
A3  Accurate, Adaptable, and Accessible Error Metrics for Predictive
Models 
abbyyR  Access to Abbyy Optical Character Recognition (OCR) API 
abc  Tools for Approximate Bayesian Computation (ABC) 
ABCanalysis  Computed ABC Analysis 
abc.data  Data Only: Tools for Approximate Bayesian Computation (ABC) 
abcdeFBA  ABCDE_FBA: ABiologistCanDoEverything of Flux Balance
Analysis with this package 
ABCoptim  Implementation of Artificial Bee Colony (ABC) Optimization 
ABCp2  Approximate Bayesian Computational Model for Estimating P2 
abcrf  Approximate Bayesian Computation via Random Forests 
abctools  Tools for ABC Analyses 
abd  The Analysis of Biological Data 
abf2  Load GapFree Axon ABF2 Files 
ABHgenotypeR  Easy Visualization of ABH Genotypes 
abind  Combine Multidimensional Arrays 
abn  Modelling Multivariate Data with Additive Bayesian Networks 
abodOutlier  AngleBased Outlier Detection 
AbsFilterGSEA  Improved False Positive Control of GenePermuting GSEA with
Absolute Filtering 
abundant  Abundant regression and highdimensional principal fitted
components 
ACA  Abrupt ChangePoint or Aberration Detection in Point Series 
acc  Functions for Processing and Analyzing Accelerometer Data 
accelerometry  Functions for Processing MinutetoMinute Accelerometer Data 
accelmissing  Missing Value Imputation for Accelerometer Data 
AcceptanceSampling  Creation and Evaluation of Acceptance Sampling Plans 
ACCLMA  ACC & LMA Graph Plotting 
accrual  Bayesian Accrual Prediction 
accrued  Data Quality Visualization Tools for Partially Accruing Data 
ACD  Categorical data analysis with complete or missing responses 
ACDm  Tools for Autoregressive Conditional Duration Models 
acepack  ace() and avas() for selecting regression transformations 
ACEt  Estimating Dynamic Heritability and Twin Model Comparison 
acid  Analysing Conditional Income Distributions 
acm4r  AlignandCount Method comparisons of RFLP data 
acmeR  Implements ACME Estimator of Bird and Bat Mortality by Wind
Turbines 
ACNE  Affymetrix SNP ProbeSummarization using NonNegative Matrix
Factorization 
acnr  Annotated CopyNumber Regions 
acopula  Modelling dependence with multivariate Archimax (or any
userdefined continuous) copulas 
acp  Autoregressive Conditional Poisson 
aCRM  Convenience functions for analytical Customer Relationship
Management 
acs  Download, Manipulate, and Present American Community Survey and
Decennial Data from the US Census 
ACSNMineR  Gene Enrichment Analysis from ACSN Maps or GMT Files 
acss  Algorithmic Complexity for Short Strings 
acss.data  Data Only: Algorithmic Complexity of Short Strings (Computed via
Coding Theorem Method) 
ACSWR  A Companion Package for the Book "A Course in Statistics with R" 
ACTCD  Asymptotic Classification Theory for Cognitive Diagnosis 
Actigraphy  Actigraphy Data Analysis 
activity  Animal Activity Statistics 
activpalProcessing  Process activPAL Events Files 
actuar  Actuarial Functions and Heavy Tailed Distributions 
ActuDistns  Functions for actuarial scientists 
ada  The R Package Ada for Stochastic Boosting 
adabag  Applies Multiclass AdaBoost.M1, SAMME and Bagging 
adagio  Discrete and Global Optimization Routines 
AdapEnetClass  A Class of Adaptive Elastic Net Methods for Censored Data 
adaptDA  Adaptive Mixture Discriminant Analysis 
AdaptFit  Adaptive Semiparametic Regression 
AdaptFitOS  Adaptive Semiparametric Regression with Simultaneous Confidence
Bands 
AdaptGauss  Gaussian Mixture Models (GMM) 
AdaptiveSparsity  Adaptive Sparsity Models 
adaptivetau  Tauleaping stochastic simulation 
adaptMCMC  Implementation of a generic adaptive Monte Carlo Markov Chain
sampler 
adaptsmoFMRI  Adaptive Smoothing of FMRI Data 
adaptTest  Adaptive twostage tests 
