointFPM A Parametric Model for Estimating the Mean Number of Events Julia Fractal Image Data Generator JuliaCall Seamless Integration Between R and 'Julia' JuliaConnectoR A Functionally Oriented Interface for Integrating 'Julia' with R JuliaFormulae Translate R Regression Model Formulae to 'Julia' Syntax JumpDiffSim Jump Diffusion Simulation and Calibration for Merton and Kou Models JustifyAlpha Justifying Alpha Levels for Hypothesis Tests K4PrestasiSiswa Student Achievement Data Files for TIMSS 2023 Grade 4 K4ProsesSiswa Student Process Data Files for TIMSS 2023 Grade 4 K4Sekolah School Context Data Files for TIMSS 2023 Grade 4 KCSKNNShiny K-Nearest Neighbour Classifier KCSNBShiny Naive Bayes Classifier KDEmcmc Kernel Density Estimation with a Markov Chain Monte Carlo Sample KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor KEPTED Kernel-Embedding-of-Probability Test for Elliptical Distribution KFAS Kalman Filter and Smoother for Exponential Family State Space Models KFPCA Kendall Functional Principal Component Analysis KFPLS Kernel Functional Partial Least Squares KGode Kernel Based Gradient Matching for Parameter Inference in Ordinary Differential Equations KHQ Methods for Calculating 'KHQ' Scores and 'KHQ5D' Utility Index Scores KINSIMU Panel Evaluation in Forensic Kinship Analysis KLINK Kinship Analysis with Linked Markers KLexp Kernel_lasso Expansion KMD Kernel Measure of Multi-Sample Dissimilarity KMEANS.KNN KMeans and KNN Clustering Package KMLtoSHAPE Preserving Attribute Values: Converting KML to Shapefile KMsurv Datasets from Klein and Moeschberger (1997), Survival Analysis KMunicate KMunicate-Style Kaplan–Meier Plots KNNShiny Interactive Document for Working with KNN Analysis KODAMA Knowledge Discovery by Accuracy Maximization KOFM Test the Kronecker Product Structure in Tensor Factor Models KOGMWU Functional Summary and Meta-Analysis of Gene Expression Data KOLaide Pick and Plot Key Opinion Leaders from a Network Given Constraints KONPsurv KONP Tests: Powerful K-Sample Tests for Right-Censored Data KOR.addrlink Matching Address Data to Reference Index KPC Kernel Partial Correlation Coefficient KQM K Quantiles Medoids (KQM) Clustering KRIS Keen and Reliable Interface Subroutines for Bioinformatic Analysis KRLS Kernel-Based Regularized Least Squares KRMM Kernel Ridge Mixed Model KRONX Clock of Regimes for Regime-Switching Fragility Analysis KSA Retained Component Criterion for Principal Component Analysis KSEAapp Kinase-Substrate Enrichment Analysis KSIC Korea Standard Industrial Classification (KSIC) KSPM Kernel Semi-Parametric Models KScorrect Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests KSgeneral Computing P-Values of the One-Sample K-S Test and the Two-Sample K-S and Kuiper Tests for (Dis)Continuous Null Distribution KTensorGraphs Co-Tucker3 Analysis of Two Sequences of Matrices KWCChangepoint Robust Changepoint Detection for Functional and Multivariate Data KWELA Hierarchical Adaptive 'RT-QuIC' Classification for Complex Matrices KappaGUI An R-Shiny Application for Calculating Cohen's and Fleiss' Kappa Karen Kalman Reaction Networks KarsTS An Interface for Microclimate Time Series Analysis KbMvtSkew Khattree-Bahuguna's Univariate and Multivariate Skewness Kcop Smooth Test for Equality of Copulas and Clustering Multivariate Kendall Kendall Rank Correlation and Mann-Kendall Trend Test Keng Knock Errors Off Nice Guesses KernSmoothIRT Nonparametric Item Response Theory KernelKnn Kernel k Nearest Neighbors Kernelheaping Kernel Density Estimation for Heaped and Rounded Data Keyboard Bayesian Designs for Early Phase Clinical Trials Kifidi Summary Table and Means Plots KinMixLite Inference About Relationships from DNA Mixtures KinformR Relationship-Informed Pedigree and Variant Scoring KingCountyHouses Data on House Sales in King County WA Kira Machine Learning KlerRSS Intelligent Ranked Set Sampling with 'Excel' Integration and SRS Comparison Kmedians K-Medians KnapsackSampling Generate Feasible Samples of a Knapsack Problem KneeArrower Finds Cutoff Points on Knee Curves KnockoffHybrid Hybrid Analysis of Population and Trio Data with Knockoff Statistics for FDR Control KnockoffTrio GWAS with Trio and Duo Data using Knockoff Statistics for FDR Control KnowBR Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases KoboconnectR Download Data from Kobotoolbox to R Kpart Cubic Spline Fitting with Knot Selection KrakenR Comprehensive R Interface for Accessing Kraken Cryptocurrency Exchange REST API KraljicMatrix A Quantified Implementation of the Kraljic Matrix KrigInv Kriging-Based Inversion for Deterministic and Noisy Computer Experiments Kurt Performs Kurtosis-Based Statistical Analyses L0Learn Fast Algorithms for Best Subset Selection L0TFinv A Splicing Approach to the Inverse Problem of L0 Trend Filtering L0cpt Change Point Detection with L0 Penalty L0ggm Smooth L0 Penalty Approximations for Gaussian Graphical Models L1centrality Graph/Network Analysis Based on L1 Centrality L1pack Routines for L1 Estimation L2DensityGoFtest Density Goodness-of-Fit Test L2E Robust Structured Regression via the L2 Criterion L2hdchange L2 Inference for Change Points in High-Dimensional Time Series LA Lioness Algorithm (LA) LABTNSCPSS Calculation of Comorbidity and Frailty Scores LAD Derive Leaf Angle Distribution (LAD) from Measured Leaf Inclination Angles LAGOSNE Interface to the Lake Multi-Scaled Geospatial and Temporal Database LAIr Converting NDVI to LAI of Field, Proximal and Satellite Data LAM Some Latent Variable Models LARisk Estimation of Lifetime Attributable Risk of Cancer from Radiation Exposure LATERmodel Linear Approach to Threshold with Ergodic Rate for Reaction Times LAWBL Latent (Variable) Analysis with Bayesian Learning LBBNN Latent Binary Bayesian Neural Networks Using 'torch' LBDiscover Literature-Based Discovery Tools for Biomedical Research LBI Likelihood Based Inference LBPG The Length-Biased Power Garima Distribution LBSPR Length-Based Spawning Potential Ratio LCAextend Latent Class Analysis (LCA) with Familial Dependence in Extended Pedigrees LCCR Latent Class Capture-Recapture Models LCCkNN Adaptive k-Nearest Neighbor Classifier Based on Local Curvature Estimation LCFdata Data sets for package ``LMERConvenienceFunctions'' LCMCR Bayesian Non-Parametric Latent-Class Capture-Recapture LCMSQA Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment LCPA A General Framework for Latent Classify and Profile Analysis LDAShiny Interactive Topic Modeling and Bibliometric Analysis via Shiny LDATS Latent Dirichlet Allocation Coupled with Time Series Analyses LDATree Oblique Classification Trees with Uncorrelated Linear Discriminant Analysis Splits LDAandLDAS Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS) LDAcoop Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation LDAvis Interactive Visualization of Topic Models LDM Testing Hypotheses About the Microbiome using the Linear Decomposition Model LDNN Longitudinal Data Neural Network LDRTools Tools for Linear Dimension Reduction LDcorSV Linkage Disequilibrium Corrected by the Structure and the Relatedness LDlinkR Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest LEA LEA: an R package for Landscape and Ecological Association Studies LEAVcore Constitution of Core Collections using Length of Encoded Attribute Values LEGIT Latent Environmental & Genetic InTeraction (LEGIT) Model LEdecomp Decompose Life Expectancy by Age (and Cause) LFApp Shiny Apps for Lateral Flow Assays LFDR.MLE Estimation of the Local False Discovery Rates by Type II Maximum Likelihood Estimation LFDR.MME Estimating Local False Discovery Rates Using the Method of Moments LFDREmpiricalBayes Estimating Local False Discovery Rates Using Empirical Bayes Methods LGCU Implementation of Learning Gamma CUSUM (Cumulative Sum) Control Charts LGDtoolkit Collection of Tools for LGD Rating Model Development LGEWIS Tests for Genetic Association/Gene-Environment Interaction in Longitudinal Studies LGRF Set-Based Tests for Genetic Association in Longitudinal Studies LHD Latin Hypercube Designs (LHDs) LIC The LIC Criterion for Optimal Subset Selection LINselect Selection of Linear Estimators LISTO Performing Comprehensive Overlap Assessments LJexm Extract, Convert, and Merge 'pdf' Files from 'zip' Files LJmp3converter Convert Video Files to 'mp3' Format, Merge or Trim Audio Files using 'FFmpeg' LKT Logistic Knowledge Tracing LLM Logit Leaf Model Classifier for Binary Classification LLMAgentR Language Model Agents in R for AI Workflows and Research LLMR Interface for Large Language Model APIs in R LLMTranslate 'shiny' App for TRAPD/ISPOR Survey Translation with LLMs LLMing Large Language Model (LLM) Tools for Psychological Text Analysis LLSR Data Analysis of Liquid-Liquid Systems using R LMD A Self-Adaptive Approach for Demodulating Multi-Component Signal LMERConvenienceFunctions Model Selection and Post-Hoc Analysis for (G)LMER Models LMMsolver Linear Mixed Models with Sparse Matrix Methods and Smoothing LMMstar Repeated Measurement Models for Discrete Times LMN Inference for Linear Models with Nuisance Parameters LMPdata Easy Import of the EU Labour Market Policy Data LMest Generalized Latent Markov Models LMfilteR Filter Methods for Parameter Estimation in Linear and Non Linear Regression Models LMoFit Advanced L-Moment Fitting of Distributions LNIRT LogNormal Response Time Item Response Theory Models LNPar Estimation and Testing for a Lognormal-Pareto Mixture LOCOM2 A Logistic Regression Model for Testing Microbial Differential Abundance LOCUS Low-Rank Decomposition of Brain Connectivity Matrices with Uniform Sparsity LOGAN Log File Analysis in International Large-Scale Assessments LOMAR Localization Microscopy Data Analysis LOPART Labeled Optimal Partitioning LOST Missing Morphometric Data Simulation and Estimation LPBkg Detecting New Signals under Background Mismodelling LPCM Local Principal Curve Methods LPDynR Land Productivity Dynamics Indicator LPM Linear Parametric Models Applied to Hydrological Series LPStimeSeries Learned Pattern Similarity and Representation for Time Series LPWC Lag Penalized Weighted Correlation for Time Series Clustering LPmerge Merging Linkage Maps by Linear Programming LREP Estimate and Test Exponential vs. Pareto Distributions LRMF3 Low Rank Matrix Factorization S3 Objects LRMiss Linear Regression with Missing Data LRQVB Low Rank Correction Quantile Variational Bayesian Algorithm for Multi-Source Heterogeneous Models LRTesteR Likelihood Ratio Tests and Confidence Intervals LS2W Locally Stationary Two-Dimensional Wavelet Process Estimation Scheme LS2Wstat A Multiscale Test of Spatial Stationarity for LS2W Processes LSAMBA Lasso-SAMBA Algorithm LSAfun Applied Latent Semantic Analysis (LSA) Functions LSAmitR Daten, Beispiele und Funktionen zu 'Large-Scale Assessment mit R' LSD Lots of Superior Depictions LSDinterface Interface Tools for 'LSD' Simulation Results Files LSDirf Impulse-Response Function Analysis for Agent-Based Models LSDsensitivity Sensitivity Analysis Tools for 'LSD' Simulations LSE Constrained Least Squares and Generalized QR Factorization LSEbootLS Bootstrap Methods for Regression Models with Locally Stationary Errors LSMjml Fitting Latent Space Item Response Models using Joint Maximum Likelihood Estimation LSMonteCarlo American options pricing with Least Squares Monte Carlo method LSPFP Lysate and Secretome Peptide Feature Plotter LSRS Land Surface Remote Sensing LST Land Surface Temperature Retrieval for Landsat 8 LSTMfactors Determining the Number of Factors in Exploratory Factor Analysis by LSTM LSTS Locally Stationary Time Series LSTbook Data and Software for "Lessons in Statistical Thinking" LSVAR Estimation of Low Rank Plus Sparse Structured Vector Auto-Regressive (VAR) Model LSWPlib Simulation and Spectral Estimation of Locally Stationary Wavelet Packet Processes LSX Semi-Supervised Algorithm for Document Scaling LTASR Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R LTCDM Latent Transition Cognitive Diagnosis Model with Covariates LTFGRS Implementation of Several Phenotype-Based Family Genetic Risk Scores LTFHPlus Implementation of LT-FH++ LTPDvar LTPD and AOQL Plans for Acceptance Sampling Inspection by Variables LTRCtrees Survival Trees to Fit Left-Truncated and Right-Censored and Interval-Censored Survival Data LUCIDus LUCID with Multiple Omics Data LVGP Latent Variable Gaussian Process Modeling with Qualitative and Quantitative Input Variables LWFBrook90R Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90 LZeroSpikeInference Exact Spike Train Inference via L0 Optimization LaF Fast Access to Large ASCII Files LabApplStat Miscellaneous Scripts from the Data Science Laboratory (UCPH) LabRS Laboratorio di Ricerca Sociale con R LabourMarketAreas Identification, Tuning, Visualisation and Analysis of Labour Market Areas LactCurveModels Lactation Curve Model Fitting for Dairy Animals LadderFuelsR Automated Tool for Vertical Fuel Continuity Analysis using Airborne Laser Scanning Data LagSequential Lag-Sequential Categorical Data Analysis Lahman Sean 'Lahman' Baseball Database LakeMetabolizer Tools for the Analysis of Ecosystem Metabolism LambertW Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data LandComp Analysing Landscape Composition and Structure at Multiple Scales Landmarking Analysis using Landmark