addhaz  Binomial and Multinomial Additive Hazards Models 
addhazard  Fit Additive Hazards Models for Survival Analysis 
addinslist  Discover and Install Useful RStudio Addins 
additivityTests  Additivity Tests in the Two Way Anova with Single Subclass
Numbers 
addreg  Additive Regression for Discrete Data 
ADDT  A Package for Analysis of Accelerated Destructive Degradation
Test Data 
ade4  Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences 
ade4TkGUI  'ade4' Tcl/Tk Graphical User Interface 
adegenet  Exploratory Analysis of Genetic and Genomic Data 
adegraphics  An S4 LatticeBased Package for the Representation of
Multivariate Data 
adehabitat  Analysis of Habitat Selection by Animals 
adehabitatHR  Home Range Estimation 
adehabitatHS  Analysis of Habitat Selection by Animals 
adehabitatLT  Analysis of Animal Movements 
adehabitatMA  Tools to Deal with Raster Maps 
adephylo  adephylo: exploratory analyses for the phylogenetic comparative
method 
AdequacyModel  Adequacy of Probabilistic Models and General Purpose
Optimization 
adespatial  Multivariate Multiscale Spatial Analysis 
ADGofTest  AndersonDarling GoF test 
adhoc  calculate ad hoc distance thresholds for DNA barcoding
identification 
adimpro  Adaptive Smoothing of Digital Images 
adlift  An adaptive lifting scheme algorithm 
ADM3  An Interpretation of the ADM method  automated detection
algorithm 
AdMit  Adaptive Mixture of Studentt distributions 
admixturegraph  Admixture Graph Manipulation and Fitting 
ADMMnet  Regularized Model with Selecting the Number of NonZeros 
ADPclust  Fast Clustering Using Adaptive Density Peak Detection 
ads  Spatial point patterns analysis 
AdvBinomApps  Upper ClopperPearson Confidence Limits for Burnin Studies
under Additional Available Information 
adwave  Wavelet Analysis of Genomic Data from Admixed Populations 
AEDForecasting  Change Point Analysis in ARIMA Forecasting 
aemo  Download and process AEMO price and demand data 
AER  Applied Econometrics with R 
AF  ModelBased Estimation of ConfounderAdjusted Attributable
Fractions 
afex  Analysis of Factorial Experiments 
AFLPsim  Hybrid Simulation and Genome Scan for Dominant Markers 
AFM  Atomic Force Microscope Image Analysis 
after  Run Code in the Background 
aftgee  Accelerated Failure Time Model with Generalized Estimating
Equations 
AGD  Analysis of Growth Data 
AggregateR  Aggregate Numeric, Date and Categorical Variables by an ID 
agop  Aggregation Operators and Preordered Sets 
agRee  Various Methods for Measuring Agreement 
Agreement  Statistical Tools for Measuring Agreement 
agricolae  Statistical Procedures for Agricultural Research 
agridat  Agricultural Datasets 
agrmt  Calculate Agreement or Consensus in Ordered Rating Scales 
AGSDest  Estimation in Adaptive Group Sequential Trials 
agsemisc  Miscellaneous plotting and utility functions 
ahaz  Regularization for semiparametric additive hazards regression 
ahp  Analytic Hierarchy Process 
AHR  Estimation and Testing of Average Hazard Ratios 
AICcmodavg  Model Selection and Multimodel Inference Based on (Q)AIC(c) 
AID  Estimation of BoxCox Power Transformation Parameter 
aidar  Tools for reading AIDA (http://aida.freehep.org/) files into R 
AIM  AIM: adaptive index model 
aimPlot  Create Pie Like Plot for Completeness 
Ake  Associated Kernel Estimations 
akima  Interpolation of Irregularly and Regularly Spaced Data 
akmeans  Adaptive Kmeans algorithm based on threshold 
alabama  Constrained Nonlinear Optimization 
alakazam  Immunoglobulin Clonal Lineage and Diversity Analysis 
ald  The Asymmetric Laplace Distribution 
ALDqr  Quantile Regression Using Asymmetric Laplace Distribution 
aLFQ  Estimating Absolute Protein Quantities from LabelFree LCMS/MS
Proteomics Data 