Models Langevin Langevin Analysis in One and Two Dimensions LangevinFlow Langevin Diffusion Samplers with a C++ Backend LaplacesDemon Complete Environment for Bayesian Inference Largevars Testing Large VARs for the Presence of Cointegration LassoBacktracking Modelling Interactions in High-Dimensional Data with Backtracking LassoHiDFastGibbs Fast High-Dimensional Gibbs Samplers for Bayesian Lasso Regression LassoNet 3CoSE Algorithm LassoSIR Sparsed Sliced Inverse Regression via Lasso LatSquare Analysis of Latin Square and Semi-Latin Square Designs Latamverse Latin American Data via 'RESTful' APIs and Curated Datasets LatentBMA Bayesian Model Averaging for Univariate Link Latent Gaussian Models Laterality Functions to Calculate Common Laterality Statistics in Primatology LatticeDesign Lattice-Based Space-Filling Designs LatticeKrig Multi-Resolution Kriging Based on Markov Random Fields LeArEst Border and Area Estimation of Data Measured with Additive Error LeMaRns Length-Based Multispecies Analysis by Numerical Simulation LePage LePage Type Tests LeadSense Medtronic Brain Sense Local Field Potencial Analysis LeafArea Rapid Digital Image Analysis of Leaf Area LearnBayes Functions for Learning Bayesian Inference LearnClust Learning Hierarchical Clustering Algorithms LearnGeom Learning Plane Geometry LearnNonparam 'R6'-Based Flexible Framework for Permutation Tests LearnPCA Functions, Data Sets and Vignettes to Aid in Learning Principal Components Analysis (PCA) LearnSL Learn Supervised Classification Methods Through Examples and Code LearnVizLMM Learning and Communicating Linear Mixed Models Without Data LearningRlab Statistical Learning Functions LearningStats Elemental Descriptive and Inferential Statistics LeaveOutKSS Leave-Out Variance Component Estimation for Two-Way Fixed Effects Models LexFindR Find Related Items and Lexical Dimensions in a Lexicon LexisNexisTools Working with Files from 'LexisNexis' LexisPlotR Plot Lexis Diagrams for Demographic Purposes LiblineaR Linear Predictive Models Based on the LIBLINEAR C/C++ Library Libra Linearized Bregman Algorithms for Generalized Linear Models LifeHist Life History Models of Individuals LifeInsuranceContracts Framework for Traditional Life Insurance Contracts LifeInsureR Modelling Traditional Life Insurance Contracts LifeTableBuilder Interactive 'shiny' Application for Constructing Life Tables LifeTableFertility 'shiny' Application for Life Table and Fertility Analysis LifemapR Data Visualisation on 'Lifemap' Tree Lifertable Life and Fertility Tables Specially for Insects LiftTest A Bootstrap Proportion Test for Brand Lift Testing LightFitR Design Complex Light Regimes LightLogR Process Data from Wearable Light Loggers and Optical Radiation Dosimeters LikertEZ Easy Analysis and Visualization of Likert Scale Data LikertMakeR Synthesise and Correlate Likert Scale and Rating-Scale Data Based on Summary Statistics LilRhino For Implementation of Feed Reduction, Learning Examples, NLP and Code Management LimnoPalettes A Limnology Themed Palette Generator LinCal Static Univariate Frequentist and Bayesian Linear Calibration LinRegInteractive Interactive Interpretation of Linear Regression Models Linda Line Transect-Based Nearest Neighbor Distance Analysis LindenmayeR Functions to Explore L-Systems (Lindenmayer Systems) LindleyPowerSeries Lindley Power Series Distribution LinearRegressionMDE Minimum Distance Estimation in Linear Regression Model Linkage Clustering Communication Networks Using the Stochastic Topic Block Model Through Linkage.fr LinkedGASP Linked Emulator of a Coupled System of Simulators LinkedMatrix Column-Linked and Row-Linked Matrices Linnorm Linear model and normality based normalization and transformation method (Linnorm) LipidMS Lipid Annotation for LC-MS/MS DDA or DIA Data LipidomicsR Elegant Tools for Processing and Visualization of Lipidomics Data LipinskiFilters Computes and Visualize Lipinski's Parameters LitFetchR Automatically Fetching References Metadata from Literature Databases Lmoments L-Moments and Quantile Mixtures LncFinder LncRNA Identification and Analysis Using Heterologous Features LoBrA Generalized Spline Mixed Effect Models for Longitudinal Breath Data LoTTA Bayesian Inference in Regression Discontinuity Designs LocKer Locally Sparse Estimator of Generalized Varying Coefficient Model for Asynchronous Longitudinal Data LocaTT Geographically-Conscious Taxonomic Assignment for Metabarcoding LocalControl Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence LocalCop Local Likelihood Inference for Conditional Copula Models Lock5Data Datasets for "Statistics: UnLocking the Power of Data" LogConcDEAD Log-Concave Density Estimation in Arbitrary Dimensions LogRegEquiv Logistic Regression Equivalence LogicForest Logic Forest LogicReg Logic Regression LogisticCopula A Copula Based Extension of Logistic Regression LogisticCurveFitting Logistic Curve Fitting by Rhodes Method LogisticEnsembles Automatically Runs 18 Logistic Models-14 Individual Logistic Models and 4 Ensembles of Models LogisticRCI Linear and Logistic Regression-Based Reliable Change Index LongCART Recursive Partitioning for Longitudinal Data and Right Censored Data Using Baseline Covariates LongDat A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data LongDecompHE Longitudinal Decomposition of Health Expectancy by Age and Cause LoopAnalyst A Collection of Tools to Conduct Levins' Loop Analysis LoopDetectR Comprehensive Feedback Loop Detection in ODE Models LoopRig Integration and Analysis of Chromatin Loop Data LorMe Lightweight One-Line Resolving Microbial Ecology Program LorenzRegression Lorenz and Penalized Lorenz Regressions LowRankQP Low Rank Quadratic Programming LqG Robust Group Variable Screening Based on Maximum Lq-Likelihood Estimation Luminescence Comprehensive Luminescence Dating Data Analysis M2SMF Multi-Modal Similarity Matrix Factorization for Integrative Multi-Omics Data Analysis M2SMJF Multi-Modal Similarity Matrix Joint Factorization M3 Reading M3 Files M3C Monte Carlo Reference-based Consensus Clustering M3JF Multi-Modal Matrix Joint Factorization for Integrative Multi-Omics Data Analysis MACER Molecular Acquisition, Cleaning, and Evaluation in R 'MACER' MADMMplasso Multi Variate Multi Response ADMM with Interaction Effects MADtests Hypothesis Tests and Confidence Intervals for Median Absolute Deviations MAFLD Diagnosis of Metabolic Dysfunction Associated Fatty Liver Disease MAGEE Mixed Model Association Test for GEne-Environment Interaction MAGMA.R MAny-Group MAtching MAGNAMWAR A Pipeline for Meta-Genome Wide Association MAICtools Performing Matched-Adjusted Indirect Comparisons (MAIC) MAIHDA Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy MAINT.Data Model and Analyse Interval Data MAIVE Meta Analysis Instrumental Variable Estimator MAKL Multiple Approximate Kernel Learning (MAKL) MALDIquant Quantitative Analysis of Mass Spectrometry Data MALDIquantForeign Import/Export Routines for 'MALDIquant' MALDIrppa MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis MAMS Designing Multi-Arm Multi-Stage Studies MANOVA.RM Resampling-Based Analysis of Multivariate Data and Repeated Measures Designs MAP Multimodal Automated Phenotyping MAPA Multiple Aggregation Prediction Algorithm MAPCtools Multivariate Age-Period-Cohort (MAPC) Modeling for Health Data MARMoT Matching on Poset-Based Average Rank for Multiple Treatments (MARMoT) MARSANNhybrid MARS Based ANN Hybrid Model MARSGWR A Hybrid Spatial Model for Capturing Spatially Varying Relationships Between Variables in the Data MARSS Multivariate Autoregressive State-Space Modeling MARSSVRhybrid MARS SVR Hybrid MASSExtra Some 'MASS' Enhancements MASSTIMATE Body Mass Estimation Equations for Vertebrates MAST Model-based Analysis of Single Cell Transcriptomics MAT Multidimensional Adaptive Testing MATA Model-Averaged Tail Area (MATA) Confidence Interval and Distribution MATES Multi-View Aggregated Two Sample Tests MAVE Methods for Dimension Reduction MAZE Mediation Analysis for Zero-Inflated Mediators MAd Meta-Analysis with Mean Differences MAnorm2 Tools for Normalizing and Comparing ChIP-seq Samples MB The Use of Marginal Distributions in Conditional Forecasting MBA Multilevel B-Spline Approximation MBAnalysis Multiblock Exploratory and Predictive Data Analysis MBBEFDLite Statistical Functions for the Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of Distributions MBC Multivariate Bias Correction of Climate Model Outputs MBCbook Companion Package for the Book "Model-Based Clustering and Classification for Data Science" MBESS The MBESS R Package MBGapp Interactive 'shiny' Application for Model-Based Geostatistics MBHdesign Spatial Designs for Ecological and Environmental Surveys MBMethPred Medulloblastoma Subgroups Prediction MBNMAdose Dose-Response MBNMA Models MBNMAtime Run Time-Course Model-Based Network Meta-Analysis (MBNMA) Models MBRM Mixed Regression Models with Generalized Log-Gamma Random Effects MBSGS Multivariate Bayesian Sparse Group Selection with Spike and Slab MBSP Multivariate Bayesian Model with Shrinkage Priors MBmca Nucleic Acid Melting Curve Analysis MCARtest Optimal Nonparametric Testing of Missing Completely at Random MCAvariants Multiple Correspondence Analysis Variants MCBackscattering Monte Carlo Simulation for Surface Backscattering MCCM Mixed Correlation Coefficient Matrix MCI Multiplicative Competitive Interaction (MCI) Model MCID Estimating the Minimal Clinically Important Difference MCL Markov Cluster Algorithm MCM Estimating and Testing Intergenerational Social Mobility Effect MCMC.qpcr Bayesian Analysis of qRT-PCR Data MCMC4Extremes Posterior Distribution of Extreme Value Models in R MCMCglmm MCMC Generalised Linear Mixed Models MCMChybridGP Hybrid Markov Chain Monte Carlo Using Gaussian Processes MCMCpack Markov Chain Monte Carlo (MCMC) Package MCMCprecision Precision of Discrete Parameters in Transdimensional MCMC MCMCvis Tools to Visualize, Manipulate, and Summarize MCMC Output MCOE Creates New Folders and Loads Standard Practices for Monterey County Office of Education MCPAN Multiple Comparisons Using Normal Approximation MCPMod Design and Analysis of Dose-Finding Studies MCPModBC Improved Inference in Multiple Comparison Procedure – Modelling MCPModGeneral A Supplement to the 'DoseFinding' Package for the General Case MCPModPack Simulation-Based Design and Analysis of Dose-Finding Trials MCPtests Multiples Comparisons Procedures MCS Model Confidence Set Procedure MCSim Determine the Optimal Number of Clusters MCSimMod Working with 'MCSim' Models MCTrend Monte Carlo Trend Analysis MChtest Monte Carlo Hypothesis Tests with Sequential Stopping MCseqReplic Monte Carlo Simulations of Time Changes in Sequences MD2sample Various Methods for the Two Sample Problem in D>1 Dimensions MDCcure Martingale Dependence Tools and Testing for Mixture Cure Models MDDC Modified Detecting Deviating Cells Algorithm in Pharmacovigilance MDFS MultiDimensional Feature Selection MDMA Mathijs Deen's Miscellaneous Auxiliaries MDMR Multivariate Distance Matrix Regression MDOLS Inference of Quadratic Functional for Moderate-Dimensional OLS MDP2 Markov Decision Processes (MDPs) MDPIexploreR Web Scraping and Bibliometric Analysis of MDPI Journals MDPtoolbox Markov Decision Processes Toolbox MDSMap High Density Genetic Linkage Mapping using Multidimensional Scaling MDSPCAShiny Interactive Document for Working with Multidimensional Scaling and Principal Component Analysis MDSS Modeling Human Dentin Serial Sectioning MDgof Various Methods for the Goodness-of-Fit Problem in D>1 Dimensions MDimNormn Multi-Dimensional MA Normalization for Plate Effect MEAanalysis Analyse and Visualise Multi Electrode Array Burst Data MECfda Scalar-on-Function Regression with Measurement Error Correction MED Mediation by Tilted Balancing MEDesigns Mating Environmental Designs MEDseq Mixtures of Exponential-Distance Models with Covariates MEFM Perform MEFM Estimation on Matrix Time Series MEGB Gradient Boosting for Longitudinal Data MEMSS Data Sets from Mixed-Effects Models in S MERO Performing Monte Carlo Expectation Maximization Random Forest Imputation for Biological Data MESS Miscellaneous Esoteric Statistical Scripts MEclustnet Fit the Mixture of Experts Latent Position Cluster Model to Network Data MEsreg Generalized Maximum Entropy Estimation for Smooth Transition and Kink Regression Models MF.beta4 Measuring Ecosystem Multi-Functionality and Its Decomposition MFAg Multiple Factor Analysis (MFA) MFDFA MultiFractal Detrended Fluctuation Analysis MFF Meta Fuzzy Functions MFO Maximal Fat Oxidation and Kinetics Calculation MFPCA Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains MFRCD Optimal Row-Column Designs for Asymmetrical Factorial Experiments MFSD Multivariate Functional Spatial Data MFSIS Model-Free Sure Independent Screening Procedures MGBT Multiple Grubbs-Beck Low-Outlier Test MGDrivE Mosquito Gene Drive Explorer MGDrivE2 Mosquito Gene Drive Explorer 2 MGL Module Graphical Lasso MGLM Multivariate Response Generalized Linear Models MGMM Missingness-Aware Gaussian Mixture Models MGPSDK Interact with the Maxar 'MGP' Application Programming Interfaces MGSDA Multi-Group Sparse Discriminant Analysis MHCtools Analysis of MHC Data in Non-Model Species MHD Metric Halfspace Depth MHDA Massive Hierarchically