AlgDesign  Algorithmic Experimental Design 
AlgebraicHaploPackage  Haplotype Two Snips Out of a Paired Group of Patients 
algstat  Algebraic statistics in R 
AlignStat  Comparison of Alternative Multiple Sequence Alignments 
alineR  Alignment of Phonetic Sequences Using the 'ALINE' Algorithm 
ALKr  Generate AgeLength Keys for fish populations 
allan  Automated Large Linear Analysis Node 
allanvar  Allan Variance Analysis 
alleHap  Allele Imputation and Haplotype Reconstruction from Pedigree
Databases 
allelematch  Identifying unique multilocus genotypes where genotyping error
and missing data may be present 
AlleleRetain  Allele Retention, Inbreeding, and Demography 
allelic  A fast, unbiased and exact allelic exact test 
AllPossibleSpellings  Computes all of a word's possible spellings 
alm  R Client for the Lagotto Altmetrics Platform 
alphahull  Generalization of the Convex Hull of a Sample of Points in the
Plane 
alphaOutlier  Obtain AlphaOutlier Regions for WellKnown Probability
Distributions 
alphashape3d  Implementation of the 3D AlphaShape for the Reconstruction of
3D Sets from a Point Cloud 
alr3  Data to accompany Applied Linear Regression 3rd edition 
alr4  Data to accompany Applied Linear Regression 4rd edition 
ALS  Multivariate Curve Resolution Alternating Least Squares
(MCRALS) 
ALSCPC  Accelerated line search algorithm for simultaneous orthogonal
transformation of several positive definite symmetric matrices
to nearly diagonal form 
altmeta  Alternative MetaAnalysis Methods 
ALTopt  Optimal Experimental Designs for Accelerated Life Testing 
amap  Another Multidimensional Analysis Package 
AMAP.Seq  Compare Gene Expressions from 2Treatment RNASeq Experiments 
AMCP  A Multiple Comparison Perspective 
ameco  European Commission Annual MacroEconomic (AMECO) Database 
amei  Adaptive Management of Epidemiological Interventions 
Amelia  A Program for Missing Data 
amen  Additive and Multiplicative Effects Models for Networks and
Relational Data 
AmericanCallOpt  This package includes pricing function for selected American
call options with underlying assets that generate payouts 
AMGET  Postprocessing tool for ADAPT 5 
aml  Adaptive Mixed LASSO 
AMOEBA  A Multidirectional Optimum EcotopeBased Algorithm 
AMORE  A MORE flexible neural network package 
AmostraBrasil  Generates Samples or Complete List of Brazilian IBGE (Instituto
Brasileiro De Geografia e Estatistica) Census Households,
Geocoding it by Google Maps 
AmpliconDuo  Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts 
anacor  Simple and Canonical Correspondence Analysis 
analogsea  Interface to 'Digital Ocean' 
analogue  Analogue and Weighted Averaging Methods for Palaeoecology 
analogueExtra  Additional Functions for Use with the Analogue Package 
analyz  Model Layer for Automatic Data Analysis via CSV File
Interpretation 
AnalyzeFMRI  Functions for analysis of fMRI datasets stored in the ANALYZE or
NIFTI format 
AnalyzeTS  Analyze (Fuzzy) Time Series 
anapuce  Tools for microarray data analysis 
AncestryMapper  Assigning Ancestry Based on Population References 
anchors  Statistical analysis of surveys with anchoring vignettes 
AnDE  An extended Bayesian Learning Technique developed by Dr. Geoff
Webb 
andrews  Andrews curves 
anesrake  ANES Raking Implementation 
anfis  Adaptive Neuro Fuzzy Inference System in R 
AnglerCreelSurveySimulation  Simulate a Bus Route Creel Survey of Anglers 
animalTrack  Animal track reconstruction for high frequency 2dimensional
(2D) or 3dimensional (3D) movement data 
animation  A Gallery of Animations in Statistics and Utilities to Create
Animations 
anim.plots  Simple Animated Plots For R 
ANLP  Build Text Prediction Model 
AnnotLists  AnnotLists: A tool to annotate multiple lists from a specific
annotation file 
anoint  Analysis of Interactions 
ANOM  Analysis of Means 
anominate  alphaNOMINATE Ideal Point Estimator 
anonymizer  Anonymize Data Containing Personally Identifiable Information 
AntAngiCool  AntiAngiogenic 
AnthropMMD  A GUI for Mean Measures of Divergence 
Anthropometry  Statistical Methods for Anthropometric Data 
antitrust  Tools for Antitrust Practitioners 
AntWeb  programmatic interface to the AntWeb 
aod  Analysis of Overdispersed Data 
aods3  Analysis of Overdispersed Data using S3 methods 
aoos  Another Object Orientation System 
aop  Adverse Outcome Pathway Analysis 
aoristic  aoristic analysis with spatial output (kml) 
ApacheLogProcessor  Process the Apache Web Server Log Combined Files 
apaStyle  Generate APA Tables for MS Word 
apaTables  Create American Psychological Association (APA) Style Tables 
apc  AgePeriodCohort Analysis 
apcluster  Affinity Propagation Clustering 
ape  Analyses of Phylogenetics and Evolution 
apex  Phylogenetic Methods for Multiple Gene Data 
aplore3  Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic
Regression" (3rd ed.) 
aplpack  Another Plot PACKage: stem.leaf, bagplot, faces, spin3R,
plotsummary, plothulls, and some slider functions 
apmsWAPP  Pre and Postprocessing for APMS data analysis based on
spectral counts 
appell  Compute Appell's F1 hypergeometric function 
apple  Approximate Path for Penalized Likelihood Estimators 
AppliedPredictiveModeling  Functions and Data Sets for 'Applied Predictive Modeling' 
appnn  Amyloid Propensity Prediction Neural Network 
approximator  Bayesian prediction of complex computer codes 
aprean3  Datasets from Draper and Smith "Applied Regression Analysis"
(3rd Ed., 1998) 
apricom  Tools for the a Priori Comparison of Regression Modelling
Strategies 
aprof  Amdahl's Profiler, Directed Optimization Made Easy 
APSIM  General Utility Functions for the 'Agricultural Production
Systems Simulator' 
APSIMBatch  Analysis the output of Apsim software 
apsimr  Edit, Run and Evaluate APSIM Simulations Easily Using R 
apsrtable  apsrtable modeloutput formatter for social science 
apt  Asymmetric Price Transmission 
APtools  Average Positive Predictive Values (AP) for Binary Outcomes and
Censored Event Times 
apTreeshape  Analyses of Phylogenetic Treeshape 
aqfig  Functions to help display air quality model output and
monitoring data 
aqp  Algorithms for Quantitative Pedology 
aqr  Interface methods to use with an ActiveQuant Master Server 
AquaEnv  AquaEnv  an integrated development toolbox for aquatic chemical
model generation 
AR1seg  Segmentation of an autoregressive Gaussian process of order 1 
arabicStemR  Arabic Stemmer for Text Analysis 
ArArRedux  Rigorous Data Reduction and Error Propagation of Ar40 / Ar39
Data 
ARCensReg  Fitting Univariate Censored Linear Regression Model with
Autoregressive Errors 
archdata  Example Datasets from Archaeological Research 
archetypes  Archetypal Analysis 
archiDART  Plant Root System Architecture Analysis Using DART and RSML
Files 
archivist  Tools for Storing, Restoring and Searching for R Objects 
archivist.github  Tools for Archiving, Managing and Sharing R Objects via GitHub 
ArDec  Time series autoregressivebased decomposition 
arf3DS4  Activated Region Fitting, fMRI data analysis (3D) 
arfima  Fractional ARIMA (and Other Long Memory) Time Series Modeling 
ArfimaMLM  ArfimaMLM Estimation For Repeated CrossSectional Data 
argosfilter  Argos locations filter 
argparse  Command line optional and positional argument parser 
argparser  CommandLine Argument Parser 
ArgumentCheck  Improved Communication to Users with Respect to Problems in
Function Arguments 
arm  Data Analysis Using Regression and Multilevel/Hierarchical
Models 