Data Analysis MHQoL Mental Health Quality of Life Toolkit MHTdiscrete Multiple Hypotheses Testing for Discrete Data MHTmult Multiple Hypotheses Testing for Multiple Families/Groups Structure MHTrajectoryR Bayesian Model Selection in Logistic Regression for the Detection of Adverse Drug Reactions MIAmaxent A Modular, Integrated Approach to Maximum Entropy Distribution Modeling MIC Analysis of Antimicrobial Minimum Inhibitory Concentration Data MICsplines The Computing of Monotonic Spline Bases and Constrained Least-Squares Estimates MIDASim Simulating Realistic Microbiome Data using 'MIDASim' MIDN Nearly Exact Sample Size Calculation for Exact Powerful Nonrandomized Tests for Differences Between Binomial Proportions MIGEE Impute Missing Values and Fitting Linear Mixed Effect Model MIIPW IPW and Mean Score Methods for Time-Course Missing Data MIIVefa Exploratory Factor Analysis Using Model Implied Instrumental Variables MIIVsem Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models MIMER Data Wrangling for Antimicrobial Resistance Studies MIMSunit Algorithm to Compute Monitor Independent Movement Summary Unit (MIMS-Unit) MINTplates Encode "License-Plates" from Sequences and Decode Them Back MIRDD Diagnostic Tool by Multiple Imputation for Regression Discontinuity Designs MIXFIM Evaluation of the FIM in NLMEMs using MCMC MJMbamlss Multivariate Joint Models with 'bamlss' MKLE Maximum Kernel Likelihood Estimation MKMeans A Modern K-Means (MKMeans) Clustering Algorithm MKclass Statistical Classification MKdescr Descriptive Statistics MKendall Matrix Kendall's Tau and Matrix Elliptical Factor Model MKinfer Inferential Statistics MKmisc Miscellaneous Functions from M. Kohl MKomics Omics Data Analysis MKpower Power Analysis and Sample Size Calculation ML.MSBD Maximum Likelihood Inference on Multi-State Trees ML2Pvae Variational Autoencoder Models for IRT Parameter Estimation MLBC Bias Correction Methods for Models Using Synthetic Data MLCIRTwithin Latent Class Item Response Theory (LC-IRT) Models under Within-Item Multidimensionality MLCM Maximum Likelihood Conjoint Measurement MLCausal Causal Inference Methods for Multilevel and Clustered Data MLDS Maximum Likelihood Difference Scaling MLDataR Collection of Machine Learning Datasets for Supervised Machine Learning MLE Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions MLEce Asymptotic Efficient Closed-Form Estimators for Multivariate Distributions MLEcens Computation of the MLE for Bivariate Interval Censored Data MLFDR High Dimensional Mediation Analysis using Local False Discovery Rates MLFS Machine Learning Forest Simulator MLGL Multi-Layer Group-Lasso MLGdata Datasets for Use with Salvan, Sartori and Pace (2020) MLID Multilevel Index of Dissimilarity MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers MLML2R Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions MLMOI Estimating Frequencies, Prevalence and Multiplicity of Infection MLMusingR Practical Multilevel Modeling MLPUGS Multi-Label Prediction Using Gibbs Sampling (and Classifier Chains) MLSP Machine Learning Models for Soil Properties MLZ Mean Length-Based Estimators of Mortality using TMB MLeval Machine Learning Model Evaluation MLmetrics Machine Learning Evaluation Metrics MLmorph Integrating Morphological Modeling and Machine Learning for Decision Support MLpreemption Maximum Likelihood Estimation of the Niche Preemption Model MLwrap Machine Learning Modelling for Everyone MM The Multiplicative Multinomial Distribution MM4LMM Inference of Linear Mixed Models Through MM Algorithm MMAC Data for Mathematical Modeling and Applied Calculus MMAD Minorization-Maximization via Assembly-Decomposition Technology MMD Minimal Multilocus Distance (MMD) for Source Attribution and Loci Selection MMDCopula Robust Estimation of Copulas by Maximum Mean Discrepancy MMDai Multivariate Multinomial Distribution Approximation and Imputation for Incomplete Categorical Data MMDvariance Detecting Differentially Variable Genes Using the Mixture of Marginal Distributions MMGFM Multi-Study Multi-Modality Generalized Factor Model MMINP Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor MMLR Fitting Markov-Modulated Linear Regression Models MMOC Multi-Omic Spectral Clustering using the Flag Manifold MMRcaseselection Case Classification and Selection Based on Regression Results MMWRweek Convert Dates to MMWR Day, Week, and Year MMeM Multivariate Mixed Effects Model MN Matrix Normal Distribution MNARclust Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models MNB Diagnostic Tools for a Multivariate Negative Binomial Regression Model MNLR Interactive Shiny Presentation for Working with Multinomial Logistic Regression MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks MNP Fitting the Multinomial Probit Model MNS Mixed Neighbourhood Selection MNormTest Multivariate Normal Hypothesis Testing MOCCA Multi-Objective Optimization for Collecting Cluster Alternatives MODISTools Interface to the 'MODIS Land Products Subsets' Web Services MOEADr Component-Wise MOEA/D Implementation MOFA2 Multi-Omics Factor Analysis v2 MOFAT Maximum One-Factor-at-a-Time Designs MOLHD Multiple Objective Latin Hypercube Design MOM Estimation and Testing of Hypothesis MOODE Multi-Objective Optimal Design of Experiments MOQA Basic Quality Data Assurance for Epidemiological Research MOSAlloc Constraint Multiobjective Sample Allocation MOST Multiphase Optimization Strategy MOTE Effect Size and Confidence Interval Calculator MOsemiind Marshall-Olkin Shock Models with Semi-Independent Time MOutliers Multivariate Outlier Detection Methods MPBoost Treatment Allocation in Clinical Trials by the Maximal Procedure MPCI Multivariate Process Capability Indices (MPCI) MPCR Multi Precision Computing MPDiR Data Sets and Scripts for Modeling Psychophysical Data in R MPGE A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes MPI Computation of Multidimensional Poverty Index (MPI) MPN Most Probable Number and Other Microbial Enumeration Techniques MPS Estimating Through the Maximum Product Spacing Approach MPSEM Modelling Phylogenetic Signals using Eigenvector Maps MPTinR Analyze Multinomial Processing Tree Models MPV Data Sets from Montgomery, Peck and Vining MPsychoR Modern Psychometrics with R MQMF Modelling and Quantitative Methods in Fisheries MR.RGM Fitting Multivariate Bidirectional Mendelian Randomization Networks Using Bayesian Directed Cyclic Graphical Models MRAM Multivariate Regression Association Measure MRCE Multivariate Regression with Covariance Estimation MRCV Methods for Analyzing Multiple Response Categorical Variables (MRCVs) MRFA Fitting and Predicting Large-Scale Nonlinear Regression Problems using Multi-Resolution Functional ANOVA (MRFA) Approach MRFcov Markov Random Fields with Additional Covariates MRG Create Non-Confidential Multi-Resolution Grids MRHawkes Multivariate Renewal Hawkes Process MRIreduce ROI-Based Transformation of Neuroimages into High-Dimensional Data Frames MRMCaov Multi-Reader Multi-Case Analysis of Variance MRMCbinary Multi-Reader Multi-Case Analysis of Binary Diagnostic Tests MRMCsamplesize Sample Size Estimations for Planning Multi-Reader Multi-Case (MRMC) Studies Without Pilot Data MRPC PC Algorithm with the Principle of Mendelian Randomization MRQoL Minimal Clinically Important Difference and Response Shift Effect for Health-Related Quality of Life MRReg MDL Multiresolution Linear Regression Framework MRStdCRT Model-Robust Standardization in Cluster-Randomized Trials MRStdLCRT Model-Robust Standardization for Longitudinal Cluster-Randomized Trials MRTAnalysis Assessing Proximal, Distal, and Mediated Causal Excursion Effects for Micro-Randomized Trials MRTSampleSize A Sample Size Calculator for Micro-Randomized Trials MRTSampleSizeBinary Sample Size Calculator for MRT with Binary Outcomes MRZero Diet Mendelian Randomization MRgrowth Mark-Recapture Growth Models MRmediation A Causal Mediation Method with Methylated Region (MR) as the Mediator MSBStatsData Data Sets for Courses at the Münster School of Business MSCCT Multiple Survival Crossing Curves Tests MSCMT Multivariate Synthetic Control Method Using Time Series MSCquartets Analyzing Gene Tree Quartets under the Multi-Species Coalescent MSCsimtester Tests of Multispecies Coalescent Gene Tree Simulator Output MSEtool Management Strategy Evaluation Toolkit MSG Data and Functions for the Book Modern Statistical Graphics MSGARCH Markov-Switching GARCH Models MSGARCHelm Hybridization of MS-GARCH and ELM Model MSIMST Bayesian Monotonic Single-Index Regression Model with the Skew-T Likelihood MSMGOptimizer Mine Sustainability Modeling Group (MSMG) 'SimaPro' CSV Optimizer MSML Model Selection Based on Machine Learning (ML) MSMU Descriptive Statistics Functions for Numeric Data MSMwRA Multivariate Statistical Methods with R Applications MSN Multivariate Survival Data with Network Structures MSPRT A Modified Sequential Probability Ratio Test (MSPRT) MSSQL Tools to Work with Microsoft SQL Server Databases via 'RODBC' MST Multivariate Survival Trees MSTest Hypothesis Testing for Markov Switching Models MSUthemes Michigan State University (MSU) Palettes and Themes MSbox Mass Spectrometry Tools MSclassifR Automated Classification of Mass Spectra MSclust Multiple-Scaled Clustering MScombine Combine Data from Positive and Negative Ionization Mode Finding Common Entities MSigSeg Multiple SIGnal SEGmentation MSinference Multiscale Inference for Nonparametric Time Trend(s) MSnbase Base Functions and Classes for Mass Spectrometry and Proteomics MSoutcomes CORe Multiple Sclerosis Outcomes Toolkit MSwM Fitting Markov Switching Models MTA Multiscalar Territorial Analysis MTAR Multi-Trait Analysis of Rare-Variant Association Study MTE Maximum Tangent Likelihood Estimation for Robust Linear Regression and Variable Selection MTLR Survival Prediction with Multi-Task Logistic Regression MTPS Multi-Task Prediction using Stacking Algorithms MTS All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models MTSYS Methods in Mahalanobis-Taguchi (MT) System MTest A Procedure for Multicollinearity Testing using Bootstrap MUACz Generate MUAC and BMI z-Scores and Percentiles for Children and Adolescents MUGS Multisource Graph Synthesis with EHR Data MUS Monetary Unit Sampling and Estimation Methods, Widely Used in Auditing MUVR2 Multivariate Methods with Unbiased Variable Selection MVA An Introduction to Applied Multivariate Analysis with R MVET Multivariate Estimates and Tests MVN Multivariate Normality Tests MVNBayesian Bayesian Analysis Framework for MVN (Mixture) Distribution MVNGmod Matrix-Variate Non-Gaussian Linear Regression Models MVOPR Multi-View Orthogonal Projection Regression for Multi-Modality Integration MVPBT Publication Bias Tests for Meta-Analysis of Diagnostic Accuracy Test MVQuickGraphs Quick Multivariate Graphs MVR Mean-Variance Regularization MVSKmod Matrix-Variate Skew Linear Regression Models MVT Estimation and Testing for the Multivariate t-Distribution MVTests Multivariate Hypothesis Tests MVar Multivariate Analysis MVar.pt Analise multivariada (brazilian portuguese) MVisAGe Compute and Visualize Bivariate Associations MWright Mainardi-Wright Family of Distributions MaOEA Many Objective Evolutionary Algorithm MacBehaviour Behavioural Studies of Large Language Models MachineShop Machine Learning Models and Tools MacroFilters Robust Trend-Cycle Decomposition for Macroeconomic Time Series MacroZooBenthosWaterA Fresh Water Quality Analysis Based on Macrozoobenthos MaddisonData Maddison Project Data Maeswrap Wrapper Functions for MAESTRA/MAESPA MagmaClustR Clustering and Prediction using Multi-Task Gaussian Processes with Common Mean MainExistingDatasets Main Existing Human Datasets MajKMeans k-Means Algorithm with a Majorization-Minimization Method MajMinKmeans k-Means Algorithm with a Majorization-Minimization Method MakefileR Create 'Makefiles' Using R ManagedCloudProvider Providing the Kubernetes-Like Functions for the Non-Kubernetes Cloud Service MandalaR Building Mandalas from Parametric Equations of Classical Curves Mangrove Risk Prediction on Trees ManifoldOptim An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization ManlyMix Manly Mixture Modeling and Model-Based Clustering MannWhitneyCopula Computing Mann-Whitney Effect Based on Copulas MantaID A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs ManyIVsNets Environmental Phillips Curve Analysis with Multiple Instrumental Variables and Networks ManyTests Multiple Testing Procedures of Cox (2011) and Wong and Cox (2007) Map2NCBI Mapping Markers to the Nearest Genomic Feature MapGAM Mapping Smoothed Effect Estimates from Individual-Level Data Mapinguari Process-Based Biogeographical Analysis MapperAlgo Topological Data Analysis: Mapper Algorithm MappingCalc Mapping Calculator for EQ-5D Utility Scores MarZIC Marginal Mediation Effects with Zero-Inflated Compositional Mediator MareyMap Estimation of Meiotic Recombination Rates Using Marey Maps MarginalMaxTest Max-Type Test for Marginal Correlation with Bootstrap MarginalMediation Marginal Mediation MariNET Build Network Based on Linear Mixed Models from EHRs MarineChain Blockchain-Enabled Maritime Transportation System Simulator MarketMatching Market Matching and Causal Impact Inference Markovchart Markov Chain-Based Cost-Optimal Control Charts MarkowitzR Statistical Significance of the Markowitz Portfolio MassSpecWavelet Peak Detection for Mass Spectrometry data using wavelet-based algorithms MassWateR Quality Control and Analysis of Massachusetts Water Quality Data Massign Simple Matrix Construction MasterBayes Maximum Likelihood and Markov Chain Monte Carlo (MCMC) Methods for Pedigree Reconstruction and Analysis MatchGATE Estimate Group Average Treatment Effects with Matching MatchIt Nonparametric Preprocessing for Parametric Causal Inference MatchLinReg Combining Matching and Linear Regression for Causal Inference MatchThem Matching and Weighting Multiply Imputed Datasets Matching Multivariate and Propensity Score Matching with Balance Optimization MatchingPursuit Processing Time Series Data Using the Matching Pursuit Algorithm MatrixCorrelation Matrix Correlation Coefficients MatrixEQTL Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations MatrixExtra Extra Methods for Sparse Matrices MatrixGenerics S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects MatrixHMM Parsimonious Families of Hidden Markov Models for Matrix-Variate Longitudinal Data MatrixMixtures Model-Based Clustering via Matrix-Variate Mixture Models MatrixModels Modelling with Sparse and Dense Matrices MaxIntTools Testing Maximal Interaction in Two-Mode Clustering via a Permutation Based Procedure MaxMC Maximized Monte Carlo MaxPro Maximum Projection Designs MaxSkew Orthogonal Data Projections with Maximal Skewness MaxWiK Machine Learning Method Based on Isolation Kernel Mean Embedding MaxentVariableSelection Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling MaximinInfer Inference for Maximin Effects in High-Dimensional Settings MazamaCoreUtils Utility Functions for Production R Code MazamaLocationUtils Manage Spatial Metadata for Known Locations MazamaRollUtils Efficient Rolling Functions MazamaSpatialPlots Thematic Plots for Mazama Spatial Datasets MazamaSpatialUtils Spatial Data Download and Utility Functions MazamaTimeSeries Core Functionality for Environmental Time Series McMiso Multicore Multivariable Isotonic Regression Mcomp Data from the M-Competitions MeTo Meteorological Tools Meanimiles Estimation of Meanimiles MeasurementDiagnostics Diagnostics for Lists of Codes Based on Measurements MedDataSets Comprehensive Medical, Disease, Treatment, and Drug Datasets MedDietCalc Multi Calculator to Compute Scores of Adherence to Mediterranean Diet MedLEA Morphological and Structural Features of Medicinal Leaves MedZIsc Statistical Framework for Co-Mediators of Zero-Inflated Single-Cell Data MediaK Calculate MeDiA_K Distance Mediana Clinical Trial Simulations MedianaDesigner Power and Sample Size Calculations for Clinical Trials MedxR Access Drug Regulatory Data via FDA and Health Canada APIs MendelianRandomization Mendelian Randomization Package Mercator Clustering and Visualizing Distance Matrices Mestim Computes the Variance-Covariance Matrix of Multidimensional Parameters Using M-Estimation MetAlyzer Read and Analyze 'MetIDQ™' Software Output Files MetBrewer Color Palettes Inspired by Works at the Metropolitan Museum of Art MetSizeR A Shiny App for Sample Size Estimation in Metabolomic Experiments MetaAnalyser An Interactive Visualisation of Meta-Analysis as a Physical Weighing Machine MetaCycle Evaluate Periodicity in Large Scale Data MetaDose Dose-Response Meta-Regression for Meta-Analysis MetaEntropy Functional Shannon Entropy for Virome Mutational Analysis MetaHD A Multivariate Meta-Analysis Model for High-Dimensional Data MetaHunt Privacy-Preserving Meta-Analysis via Low-Rank Basis Hunting MetaIntegration Ensemble Meta-Prediction Framework MetaLandSim Landscape and Range Expansion Simulation MetaNLP Natural Language Processing for Meta Analysis MetaNet Network Analysis for Omics Data MetaRVM Meta-Population Compartmental Model for Respiratory Virus Diseases MetaSKAT Meta Analysis for SNP-Set (Sequence) Kernel Association Test MetaSubtract Subtracting Summary Statistics of One or more Cohorts from Meta-GWAS Results MetaUtility Utility Functions for Conducting and Interpreting Meta-Analyses MetaboCoreUtils Core Utils for Metabolomics Data MetaboQC Normalize Metabolomic Data using QC Signal MetabolAnalyze Probabilistic Latent Variable Models for Metabolomic Data MetabolSSMF Simplex-Structured Matrix Factorisation for Metabolomics Analysis MetabolicSurv A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature MetabolicSyndrome Diagnosis of Metabolic Syndrome MetabolomicsBasics Basic Functions to Investigate Metabolomics Data Matrices MethComp Analysis of Agreement in Method Comparison Studies MethEvolSIM Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies MethScope Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding MethodCompare Evaluating Bias and Precision in Method Comparison Studies MethodOpt Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation MetricGraph Random Fields on Metric Graphs Metrics Evaluation Metrics for Machine Learning MetricsWeighted Weighted Metrics and Performance Measures for Machine Learning MexBrewer Color Palettes Inspired by Works of Mexican Painters and Muralists MexicoDataAPI Access Mexican Data via APIs and Curated Datasets MfUSampler Multivariate-from-Univariate (MfU) MCMC Sampler Mfuzz Soft clustering of omics time series data Mhorseshoe Approximate Algorithm for Horseshoe Prior MiRKAT Microbiome Regression-Based Kernel Association Tests MiRNAQCD Micro-RNA Quality Control and Diagnosis MiRSEA 'MicroRNA' Set Enrichment Analysis MicSim Performing Continuous-Time Microsimulation MicroDatosEs Utilities for Official Spanish Microdata MicroMacroMultilevel Micro-Macro Multilevel Modeling MicroMoB Discrete Time Simulation of Mosquito-Borne Pathogen Transmission MicroNiche Microbial Niche Measurements MicrobTiSDA Microbiome Time-Series Data Analysis MicrobialGrowth Estimates Growth Parameters from Models and Plots the Curve MicrobiomeStat Statistical Methods for Microbiome Compositional Data MicrobiomeSurv Biomarker Validation for Microbiome-Based Survival Classification and Prediction Microsoft365R Interface to the 'Microsoft 365' Suite of Cloud Services MigConnectivity Estimate Migratory Connectivity for Migratory Animals MigrationDetectR Segment-Based Migration Detection Algorithm MinEDfind A Bayesian Design for Minimum Effective Dosing-Finding Trial MinTriadic Extension to the 'Lolog' Package for 'Triadic' Network Statistics MindOnStats Data sets included in Utts and Heckard's Mind on Statistics Minirand Minimization Randomization MisRepARMA Misreported Time Series Analysis MiscMath Miscellaneous Mathematical Tools MiscMetabar Miscellaneous Functions for Metabarcoding Analysis MissCP Change Point Detection with Missing Values MissMech Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random MissingHandle Handles Missing Dates and Data and Converts into Weekly and Monthly from Daily MissingPlotLSD Missing Plot in LSD MissingPlotRBD Missing Plot in RBD Missplot Missing Plot Technique in Design of Experiment MitoHEAR Quantification of Mitochondrial DNA Heteroplasmy MittagLeffleR Mittag-Leffler Family of Distributions MixFrac Fractional Factorial Designs with Alias and Trend-Free Analysis MixGHD Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions MixLFA Mixture of Longitudinal Factor Analysis Methods MixMashNet Tools for Multilayer and Single Layer Network Modeling MixMatrix Classification with Matrix Variate Normal and t Distributions MixOptim Mixture Optimization Algorithm MixRF A Random-Forest-Based Approach for Imputing Clustered Incomplete Data MixSAL Mixtures of Multivariate Shifted Asymmetric Laplace (SAL) Distributions MixSIAR Bayesian Mixing Models in R MixSemiRob Mixture Models: Parametric, Semiparametric, and Robust MixSim Simulating Data to Study Performance of Clustering Algorithms MixStable Parameter Estimation for Stable Distributions and Their Mixtures MixTwice Large-Scale Hypothesis Testing by Variance Mixing MixedIndTests Tests of Randomness and Tests of Independence MixedLevelRSDs Mixed Level Response Surface Designs MixedPoisson Mixed Poisson Models MixedPsy Statistical Tools for the Analysis of Psychophysical Data MixedTS Mixed Tempered Stable Distribution MixfMRI Mixture fMRI Clustering Analysis MixtureFitting Fitting of Univariate Mixture Distributions to Data using Various Approaches MixtureMissing Robust and Flexible Model-Based Clustering for Data Sets with Missing Values at Random Mmcsd Modeling Complex Longitudinal Data in a Quick and Easy Way MoBPS Modular Breeding Program Simulator MoEClust Gaussian Parsimonious Clustering Models with Covariates and a Noise Component MoNAn Mobility Network Analysis MoTBFs Learning Hybrid Bayesian Networks using Mixtures of Truncated Basis Functions ModEstM Mode Estimation, Even in the Multimodal Case ModLR Information-Theoretic Approach for Moderation Analysis ModStatR Statistical Modelling in Action with R ModTools Building Regression and Classification Models ModalCens Parametric Modal Regression with Right Censoring ModalForecast Parametric Modal ARIMA Models using the SKD Family Modalclust Hierarchical Modal Clustering ModelMap Modeling and Map Production using Random Forest and Related Stochastic Models ModelMatrixModel Create Model Matrix and Save the Transforming Parameters ModelMetrics Rapid Calculation of Model Metrics Modelcharts Classification Model Charts Modeler Classes and Methods for Training and Using Binary Prediction Models MolgenisArmadillo Armadillo Client for the Armadillo Service MolgenisAuth 'OpenID Connect' Discovery and Authentication MomTrunc Moments of Folded and Doubly Truncated Multivariate Distributions Mondrian A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events MonoPhy Explore Monophyly of Taxonomic Groups in a Phylogeny MonoPoly Functions to Fit Monotone Polynomials MonotoneHazardRatio Nonparametric Estimation and Inference of a Monotone Hazard Ratio Function MonotonicityTest Nonparametric Bootstrap Test for Regression Monotonicity Monte.Carlo.se Monte Carlo Standard Errors MonteCarloSEM Monte Carlo Simulation for Structural Equation Modeling MoonShineR Predict Moonlight, Sunlight, and/or Twilight Ground Illuminance MorphSim Simulate Discrete Character Data along Phylogenetic Trees Morpho Calculations and Visualisations Related to Geometric Morphometrics MorphoRegions Analysis of Regionalization Patterns in Serially Homologous Structures MorphoTools2 Multivariate Morphometric Analysis MortCast Estimation and Projection of Age-Specific Mortality Rates MortalityGaps The Double-Gap Life Expectancy Forecasting Model MortalityLaws Parametric Mortality Models, Life Tables and HMD MortalityTables A Framework for Various Types of Mortality / Life Tables MplusAutomation An R Package for Facilitating Large-Scale Latent Variable Analyses in Mplus MplusLGM Automate Latent Growth Mixture Modelling in 'Mplus' MplusTrees Decision Trees with Structural Equation Models Fit in 'Mplus' Mqrcm M-Quantile Regression Coefficients Modeling MsCoreUtils Core Utils for Mass Spectrometry Data MsExperiment Infrastructure for Mass Spectrometry Experiments MsFeatures Functionality for Mass Spectrometry Features MuChPoint Multiple Change Point MuFiMeshGP Multi-Fidelity Emulator for Computer Experiments with Tunable Fidelity Levels MuMIn Multi-Model Inference MuPETFlow Multiple Ploidy Estimation Tool for all Species Compatible with Flow Cytometry MuViCP MultiClass Visualizable Classification using Combination of Projections MultANOVA Analysis of Designed High-Dimensional Data using the Comprehensive MultANOVA Framework MultBiplotR Multivariate Analysis Using Biplots in R MultEq Multiple Equivalence Tests and Simultaneous Confidence Intervals MultNonParam Multivariate Nonparametric Methods MultOrdRS Model Multivariate Ordinal Responses Including Response Styles MultRegCMP Bayesian Multivariate Conway-Maxwell-Poisson Regression Model for Correlated Count Data MultSurvTests Permutation Tests for Multivariate Survival Analysis MultiATSM Multicountry Term Structure of Interest Rates Models MultiAssayExperiment Software for the integration of multi-omics experiments in Bioconductor MultiBD Multivariate Birth-Death Processes MultiCOAP High-Dimensional Covariate-Augmented Overdispersed Multi-Study Poisson Factor Model MultiClassROC ROC Curves for Multi-Class Analysis MultiDataSet Implementation of MultiDataSet and ResultSet MultiDiscreteRNG Generate Multivariate Discrete Data MultiFit Multiscale Fisher's Independence Test for Multivariate Dependence MultiGlarmaVarSel Variable Selection in Sparse Multivariate GLARMA Models MultiGrey Fitting and Forecasting of Grey Model for Multivariate Time Series Data MultiGroupO MultiGroup Method and Simulation Data Analysis MultiGroupSequential Group-Sequential Procedures with Multiple Hypotheses MultiJoin Enables Efficient Joining of Data File on Common Fields using the Unix Utility Join MultiKink Estimation and Inference for Multi-Kink Quantile Regression MultiLCIRT Multidimensional Latent Class Item Response Theory Models MultiLevelOptimalBayes Regularized Bayesian Estimator for Two-Level Latent Variable Models MultiModalR Fast Bayesian Probability Estimation for Multimodal Categorical Data MultiNMix Multi-Species N-Mixture (MNM) Models with 'nimble' MultiObjMatch Multi-Objective Matching Algorithm MultiOrd