arnie  "Arnie" box office records 19822014 
aroma.affymetrix  Analysis of Large Affymetrix Microarray Data Sets 
aroma.apd  A ProbeLevel Data File Format Used by 'aroma.affymetrix'
[deprecated] 
aroma.cn  CopyNumber Analysis of Large Microarray Data Sets 
aroma.core  Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework 
ARPobservation  Tools for Simulating Direct Behavioral Observation Recording
Procedures Based on Alternating Renewal Processes 
aRpsDCA  Arps Decline Curve Analysis in R 
arrApply  Apply a Function to a Margin of an Array 
ArrayBin  Binarization of numeric data arrays 
arrayhelpers  Convenience Functions for Arrays 
ars  Adaptive Rejection Sampling 
ART  Aligned Rank Transform for Nonparametric Factorial Analysis 
artfima  ARTFIMA Model Estimation 
ARTIVA  TimeVarying DBN Inference with the ARTIVA (Auto Regressive TIme
VArying) Model 
ARTool  Aligned Rank Transform 
ARTP  Gene and Pathway pvalues computed using the Adaptive Rank
Truncated Product 
ARTP2  Pathway and GeneLevel Association Test 
arules  Mining Association Rules and Frequent Itemsets 
arulesNBMiner  Mining NBFrequent Itemsets and NBPrecise Rules 
arulesSequences  Mining Frequent Sequences 
arulesViz  Visualizing Association Rules and Frequent Itemsets 
aRxiv  Interface to the arXiv API 
asaur  Data Sets for "Applied Survival Analysis Using R"" 
asbio  A Collection of Statistical Tools for Biologists 
ascii  Export R objects to several markup languages 
as.color  Assign Random Colors to Unique Items in a Vector 
asd  Simulations for Adaptive Seamless Designs 
asdreader  Reading ASD Binary Files in R 
ash  David Scott's ASH Routines 
asht  Applied Statistical Hypothesis Tests 
AsioHeaders  'Asio' C++ Header Files 
ASMap  Linkage Map Construction using the MSTmap Algorithm 
asnipe  Animal Social Network Inference and Permutations for Ecologists 
aspace  A collection of functions for estimating centrographic
statistics and computational geometries for spatial point
patterns 
ASPBay  Bayesian Inference on Causal Genetic Variants using Affected
SibPairs Data 
aspect  A General Framework for Multivariate Analysis with Optimal
Scaling 
aSPU  Adaptive Sum of Powered Score Test 
asremlPlus  Augments the Use of 'Asreml' in Fitting Mixed Models 
assertive  Readable Check Functions to Ensure Code Integrity 
assertive.base  A Lightweight Core of the 'assertive' Package 
assertive.code  Assertions to Check Properties of Code 
assertive.data  Assertions to Check Properties of Data 
assertive.data.uk  Assertions to Check Properties of Strings 
assertive.data.us  Assertions to Check Properties of Strings 
assertive.datetimes  Assertions to Check Properties of Dates and Times 
assertive.files  Assertions to Check Properties of Files 
assertive.matrices  Assertions to Check Properties of Matrices 
assertive.models  Assertions to Check Properties of Models 
assertive.numbers  Assertions to Check Properties of Numbers 
assertive.properties  Assertions to Check Properties of Variables 
assertive.reflection  Assertions for Checking the State of R 
assertive.sets  Assertions to Check Properties of Sets 
assertive.strings  Assertions to Check Properties of Strings 
assertive.types  Assertions to Check Types of Variables 
assertr  Assertive Programming for R Analysis Pipelines 
assertthat  Easy pre and post assertions 
AssetPricing  Optimal pricing of assets with fixed expiry date 
assist  A Suite of R Functions Implementing Spline Smoothing Techniques 
ASSISTant  Adaptive Subgroup Selection in Group Sequential Trials 
AssocTests  Genetic Association Studies 
assortnet  Calculate the Assortativity Coefficient of Weighted and Binary
Networks 
AssotesteR  Statistical Tests for Genetic Association Studies 
aster  Aster Models 