Generation of Multivariate Ordinal Variates MultiPhen A Package to Test for Multi-Trait Association MultiRFM High-Dimensional Multi-Study Robust Factor Model MultiRNG Multivariate Pseudo-Random Number Generation MultiResponseR Analysis of Data from Multiple-Response Questionnaires MultiRobust Multiply Robust Methods for Missing Data Problems MultiSkew Measures, Tests and Removes Multivariate Skewness MultiSpline Spline-Based Nonlinear Modeling for Multilevel and Longitudinal Data MultiStatM Multivariate Statistical Methods MultiTraits Analyzing and Visualizing Multidimensional Plant Traits MultipleBreakpoints Estimating Multiple Breakpoints for a Sequence of Realizations of Bernoulli Variables MultipleBubbles Test and Detection of Explosive Behaviors for Time Series MultipleRegression Multiple Regression Analysis MultiplierDEA Multiplier Data Envelopment Analysis and Cross Efficiency MultiscaleDTM Multi-Scale Geomorphometric Terrain Attributes MultiscaleSCP Multiscale Systematic Conservation Planning Across Nested H3 Grids MultisiteMediation Causal Mediation Analysis in Multisite Trials MultivariateAnalysis Pacote Para Analise Multivariada MultivariateRandomForest Models Multivariate Cases Using Random Forests MultivariateTrendAnalysis Univariate and Multivariate Trend Testing MultiwayRegression Perform Tensor-on-Tensor Regression MulvariateRandomForestVarImp Variable Importance Measures for Multivariate Random Forests MvBinary Modelling Multivariate Binary Data with Blocks of Specific One-Factor Distribution My.stepwise Stepwise Variable Selection Procedures for Regression Analysis Mychisq Chi-Squared Test for Goodness of Fit and Independence Test MyoScore Transcriptomic Scoring for Human Skeletal Muscle Health N2H4 Handling Methods for Naver News Text Crawling N2R Fast and Scalable Approximate k-Nearest Neighbor Search Methods using 'N2' Library NAC Network-Adjusted Covariates for Community Detection NACHO NanoString Quality Control Dashboard NADA Nondetects and Data Analysis for Environmental Data NADA2 Data Analysis for Censored Environmental Data NAEPirtparams IRT Parameters for the National Assessment of Education Progress NAEPprimer The NAEP Primer NAM Nested Association Mapping NAP Non-Local Alternative Priors in Psychology NAPrior Network Meta-Analytic Predictive Prior for Mid-Trial SoC Changes NAVAECI Non-Asymptotically Valid and Asymptotically Exact (NAVAE) Confidence Intervals NB.MClust Negative Binomial Model-Based Clustering NBAloveR Help Basketball Data Analysis NBBDesigns Neighbour Balanced Block Designs (NBBDesigns) NBDCtools National Institutes of Health Brain Development Cohorts Data Hub Tools NBDdirichlet NBD-Dirichlet Model of Consumer Buying Behavior for Marketing Research NBDesign Design and Monitoring of Clinical Trials with Negative Binomial Endpoint NBKP Beta Kernel Process Modeling with Negative Binomial Response NBLDA Negative Binomial Linear Discriminant Analysis NBPSeq Negative Binomial Models for RNA-Sequencing Data NBR Network-Based R-Statistics using Mixed Effects Models NBShiny Interactive Document for Working with Naive Bayes Classification NBShiny2 Interactive Document for Working with Naive Bayes Classification NBShiny3 Interactive Document for Working with Naive Bayes Classification NBtsVarSel Variable Selection in a Specific Regression Time Series of Counts NCA Necessary Condition Analysis NCC Simulation and Analysis of Platform Trials with Non-Concurrent Controls NCSCopula Non-Central Squared Copula Models Estimation NCmisc Miscellaneous Functions for Creating Adaptive Functions and Scripts NCutYX Clustering of Omics Data of Multiple Types with a Multilayer Network Representation NDP Interactive Presentation for Working with Normal Distribution NDPalette Notre Dame Color Palettes for R NEpiC Network Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals NFLSimulatoR Simulating Plays and Drives in the NFL NFWdist The Standard Distribution Functions for the 3D NFW Profile NGBVS Bayesian Variable Selection for SNP Data using Normal-Gamma NGCHM Next Generation Clustered Heat Maps NGLVieweR Interactive 3D Visualization of Molecular Structures NHANES Data from the US National Health and Nutrition Examination Study NHLData Scores for Every Season Since the Founding of the NHL in 1917 NHPoisson Modelling and Validation of Non Homogeneous Poisson Processes NHSDataDictionaRy NHS Data Dictionary Toolset for NHS Lookups NHSRdatasets NHS and Healthcare-Related Data for Education and Training NHSRplotthedots Draw XmR Charts for NHS 'Making Data Count' Programme NHSRwaitinglist Waiting List Metrics Using Queuing Theory NIMAA Nominal Data Mining Analysis NIPTeR Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing NIRStat Novel Statistical Methods for Studying Near-Infrared Spectroscopy (NIRS) Time Series Data NISTnls Nonlinear least squares examples from NIST NISTunits Fundamental Physical Constants and Unit Conversions from NIST NLP Natural Language Processing Infrastructure NLPclient Stanford 'CoreNLP' Annotation Client NLPutils Natural Language Processing Utilities NLPwavelet Bayesian Wavelet Analysis Using Non-Local Priors NMA Network Meta-Analysis Based on Multivariate Meta-Analysis and Meta-Regression Models NMADTA Network Meta-Analysis of Multiple Diagnostic Tests NMAR Estimation under not Missing at Random Nonresponse NMAforest Forest Plots for Network Meta-Analysis with Proportion for Paths and Studies NMAoutlier Detecting Outliers in Network Meta-Analysis NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) NMFN Non-Negative Matrix Factorization NMMIPW Inverse Probability Weighting under Non-Monotone Missing NMOF Numerical Methods and Optimization in Finance NMRphasing Phase Error Correction and Baseline Correction for One Dimensional ('1D') 'NMR' Data NMTox Dose-Response Relationship Analysis of Nanomaterial Toxicity NMVANOVA Novice Model Variation ANOVA NMcalc Basic Calculations for PK/PD Modeling NMdata Preparation, Checking and Post-Processing Data for PK/PD Modeling NMsim Seamless 'Nonmem' Simulation Platform NNMIS Nearest Neighbor Based Multiple Imputation for Survival Data with Missing Covariates NNMoMo Neural Network Extension to 'StMoMo' for Lee-Carter Modeling NNS Nonlinear Nonparametric Statistics NO.PING.PONG Incorporating Previous Findings When Evaluating New Data NORMAgene Data-Driven qRT-PCR Normalization Using NORMAgene NOVA Neural Output Visualization and Analysis NPBBBDAefficiency A-Efficiency for Nested Partially Balanced Bipartite Block (NPBBB) Designs NPBBBdesigns Construction and a-Efficiency of Nested Partially Balanced Bipartite Block Designs NPBayesImputeCat Non-Parametric Bayesian Multiple Imputation for Categorical Data NPCD Nonparametric Methods for Cognitive Diagnosis NPCDTools The Nonparametric Classification Methods for Cognitive Diagnosis NPCirc Nonparametric Circular Methods NPCox Nonparametric and Semiparametric Proportional Hazards Model NPFD N-Power Fourier Deconvolution NPHMC Sample Size Calculation for the Proportional Hazards Mixture Cure Model NPHazardRate Nonparametric Hazard Rate Estimation NPIstats Nonparametric Predictive Inference NPLStoolbox N-Way Partial Least Squares Modelling of Multi-Way Data NPMLEcmprsk Type-Specific Failure Rate and Hazard Rate on Competing Risks Data NPP Normalized Power Prior Bayesian Analysis NPRED Predictor Identifier: Nonparametric Prediction NPStability Rank-Based Stability Index (RSI) for Genotype by Environment Studies NPflow Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data NRMSampling Sampling Design and Estimation Methods for Natural Resource Management NRMstatsML Statistical and Machine Learning Engine for Long-Term Natural Resource Management Data NRejections Metrics for Multiple Testing with Correlated Outcomes NSM3 Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition NSMM Non-Stationary Multivariate (Copula-Based) Framework, Hydrological Applications NSO1212 National Statistical Office of Mongolia's Open Data API Handler NSR 'Native Status Resolver' NST Normalized Stochasticity Ratio NScluster Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models NTLKwIEx Computation of NTLKwIEx Distribution Properties NTS Nonlinear Time Series Analysis NTSS Nonparametric Tests in Spatial Statistics NU.Learning Nonparametric and Unsupervised Learning from Cross-Sectional Observational Data NUCOMBog NUtrient Cycling and COMpetition Model Undisturbed Open Bog Ecosystems in a Temperate to Sub-Boreal Climate NUETON Nitrogen Use Efficiency Toolkit on Numerics NUSS Mixed N-Grams and Unigram Sequence Segmentation NVAR Nonlinear Vector Autoregression Models NVCSSL Nonparametric Varying Coefficient Spike-and-Slab Lasso NaileR Interpreting Latent Variables with AI NameNeedle Using Needleman-Wunsch to Match Sample Names NatParksPalettes Color Palettes Inspired by National Parks NatureSounds Animal Sounds for Bioacustic Analysis NbClust Determining the Best Number of Clusters in a Data Set NeEDS4BigData New Experimental Design Based Subsampling Methods for Big Data NeStage Effective Population Size from Stage-Structured Populations Nebulosa Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation Necklaces Necklaces and Bracelets NegBinBetaBinreg Negative Binomial and Beta Binomial Bayesian Regression Models NegativeControlOutcomeAdjustment Estimation of Vaccine Efficacy using Negative Control Outcomes Neighboot Neighborhood Bootstrap Method for RDS NeighborFinder Find Neighbor Species of a Bacteria of Interest in the Human Gut Microbiota Nematode Ecological Indices Calculator for Nematode Communities NestMRMC Single Reader Between-Cases AUC Estimator in Nested Data NestedMenu A Nested Menu Widget for 'Shiny' Applications Nestimate Network Estimation, Bootstrap, and Higher-Order Analysis NetCluster Clustering for networks NetCoupler Inference of Causal Links Between a Network and an External Variable NetDA Network-Based Discriminant Analysis Subject to Multi-Label Classes NetExplorer Network Explorer NetGreg Network-Guided Penalized Regression (NetGreg) NetIndices Estimating Network Indices, Including Trophic Structure of Foodwebs in R NetInt Methods for Unweighted and Weighted Network Integration NetLogoR Build and Run Spatially Explicit Agent-Based Models NetMix Dynamic Mixed-Membership Network Regression Model NetOrigin Origin Estimation for Propagation Processes on Complex Networks NetPreProc Network Pre-Processing and Normalization NetRep Permutation Testing Network Module Preservation Across Datasets NetSci Calculates Basic Network Measures Commonly Used in Network Medicine NetSimR Actuarial Functions for Non-Life Insurance Modelling NetSurvProx 'NetSurvProx': Network-Based Survival Analysis via Proximal Methods NetVAR Network Structures in VAR Models NetWeaver Graphic Presentation of Complex Genomic and Network Data Analysis NetworkChange Bayesian Package for Network Changepoint Analysis NetworkComparisonTest Statistical Comparison of Two Networks Based on Several Invariance Measures NetworkComparr Statistical Comparison of Networks NetworkDistance Distance Measures for Networks NetworkExtinction Extinction Simulation in Ecological Networks NetworkInference Inferring Latent Diffusion Networks NetworkReg Generalized Linear Regression Models on Network-Linked Data with Statistical Inference NetworkRiskMeasures Risk Measures for (Financial) Networks NetworkToolbox Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis NeuDist Univariate Continuous Distributions with Model Diagnostics NeuralEstimators Likelihood-Free Parameter Estimation using Neural Networks NeuralNetTools Visualization and Analysis Tools for Neural Networks NeuralSens Sensitivity Analysis of Neural Networks NeuroDataSets A Comprehensive Collection of Neuroscience and Brain-Related Datasets NeuroDecodeR Decode Information from Neural Activity NeutroCODsAnalysis Neutrosophic Analysis Crossover Designs NeutroIBDAnalysis Neutrosophic Analysis of Incomplete Block Designs NeutroRCDsAnalysis Neutrosophic Analysis of Row Column Designs NeutroSplitStripAnalysis Neutrosophic Analysis of Split-Plot and Strip-Plot Designs Newdistns Computes Pdf, Cdf, Quantile and Random Numbers, Measures of Inference for 19 General Families of Distributions NewmanOmics Extending the Newman Studentized Range Statistic to Transcriptomics NiLeDAM Monazite Dating for the NiLeDAM Team NightDay Night and Day Boundary Plot Function NipponMap Japanese Map Data and Functions NitrogenUptake2016 Data and Source Code From: Nitrogen Uptake and Allocation Estimates for Spartina Alterniflora and Distichlis Spicata NlcOptim Solve Nonlinear Optimization with Nonlinear Constraints NlinTS Models for Non Linear Causality Detection in Time Series NlsyLinks Utilities and Kinship Information for Research with the NLSY Nmisc Miscellaneous Functions Used at 'Numeract LLC' Nmix Bayesian Inference on Univariate Normal Mixtures NoSleepR Prevent System Sleep During Long R Tasks NobBS Nowcasting by Bayesian Smoothing NonCompart Noncompartmental Analysis for Pharmacokinetic Data NonNorMvtDist Multivariate Lomax (Pareto Type II) and Its Related Distributions NonParRolCor a Non-Parametric Statistical Significance Test for Rolling Window Correlation NonProbEst Estimation in Nonprobability Sampling NonlinearDiD Staggered Difference-in-Differences with Nonlinear Outcomes NonlinearTSA Nonlinear Time Series Analysis Nonpareil Metagenome Coverage Estimation and Projections for 'Nonpareil' NormData Derivation of Regression-Based Normative Data NormExpression Normalize Gene Expression Data using Evaluated Methods NormPsy Normalisation of Psychometric Tests NormalLaplace The Normal Laplace Distribution NormalityAssessment A Graphical User Interface for Testing Normality Visually NostalgiR Advanced Text-Based Plots NovelDistns Computes PDF, CDF, Quantile, Random Numbers and Measures of Inference for 3 General Families of Distributions NoviceDeveloperResources Resources to Assist Novice Developers NoviceDeveloperResources2 Further Resources to Assist Novice Developers NumericEnsembles Automatically Runs 18 Individual and 14 Ensembles of Models Numero Statistical Framework to Define Subgroups in Complex Datasets NutrienTrackeR Food Composition Information and Dietary Assessment OAIHarvester Harvest Metadata Using OAI-PMH Version 2.0 OBASpatial Objective Bayesian Analysis for Spatial Regression Models OBIC Calculate the Open Bodem Index (OBI) Score OBL Optimum Block Length OBMbpkg Estimate the Population Size for the Mb Capture-Recapture Model OBRE Optimal B-Robust Estimator Tools OBsMD Objective Bayesian Model Discrimination in Follow-Up Designs OCNet Optimal Channel Networks OCSdata Download Data from the 'Open Case Studies' Repository ODMeans OD-Means: k-Means for Origin-Destination ODRF Oblique Decision Random Forest for Classification and Regression ODS Statistical Methods for Outcome-Dependent Sampling Designs ODT Optimal Decision Trees Algorithm ODataQuery Querying on 'OData' OECD Search and Extract Data from the OECD OEFPIL Optimal Estimation of Function Parameters by Iterated Linearization OGI Objective General Index OHPL Ordered Homogeneity Pursuit Lasso for Group Variable Selection OLCPM Online Change Point Detection for Matrix-Valued Time Series OLSengine Transparent and Assisted Linear Modeling Engine OLStrajr Ordinary Least Squares Trajectory Analysis ONAM Fitting Interpretable Neural Additive Models Using Orthogonalization ONEST Observers Needed to Evaluate Subjective Tests OOBCurve Out of Bag Learning Curve OOR Optimistic Optimization in R OORRT Estimator for Optimised Optional Randomised Response Technique OPC The Online Principal Component Estimation Method OPCreg Online Principal Component Regression for Online Datasets OPDOE Optimal Design of Experiments OPI Open Perimetry Interface OPL Optimal Policy Learning OPSR Ordered Probit Switching Regression OPTS Optimization via Subsampling (OPTS) OPTeCD Optimal Partial Tetra-Allele Cross Designs OPTtesting Optimal Testing ORCME Order Restricted Clustering for Microarray Experiments ORFID Manage and Summarize Data from Oregon RFID ORMR and ORSR Antenna Readers ORION Ordinal Relations ORIONZ.G EAP Scoring in Exploratory FA Solutions with Correlated Residuals ORKM The Online Regularized K-Means Clustering Algorithm ORTH.Ord Alternating Logistic Regression with Orthogonalized Residuals for Correlated Ordinal Outcomes ORTSC Connects to Google Cloud API for Label Detection ORscraper Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar' OSAT OSAT: Optimal Sample Assignment Tool OSCARS Global Bounded Optimization by the OSCARS-II Algorithm OSCV One-Sided Cross-Validation OSDR Finds an Optimal System of Distinct Representatives OSFD Output Space-Filling Design OSIRCR Cosine Regression-Based Online Sliced Inverse Regression Algorithm OSLdecomposition Signal Component Analysis for Optically Stimulated Luminescence OSMscale Add a Scale Bar to 'OpenStreetMap' Plots OSNMTF Orthogonal Sparse Non-Negative Matrix Tri-Factorization OSsurvival Assessing Surrogacy with a Censored Outcome OTBsegm Apply Unsupervised Segmentation Algorithms from 'OTB' OTE Optimal Trees Ensembles for Regression, Classification and Class Membership Probability Estimation OTRselect Variable Selection for Optimal Treatment Decision OTUtable North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions OTclust Mean Partition, Uncertainty Assessment, Cluster Validation and Visualization Selection for Cluster Analysis OTrecod Data Fusion using Optimal Transportation Theory OUwie Analysis of Evolutionary Rates in an OU Framework OVL.CI Inference on the Overlap Coefficient OVtool Omitted Variable Tool OWEA Optimal Weight Exchange Algorithm for Optimal Designs for Three Models Oarray Arrays with Arbitrary Offsets OasisR Outright Tool for the Analysis of Spatial Inequalities and Segregation Observation Collect and Process Physical Activity Direct Observation Data OceanView Visualisation of Oceanographic Data and Model Output OddsPlotty Odds Plot to Visualise a Logistic Regression Model OdysseusCharacterizationModule Handy and Minimalistic Common Data Model Characterization OdysseusPathwayModule Cohort Pathway Analysis with Pre-Index Event Support OdysseusSurvivalModule Cohort-Based Single-Event Survival Utilities OenoKPM Modeling the Kinetics of Carbon Dioxide Production in Alcoholic Fermentation OhdsiReportGenerator Observational Health Data Sciences and Informatics Report Generator OhdsiShinyAppBuilder Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules Ohit OGA+HDIC+Trim and High-Dimensional Linear Regression Models OkNNE A k-Nearest Neighbours Ensemble via Optimal Model Selection for Regression OlinkAnalyze Facilitate Analysis of Proteomic Data from Olink OlinkAnalyzeVignettes Vignettes for Analyzing Data using 'OlinkAnalyze' OlympicRshiny 'Shiny' Application for Olympic Data OmegaG Omega-Generic: Composite Reliability of Multidimensional Measures OmicFlow Fast and Efficient (Automated) Analysis of Sparse Omics Data OmicKriging Poly-Omic Prediction of Complex TRaits OmicNavigator Open-Source Software for 'Omic' Data Analysis and Visualization OmicNetR Network-Based Integration of Multi-Omics Data Using Sparse CCA OmicSense Biosensor Development using Omics Data OmicsPLS Data Integration with Two-Way Orthogonal Partial Least Squares OmicsPrepR Unified Preprocessing Toolkit for Proteomics and Metabolomics OmicsQC Nominating Quality Control Outliers in Genomic Profiling Studies Omisc DeFries-Fulker Analysis and Univariate Bootstrapping OmopConstructor Build Tables in the OMOP Common Data Model OmopOnSpark Using a Common Data Model on 'Spark' OmopSketch Characterise Tables of an OMOP Common Data Model Instance OmopStudyBuilder Build Reproducible Network Studies for OMOP Common Data Model OmopViewer Visualise OMOP Results using 'shiny' Applications OnAge Test of Between-Group Differences in the Onset of Senescence OncoDataSets A Comprehensive Collection of Cancer Types and Cancer-Related Datasets OncoSubtype Predict Cancer Subtypes Based on TCGA Data using Machine Learning Method Oncofilterfast Aids in the Analysis of Genes Influencing Cancer Survival Oncotree Estimating Oncogenetic Trees One4All Validate, Share, and Download Data OneArm2stage Phase II Single-Arm Two-Stage Designs with Time-to-Event Outcomes OneArmTTE One-Arm Clinical Trial Designs for Time-to-Event Endpoint OneR One Rule Machine Learning Classification Algorithm with Enhancements OneSampleLogRankTest One-Sample Log-Rank Test OneSampleMR One Sample Mendelian Randomization and Instrumental Variable Analyses OneStep One-Step Estimation OneTwoSamples Deal with One and Two (Normal) Samples OnlineSurr Surrogate Evaluation for Jointly Longitudinal Outcome and Surrogate OnomasticDiversity Onomastic Diversity Measures OofAExp Order-of-Addition Experiments OpEnCAST Optimized Ensemble Model for C and A Methylation Search in Plant OpEnHiMR Optimization Based Ensemble Model for Prediction of Histone Modifications in Rice OpeNoise Environmental Noise Pollution Data Analysis Open.Visualization.Academy Content to Support Classes Taught Through the Open Visualization Academy OpenBARD Open British Arboricultural Record Dataset OpenCL Interface allowing R to use OpenCL OpenImageR An Image Processing Toolkit OpenLand Quantitative Analysis and Visualization of LUCC OpenML Open Machine Learning and Open Data Platform OpenMindat Quickly Retrieve Datasets from the 'Mindat' API OpenMx Extended Structural Equation Modelling OpenRange Code to Access Open Access Species Range Maps OpenRepGrid Tools to Analyze Repertory Grid Data OpenRepGrid.ic Interpretive Clustering for Repertory Grids OpenSourceAP.DownloadR Download Open Source Asset Pricing (OpenAP) Data Directly OpenSpecy Analyze, Process, Identify, and Share Raman and (FT)IR Spectra OpenStreetMap Access to Open Street Map Raster Images Opportunistic Routing Distribution, Broadcasts, Transmissions and Receptions in an Opportunistic Network Opt5PL Optimal Designs for the 5-Parameter Logistic Model OptCirClust Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible OptGS Near-Optimal Group-Sequential Designs for Continuous Outcomes OptHedging Estimation of value and hedging strategy of call and put options. OptHoldoutSize Estimation of Optimal Size for a Holdout Set for Updating a Predictive Score OptM Estimating the Optimal Number of Migration Edges from 'Treemix' OptOTrials Optimal Two-Stage Designs for Ordered Categorical Outcomes OptSig Optimal Level of Significance for Regression and Other Statistical Tests OptSurvCutR Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with 'OptSurvCutR' OptimModel Perform Nonlinear Regression Using 'optim' as the Optimization Engine OptimaRegion Confidence Regions for Optima of Response Surfaces OptimalBinningWoE Optimal Binning and Weight of Evidence Framework for Modeling OptimalCutpoints Computing Optimal Cutpoints in Diagnostic Tests OptimalDesign A Toolbox for Computing Efficient Designs of Experiments OptimalRerandExpDesigns Optimal Rerandomization Experimental Designs OptimalSurrogate Model Free Approach to Quantifying Surrogacy OptimalTiming Optimal Timing Identification OptionPricing Option Pricing with Efficient Simulation Algorithms OralOpioids Retrieving Oral Opioid Information Orangutan Automated Analysis of Phenotypic Data Orcs Omnidirectional R Code Snippets OrdCD Ordinal Causal Discovery OrdFacReg Least Squares, Logistic, and Cox-Regression with Ordered Predictors OrdMonReg Compute Least Squares Estimates of One Bounded or Two Ordered Isotonic Regression Curves OrdNor Concurrent Generation of Ordinal and Normal Data with Given Correlation Matrix and Marginal Distributions OrdinalCompositions Wasserstein-Based Regression for Ordinal Compositional Data OrgHeatmap Visualization Tool for Numerical Data on Human/Mouse Organs and Organelles OrgMassSpecR Organic Mass Spectrometry OrganismDbi Software to enable the smooth interfacing of different database packages OrigamiPlot A Visualization Tool Enhancing Radar Plot Visualizations for Multivariate Data OrthoPanels Dynamic Panel Models with Orthogonal Reparameterization of Fixed Effects OryzaProbe Rice Microarray Probe ID Conversion, from Probe ID to RAP-DB ID OscillatorGenerator Generation of Customizable, Discretized Time Series of Oscillating Species OssaNMA Optimal Sample Size and Allocation with a Network Meta-Analysis Ostats O-Stats, or Pairwise Community-Level Niche Overlap Statistics OtsuFire Fire Scars, Severity and Regeneration Mapping Using 'Otsu' Thresholding OtsuSeg Raster Thresholding Using Otsu´s Algorithm OutSeekR Statistical Approach to Outlier Detection in RNA-Seq and Related Data OutcomeWeights Outcome Weights of Treatment Effect Estimators OutliersLearn Educational Outlier Package with Common Outlier Detection Algorithms OutliersO3 Draws Overview of Outliers (O3) Plots OwenQ Owen Q-Function OxSR Soil Iron Oxides via Diffuse Reflectance OxyBS Processing of Oxy-Bisulfite Microarray Data PAC Partition-Assisted Clustering and Multiple Alignments of Networks PACVr Plastome Assembly Coverage Visualization PADOG Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) PAFit Generative Mechanism Estimation in Temporal Complex Networks PAGE Predictor-Assisted Graphical Models under Error-in-Variables PAGFL Joint Estimation of Latent Groups and Group-Specific Coefficients in (Time-Varying) Panel Data Models PAGWAS Pathway Analysis Methods for Genomewide Association Data PAICE Phylogeographic Analysis of Island Colonization Events PAMhm Generate Heatmaps Based on Partitioning Around Medoids (PAM) PAMmisc Miscellaneous Functions for Passive Acoustic Analysis PAMpal Load and Process Passive Acoustic Data PAMscapes Tools for Summarising and Analysing Soundscape Data PANACEA Personalized Network-Based Anti-Cancer Therapy Evaluation PANPRSnext Building PRS Models Based on Summary Statistics of GWAs PAS Polygenic Analysis System (PAS) PASSED Calculate Power and Sample Size for Two Sample Mean Tests PASWR Probability and Statistics with R PASWR2 Probability and Statistics with R, Second Edition PAutilities Streamline Physical Activity Research PBD Protracted Birth-Death Model of Diversification PBIBD Partially Balanced Incomplete Block Designs PBIR Estimating the Probability of Being in Response and Related Outcomes PBImisc A Set of Datasets Used in My Classes or in the Book 'Modele Liniowe i Mieszane w R, Wraz z Przykladami w Analizie Danych' PBNPA Permutation Based Non-Parametric Analysis of CRISPR Screen Data PBSadmb ADMB for R Using Scripts or GUI PBSddesolve Solver for Delay Differential Equations PBSmapping Mapping Fisheries Data and Spatial Analysis Tools PBSmodelling GUI Tools Made Easy: Interact with Models and Explore Data PBtDesigns Partially Balanced t-Designs (PBtDesigns) PCADSC Tools for Principal Component Analysis-Based Data Structure Comparisons PCAPAM50 Enhanced 'PAM50' Subtyping of Breast Cancer PCAmatchR Match Cases to Controls Based on Genotype Principal Components PCAmixdata Multivariate Analysis of Mixed Data PCBN Inference of Pair-Copula Bayesian Networks PCBS Principal Component BiSulfite PCDimension Finding the Number of Significant Principal Components PCFAM Computation of Ancestry Scores with Mixed Families and Unrelated Individuals PCGII Partial Correlation Graph with Information Incorporation PCGSE Principal Component Gene Set Enrichment PCL Proximal Causal Learning PCLassoReg Group Regression Models for Risk Protein Complex Identification PCMBase Simulation and Likelihood Calculation of Phylogenetic Comparative Models PCMBaseCpp Fast Likelihood Calculation for Phylogenetic Comparative Models PCMRS Model Response Styles in Partial Credit Models PCObw Bandwidth Selector with Penalized Comparison to Overfitting Criterion PCPS Principal Coordinates of Phylogenetic Structure PCRA Companion to Portfolio Construction and Risk Analysis PCRedux Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit as Described in Burdukiewicz (2022) PCS Calculate the Probability of Correct Selection (PCS) PCSinR Parallel Constraint Satisfaction Networks in R PCovR Principal Covariates Regression PCpluS Piecewise Constant Plus Smooth Regression PDE Extract Tables and Sentences from PDFs with User Interface PDEnaiveBayes Plausible Naive Bayes Classifier Using PDE PDFEstimator Multivariate Nonparametric Probability Density Estimator PDIndex Disease Intensity and Progress Curve Indices for Plant Pathology PDM Photogrammetric Distances Measurer PDMIF Fits Heterogeneous Panel Data Models PDN Personalized Disease Network PDQutils PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher Approximations PDSCE Positive Definite Sparse Covariance Estimators PDShiny 'Probability Distribution Shiny' PDXpower Time to Event Outcome in Experimental Designs of Pre-Clinical Studies PDtoolkit Collection of Tools for PD Rating Model Development and Validation PEAXAI Probabilistic Efficiency Analysis Using Explainable Artificial Intelligence PEGroupTesting Population Proportion Estimation using Group Testing PEIMAN2 Post-Translational Modification Enrichment, Integration, and Matching Analysis PEIP Geophysical Inverse Theory and Optimization PELVIS Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae PEPBVS Bayesian Variable Selection using Power-Expected-Posterior Prior PERK Predicting Environmental Concentration and Risk PERMANOVA Multivariate Analysis of Variance Based on Distances and Permutations PERSUADE Parametric Survival Model Selection for Decision-Analytic Models PEkit Partition Exchangeability Toolkit PEtests Power-Enhanced (PE) Tests for High-Dimensional Data PFCI Penalized Fast Causal Inference for High-Dimensional Structure Learning PFIM Population Fisher Information Matrix PFLR Estimating Penalized Functional Linear Regression PFW Filtering and Processing Data from Project FeederWatch PGM2 Recursive Construction of Nested Resolvable Designs and Associated Uniform Designs PGRdup Discover Probable Duplicates in Plant Genetic Resources Collections PGaGEV Power Garima-Generalized Extreme Value Distribution PGaovR Analysis of Experimental Data using ANOVA and Mean Comparison PH1XBAR Phase I Shewhart X-Bar Chart PHENIX Phenotypic Integration Index PHENTHAUproc Phenology Modelling of Thaumetopoea Processionea PHEindicatormethods Common Public Health Statistics and their Confidence Intervals PHInfiniteEstimates Tools for Inference in the Presence of a Monotone Likelihood PHSMM Penalised Maximum Likelihood Estimation for Hidden Semi-Markov Models PHYLOGR Functions for Phylogenetically Based Statistical Analyses PHclust Poisson Hurdle Clustering for Sparse Microbiome Data PHeval Evaluation of the Proportional Hazards Assumption and Test for Comparing Survival Curves with a Standardized Score Process PICBayes Bayesian Models for Partly Interval-Censored Data PIE A Partially Interpretable Model with Black-Box Refinement PINMA Improved Methods for Constructing Prediction Intervals for Network Meta-Analysis PINSPlus Clustering Algorithm for Data Integration and Disease Subtyping PINstimation Estimation of the Probability of Informed Trading PITS Power of Interrupted Time Series (ITS) Studies PJCcalculator PROs-Joint Contrast (PJC) Calculator PJFM Variational Inference for High-Dimensional Joint Frailty Model PK Basic Non-Compartmental Pharmacokinetics PKI Public Key Infrastucture for R Based on the X.509 Standard PKLMtest Classification Based MCAR Test PKNCA Perform Pharmacokinetic Non-Compartmental Analysis PKPDindex Optimal PK/PD Index Finder PKPDsim Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations PKbioanalysis Pharmacokinetic Bioanalysis Experiments Design and Exploration PKconverter The Parameter Converter of the Pharmacokinetic Models PL94171 Tabulate P.L. 94-171 Redistricting Data Summary Files PLEXI Multiplex Network Analysis PLFD Portmanteau Local Feature Discrimination for Matrix-Variate Data PLIS Multiplicity Control using Pooled LIS Statistic PLNmodels Poisson Lognormal Models PLORN Prediction with Less Overfitting and Robust to Noise PLRModels Statistical Inference in Partial Linear Regression Models PLUCR Policy Learning Under Constraint PLindleyROC Receiver Operating Characteristic Based on Power Lindley Distribution PLmixed Estimate (Generalized) Linear Mixed Models with Factor Structures PLreg Power Logit Regression for Modeling Bounded Data PMA Penalized Multivariate Analysis PMCMR Calculate Pairwise Multiple Comparisons of Mean Rank Sums PMCMRplus Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended PMEvapotranspiration Calculation of the Penman-Monteith Evapotranspiration using Weather Variables PMLE4SCR Pseudo Maximum Likelihood Estimation for Semi-Competing Risks Data PMwR Portfolio Management with R PNADCperiods Identify Reference Periods in Brazil's PNADC Survey Data PNADcIBGE Downloading, Reading and Analyzing PNADC Microdata PNAR Poisson Network Autoregressive Models PNC Phylogenetic Niche Conservatism Analysis for Ecological Communities PND.heter.cluster Estimating the Cluster Specific Treatment Effects in Partially Nested Designs PNDSIBGE Downloading, Reading and Analyzing PNDS Microdata - Package in Development PNSIBGE Downloading, Reading and Analyzing PNS Microdata PNWColors Color Palettes Inspired by Nature in the US Pacific Northwest POCRE Penalized Orthogonal-Components Regression POD Probability of Detection for Qualitative PCR Methods POET Principal Orthogonal ComplEment Thresholding (POET) Method POINT Protein Structure Guided Local Test POMADE Power for Meta-Analysis of Dependent Effects POMS Phylogenetic Organization of Metagenomic Signals POMaSPU Adaptive Association Tests for Multiple Phenotypes using Proportional Odds Model (POM-aSPU) PONG2 KIR Genotype Imputation and Model Training from SNP Array Data POPInf Assumption-Lean and Data-Adaptive Post-Prediction Inference POSSA Power Simulation for Sequential Analyses and Multiple Hypotheses POSTm Phylogeny-Guided OTU-Specific Association Test for Microbiome Data POSetR Partially Ordered Sets in R POT Generalized Pareto Distribution and Peaks Over Threshold POV Partition of Variation Variance Component Analysis Method PP Person Parameter Estimation PPCDT An Optimal Subset Selection for Distributed Hypothesis Testing PPCI Projection Pursuit for Cluster Identification PPCSexRx Prescribe Sub-Symptom Exercise for Adolescent Concussion PPMR Probabilistic Two Sample Mendelian Randomization PPMiss Copula-Based Estimator for Long-Range Dependent Processes under Missing Data PPQplan Process Performance Qualification (PPQ) Plans in Chemistry, Manufacturing and Controls (CMC) Statistical Analysis PPRL Privacy Preserving Record Linkage PPSFS Partial Profile Score Feature Selection in High-Dimensional Generalized Linear Interaction Models PPTS Point Process Time Series PPTcirc Projected Polya Tree for Circular Data PPbigdata Projection Pursuit for Big Data Based on Data Nuggets PPforest Projection Pursuit Classification Forest PPtreeExt Projection Pursuit Classification Tree Extensions PPtreeViz Projection Pursuit Classification Tree Visualization PQA Perform the Pearson-Quetelet Analysis on Two-Way Contingency Tables PRANA Pseudo-Value Regression Approach for Network Analysis (PRANA) PRBMSdesigns Partially Residual Balanced Multi-Session Designs PRDA Conduct a Prospective or Retrospective Design Analysis PRECAST Embedding and Clustering with Alignment for Spatial Omics Datasets PREPShiny Interactive Document for Preprocessing the Dataset PRIMAL Parametric Simplex Method for Sparse Learning PRIMEplus Study Design for Immunotherapy Clinical Trials PRISM.forecast Penalized Regression with Inferred Seasonality Module - Forecasting Unemployment Initial Claims using 'Google Trends' Data PRISMA Protocol Inspection and State Machine Analysis PRISMA2020 Make Interactive 'PRISMA' Flow Diagrams PRMethods D-Hondt, Sainte-Lague, and Modified Sainte-Lague Methods for Seat Allocation PRNG A Pseudo-Random Number Generator PROJ Generic Coordinate System Transformations Using 'PROJ' PROMETHEE Preference Ranking Organization METHod for Enrichment of Evaluations PROSPER Simulation of Weed Population Dynamics PROreg Patient Reported Outcomes Regression Analysis PROscorer Functions to Score Commonly-Used Patient-Reported Outcome (PRO) Measures and Other Psychometric Instruments PROscorerTools Tools to Score Patient-Reported Outcome (PRO) and Other Psychometric Measures PROsetta Linking Patient-Reported Outcomes Measures PRP Bayesian Prior and Posterior Predictive Replication Assessment PRROC Precision-Recall and ROC Curves for Weighted and Unweighted Data PRTree Probabilistic Regression Trees PReMiuM Dirichlet Process Bayesian Clustering, Profile Regression PResiduals Probability-Scale Residuals and Residual Correlations PSAWR 'Pushshift' API Wrapper for 'Reddit' Submission and Comment Search PSAboot Bootstrapping for Propensity Score Analysis PSAgraphics Propensity Score Analysis Graphics PSCBS Analysis of Parent-Specific DNA Copy Numbers PSDistr Distributions Derived from Normal Distribution PSF Forecasting of Univariate Time Series Using the Pattern Sequence-Based Forecasting (PSF) Algorithm PSGD Projected Subset Gradient Descent PSGoft Modified Lilliefors Goodness-of-Fit Normality Test PSIM Preference Selection Index Method (PSIM) PSIndependenceTest Independence Tests for Two-Way, Three-Way and Four-Way Contingency Tables PSLM2015 Pakistan Social and Living Standards Measurement Survey 2014-15 PSMatch Handling and Managing Peptide Spectrum Matches PSPI Propensity Score Predictive Inference for Generalizability PSPManalysis Analysis of Physiologically Structured Population Models PSRICalc Plant Stress Response Index Calculator PSRICalcSM Plant Stress Response Index Calculator - Softmax Method PSSIM Test of Independence & Image Structural Similarity Measure PSSIM PSSMCOOL Features Extracted from Position Specific Scoring Matrix (PSSM) PSTR Panel Smooth Transition Regression Modelling PSW Propensity Score Weighting Methods for Dichotomous Treatments PScr Estimation for the Power Series Cure Rate Model PSinference Inference for Released Plug-in Sampling Synthetic Dataset PSor Semiparametric Principal Stratification Analysis Beyond Monotonicity PSpower Sample Size and Power for Propensity Score Weighted Estimators PSsurvival Propensity Score Methods for Survival Analysis PStrata Principal Stratification Analysis in R PSweight Propensity Score Weighting for Causal Inference with Observational Studies and Randomized Trials PTAk Principal Tensor Analysis on k Modes PTE Personalized Treatment Evaluator PTERP PTE and RP for Optimally-Transformed Surrogate PTMods Managing Post-Translational Modifications in R PTSDdiag Optimize PTSD Diagnostic Criteria PTSR Positive Time Series Regression PTXQC Quality Report Generation for MaxQuant and mzTab Results PTwins Percentile Estimation of Fetal Weight for Twins by Chorionicity PUGMM Parsimonious Ultrametric Gaussian Mixture Models PUMP Power Under Multiplicity Project PUPAK Parameter Estimation, and Plot Visualization of Adsorption Kinetic Models PUPMCR Image-Based Identification of Color Based on Rayner (1970) Terminology and Known Fungal Pigments PUPMSI Moisture Sorption Isotherm Modeling Program PUlasso High-Dimensional Variable Selection with Presence-Only Data PVAClone Population Viability Analysis with Data Cloning PVBcorrect Partial Verification Bias Correction for Diagnostic Accuracy PVR Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve PWEALL Design and Monitoring of Survival Trials Accounting for Complex Situations PWEV PSO Based Weighted Ensemble Algorithm for Volatility Modelling PWEXP Piecewise Exponential Distribution Prediction Model PWIR Provides a Function to Calculate Prize Winner Indices Based on Bibliometric Data PaLMr Interface for 'Google Pathways Language Model 2 (PaLM 2)' PaRe A Way to Perform Code Review or QA on Other Packages PacketLLM AI Assistant Gadget for 'RStudio' Pade Padé Approximant Coefficients PairViz Visualization using Graph Traversal PairedData Paired Data Analysis PakPC2017 Pakistan Population Census 2017 PakPC2023 Pakistan Population Census 2023 PakPMICS2014Ch Multiple Indicator Cluster Survey (MICS) 2014 Child Questionnaire Data for Punjab, Pakistan PakPMICS2014HH Multiple Indicator Cluster Survey (MICS) 2014 Household Questionnaire Data for Punjab, Pakistan PakPMICS2014HL Multiple Indicator Cluster Survey (MICS) 2014 Household Listing Questionnaire Data for Punjab, Pakistan PakPMICS2014Wm Multiple Indicator Cluster Survey (MICS) 2014 Women Questionnaire Data for Punjab, Pakistan PakPMICS2018 Multiple Indicator Cluster Survey (MICS) 2017-18 Data for Punjab, Pakistan PakPMICS2018bh Multiple Indicator Cluster Survey (MICS) 2017-18 Birth History of Children Questionnaire Data for Punjab, Pakistan PakPMICS2018fs Multiple Indicator Cluster Survey (MICS) 2017-18 Children Age 5-17 Questionnaire Data for Punjab, Pakistan PakPMICS2018hh Multiple Indicator Cluster Survey (MICS) 2017-18 Household Questionnaire Data for Punjab, Pakistan PakPMICS2018mm Multiple Indicator Cluster Survey (MICS) 2017-18 Maternal Mortality Questionnaire Data for Punjab, Pakistan PakPMICS2018mn Multiple Indicator Cluster Survey (MICS) 2017-18 Men Questionnaire Data for Punjab, Pakistan PamBinaries Read and Process 'Pamguard' Binary Data PanJen A Semi-Parametric Test for Specifying Functional Form PanelCount Random Effects and/or Sample Selection Models for Panel Count Data PanelMatch Matching Methods for Causal Inference with Time-Series Cross-Sectional Data PanelSelect Panel Sample Selection Models PanelTM Two- And Three-Way Dynamic Panel Threshold Regression Model for Change Point Detection PantaRhei Plots Sankey Diagrams ParCC Parameter Converter and Calculator for Health Technology Assessment ParDNAcopy Parallel implementation of the "segment" function of package "DNAcopy" ParallelLogger Support for Parallel Computation, Logging, and Function Automation ParallelTree Visualizing Multilevel Data with Parallel Tree Plots ParamANOVA Fully Parameterizable ANOVA Tests ParamHelpers Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning Pareto The Pareto, Piecewise Pareto and Generalized Pareto Distribution ParetoPosStable Computing, Fitting and Validating the PPS Distribution Paris2024Colours Color Palettes Inspired by Paris 2024 Olympic and Paralympic Games ParmOff Complex Argument Matching PartCensReg Estimation and Diagnostics for Partially Linear Censored Regression Models Based on Heavy-Tailed Distributions PartialNetwork Estimating Peer Effects Using Partial Network Data PartialTL Partial Transfer Learning for Causal Estimation Partiallyoverlapping Partially Overlapping Samples Tests Path.Analysis Path Coefficient Analysis PathwaySpace Spatial Projection of Network Signals along Geodesic Paths PathwayVote Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting PatientGenerator Generator of Synthetic Patient Data for the OMOP Common Data Model PatientLevelPrediction Develop Clinical Prediction Models Using the Common Data Model PatientProfiles Identify Characteristics of Patients in the OMOP Common Data Model Patterns Deciphering Biological Networks with Patterned Heterogeneous Measurements PeakError Compute the Label Error of Peak Calls PeakSegDP Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data PeakSegDisk Disk-Based Constrained Change-Point Detection PeakSegJoint Joint Peak Detection in Several ChIP-Seq Samples PeakSegOptimal Optimal Segmentation Subject to Up-Down Constraints PearsonDS Pearson Distribution System PearsonICA Independent Component Analysis using Score Functions from the Pearson System Pedixplorer Pedigree Functions PeerPerformance Luck-Corrected Peer Performance Analysis in R PenCoxFrail Regularization in Cox Frailty Models PenIC Semiparametric Regression Analysis of Interval-Censored Data using Penalized Splines PenguinR A Comprehensive Collection of Penguin Datasets for Statistical Analysis and Experimental Design PepMapViz A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration Peptides Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences PerFit Person Fit PerMat Performance Metrics in Predictive Modeling PerRegMod Fitting Periodic Coefficients Linear Regression Models Perc Using Percolation and Conductance to Find Information Flow Certainty in a Direct Network PerfMeas Performance Measures for Ranking and Classification Tasks PerformanceAnalytics Econometric Tools for Performance and Risk Analysis PeriodicTable Periodic Table of the Elements PermAlgo Permutational Algorithm to Simulate Survival Data PermCor Robust Permutation Tests of Correlation Coefficients PermutationR Conduct Permutation Analysis of Variance in R PersomicsArray Automated Persomics Array Image Extraction PeruAPIs Access Peruvian Data via Public APIs and Curated Datasets PesticideLoadIndicator Computes Danish Pesticide Load Indicator PhaseGMM Phase-Function Based Estimation and Inference for Linear Errors-in-Variables (EIV) Models PhaseType Inference for Phase-Type Distributions PhaseTypeR General-Purpose Phase-Type Functions PheCAP High-Throughput Phenotyping with EHR using a Common Automated Pipeline PheNorm Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data PheVis Automatic Phenotyping of Electronic Health Record at Visit Resolution PhenoSpectra Multispectral Data Analysis and Visualization Phenotype A Tool for Phenotypic Data Processing PhenotypeR Assess Study Cohorts Using a Common Data Model Phi2rho Owen's T Function and Bivariate Normal Integral PhilipsHue R Interface to the Philips Hue API PhoneValidator Client for 'GenderAPI.io' Phone Number Validation and Formatter API PhotoGEA Photosynthetic Gas Exchange Analysis PhotosynQ Connect to PhotosynQ PhySortR A Fast, Flexible Tool for Sorting Phylogenetic Trees PhylogeneticEM Automatic Shift Detection using a Phylogenetic EM PhysActBedRest Marks Periods of 'Bedrest' in Actigraph Accelerometer Data PhysicalActivity Process Accelerometer Data for Physical Activity Measurement PhysioIndexR Physiological and Stress Indices for Crop Evaluation PhytoIn Vegetation Analysis and Forest Inventory PhytosanitaryCalculator Phytosanitary Calculator for Inspection Plans Based on Risks PiC Interactive Processing and Segmentation of Forest TLS Point-Cloud Data PieGlyph Axis Invariant Scatter Pie Plots Pijavski Global Univariate Minimization Pinference Probability Inference for Propositional Logic PivotalP Prediction for Future Data from Mixture Distributions Gamma, Beta, Weibull and Normal PlackettLuce Plackett-Luce Models for Rankings Planesmuestra Functions for Calculating Dodge Romig, MIL STD 105E and MIL STD 414 Acceptance Sampling Plan PlanetNICFI Processing of the 'Planet NICFI' Satellite Imagery PlasmaMutationDetector Tumor Mutation Detection in Plasma PlateVision Automated qPCR Analysis and Visual Quality Control PlatformDesign Optimal Two-Period Multiarm Platform Design with New Experimental Arms Added During the Trial PlayerChart Generate Pizza Chart: Player Stats 0-100 PlayerRatings Dynamic Updating Methods for Player Ratings Estimation PlotBivInvGaus Density Contour Plot for Bivariate Inverse Gaussian Distribution PlotContour Plot Contour Line PlotFTIR Plot FTIR Spectra PlotNormTest Graphical Univariate/Multivariate Assessments for Normality Assumption PlotPrjNetworks Useful Networking Tools for Project Management PlotTools Extended Tools for Continuous Legends, Polygon Manipulation, and Visual Display of Categorical Data PnT Peak Finder PoDBAY Vaccine Efficacy Estimation Package PoPdesign Posterior Predictive (PoP) Design for Phase I Clinical Trials PoSI Valid Post-Selection Inference for Linear LS Regression PoSIAdjRSquared Post-Selection Inference for Adjusted R Squared PogromcyDanych DataCrunchers (PogromcyDanych) is the Massive Online Open Course that Brings R and Statistics to the People PoiClaClu Classification and Clustering of Sequencing Data Based on a Poisson Model PointFore Interpretation of Point Forecasts as State-Dependent Quantiles and Expectiles PointedSDMs Fit Models Derived from Point Processes to Species Distributions using 'inlabru' PoisBinNonNor Data Generation with Poisson, Binary and Continuous Components PoisBinOrd Data Generation with Poisson, Binary and Ordinal Components PoisBinOrdNonNor Generation of Up to Four Different Types of Variables PoisBinOrdNor Data Generation with Poisson, Binary, Ordinal and Normal Components PoisNonNor Simultaneous Generation of Count and Continuous Data PoisNor Simultaneous Generation of Multivariate Data with Poisson and Normal Marginals PoissonBinomial Efficient Computation of Ordinary and Generalised Poisson Binomial Distributions PoissonMultinomial The Poisson-Multinomial Distribution PoissonPCA Poisson-Noise Corrected PCA PolarCAP Access the Polarization in Comparative Attitudes Project PolicyPortfolios Tools for Managing, Measuring and Visualizing Policy Portfolios PolisheR Interfacing 'NaileR' with 'Shiny' Poly4AT Access 'INVEKOS' API for Field Polygons PolyHaplotyper Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids PolyMigR Analysis of Polyphenol Migration from Packaging Films PolyPatEx Paternity Exclusion in Autopolyploid Species PolyTree Estimate Causal Polytree from Data Polychrome Qualitative Palettes with Many Colors PolycrossDesigns Polycross Designs ("PolycrossDesigns") PolynomF Polynomials in R Pomic Pattern Oriented Modelling Information Criterion PoolBal Balancing Central and Marginal Rejection of Pooled p-Values PoolDilutionR Calculate Gross Biogeochemical Flux Rates from Isotope Pool Dilution Data PooledCohort Predicted Risk for CVD using Pooled Cohort Equations, PREVENT Equations, and Other Contemporary CVD Risk Calculators PooledMeanGroup Pooled Mean Group Estimation of Dynamic Heterogenous Panels PopComm Population-Level Cell-Cell Communication Analysis Tools PopED Population (and Individual) Optimal Experimental Design PopGenHelpR Streamline Population Genomic and Genetic Analyses PopGenReport A Simple Framework to Analyse Population and Landscape Genetic Data PopPsiSeqR Process and Visualize Evolve & Resequence Experiments PopVar Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation PopulateR Create Data Frames for the Micro-Simulation of Human Populations PopulationGrowthR Linear Population Growth Scenarios PortalHacienda Acceder Con R a Los Datos Del Portal De Hacienda PortfolioAnalytics Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios PortfolioOptim Small/Large Sample Portfolio Optimization PortfolioTesteR Test Investment Strategies with English-Like Code PosRatioDist Quotient of Random Variables Conditioned to the Positive Quadrant PosiR Post-Selection Inference via Simultaneous Confidence Intervals PostcodesioR API Wrapper Around 'Postcodes.io' PosteriorBootstrap Non-Parametric Sampling with Parallel Monte Carlo PottsUtils Utility Functions of the Potts Models PowRPriori Power Analysis via Data Simulation for (Generalized) Linear Mixed Effects Models PoweR Computation of Power and Level Tables for Hypothesis Tests PoweREST A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics Power2Stage Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies PowerSDI Calculate Standardised Drought Indices Using NASA POWER Data PowerTOST Power and Sample Size for (Bio)Equivalence Studies PrInDT Prediction and Interpretation in Decision Trees for Classification and Regression PracTools Designing and Weighting Survey Samples PracticalEquiDesign Design of Practical Equivalence Trials PreKnitPostHTMLRender Pre-Knitting Processing and Post HTML-Rendering Processing PreProcess Basic Functions for Pre-Processing Microarrays PreProcessRecordLinkage Preprocessing Record Linkage PreProcessing Various Preprocessing Transformations of Numeric Data Matrices PreciseSums Accurate Floating Point Sums and Products PredPsych Predictive Approaches in Psychology PredTest Preparing Data For, and Calculating the Prediction Test PredictABEL Assessment of Risk Prediction Models PredictionR Prediction for Future Data from any Continuous Distribution PredictorSelect Out-of-Sample Predictability in Predictive Regressions with Many Predictor Candidates PresenceAbsence Presence-Absence Model Evaluation PressPurt Indeterminacy of Networks via Press Perturbations PrettyCols Pretty Colour Palettes PriceIndices Calculating Bilateral and Multilateral Price Indexes PriorGen Generates Prior Distributions for Proportions PrivateLR Differentially Private Regularized Logistic Regression ProAE PRO-CTCAE Scoring, Analysis, and Graphical Tools ProActive Detect Elevations and Gaps in Mapped Sequencing Read Coverage ProDenICA Product Density Estimation for ICA using Tilted Gaussian Density Estimates ProFAST Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction ProPublicaR Access Functions for ProPublica's APIs ProSGPV Penalized Regression with Second-Generation P-Values ProSportsDraftData Professional Sports Draft Data ProTrackR Manipulate and Play 'ProTracker' Modules ProTrackR2 Manipulate and Play 'ProTracker' Modules ProbBayes Probability and Bayesian Modeling ProbBreed Probability Theory for Selecting Candidates in Plant Breeding ProbMarg Computing Logit & Probit Predicted Probabilities & Marginal Effects ProbSVMs Probabilistic Support Vector Machines ProbSamplingI Probabilistic Sampling Design and Strategies ProbYX Inference for the Stress-Strength Model R = P(Y