aster2  Aster Models 
astro  Astronomy Functions, Tools and Routines 
astrochron  A Computational Tool for Astrochronology 
astrodatR  Astronomical Data 
astroFns  Astronomy: time and position functions, misc. utilities 
astrolibR  Astronomy Users Library 
astsa  Applied Statistical Time Series Analysis 
asVPC  Average Shifted Visual Predictive Checks 
asymLD  Asymmetric Linkage Disequilibrium (ALD) for Polymorphic Genetic
Data 
asymmetry  The SlideVector Model for Multidimensional Scaling of
Asymmetric Data 
asympTest  Asymptotic statistic 
AsynchLong  Regression Analysis of Sparse Asynchronous Longitudinal Data 
asypow  Calculate Power Utilizing Asymptotic Likelihood Ratio Methods 
ATE  Inference for Average Treatment Effects using Covariate
Balancing 
AtelieR  A GTK GUI for teaching basic concepts in statistical inference,
and doing elementary bayesian tests 
atmcmc  Automatically Tuned Markov Chain Monte Carlo 
ATmet  Advanced Tools for Metrology 
AtmRay  Acoustic Traveltime Calculations for 1D Atmospheric Models 
aTSA  Alternative Time Series Analysis 
atsd  Support Querying Axibase TimeSeries Database 
attribrisk  Population Attributable Risk 
AUC  Threshold independent performance measures for probabilistic
classifiers 
aucm  AUC Maximization 
AUCRF  Variable Selection with Random Forest and the Area Under the
Curve 
audio  Audio Interface for R 
audiolyzR  audiolyzR: Give your data a listen 
audit  Bounds for Accounting Populations 
auRoc  Various Methods to Estimate the AUC 
AUtests  Approximate Unconditional and Permutation Tests 
autoencoder  Sparse Autoencoder for Automatic Learning of Representative
Features from Unlabeled Data 
autoimage  Enhanced Image Plots 
automap  Automatic interpolation package 
AutoModel  Automated Hierarchical Multiple Regression with Assumptions
Checking 
autopls  Partial Least Squares Regression with Backward Selection of
Predictors 
AutoregressionMDE  Minimum Distance Estimation in Autoregressive Model 
AutoSEARCH  GeneraltoSpecific (GETS) Modelling 
autoSEM  Performs Specification Search in Structural Equation Models 
autovarCore  Automated Vector Autoregression Models and Networks 
averisk  Calculation of Average Population Attributable Fractions and
Confidence Intervals 
aws  Adaptive Weights Smoothing 
aws.alexa  Client for the Amazon Alexa Web Information Services API 
awsMethods  Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri' and 'dti' 
aws.signature  Amazon Web Services Request Signatures 
aylmer  A generalization of Fisher's exact test 
AzureML  Interface with Azure Machine Learning Datasets, Experiments and
Web Services 

B2Z  Bayesian TwoZone Model 
b6e6rl  Adaptive differential evolution, b6e6rl variant 
babar  Bayesian Bacterial Growth Curve Analysis in R 
babel  Ribosome Profiling Data Analysis 
BaBooN  Bayesian Bootstrap Predictive Mean Matching  Multiple and
Single Imputation for Discrete Data 
babynames  US Baby Names 18802014 
BACA  Bubble Chart to Compare Biological Annotations by using DAVID 
BacArena  Modeling Framework for Cellular Communities in their
Environments 
BACCO  Bayesian Analysis of Computer Code Output (BACCO) 
BACCT  Bayesian Augmented Control for Clinical Trials 
backblazer  Bindings to the Backblaze B2 API 
backpipe  Backward Pipe Operator 
backports  Reimplementations of Functions Introduced Since R3.0.0 
backShift  Learning Causal Cyclic Graphs from Unknown Shift Interventions 
backtest  Exploring PortfolioBased Conjectures About Financial
Instruments 
backtestGraphics  Interactive Graphics for Portfolio Data 
BACprior  Choice of the Hyperparameter Omega in the Bayesian Adjustment
for Confounding (BAC) Algorithm 
bacr  Bayesian Adjustment for Confounding 
badgecreatr  Create Badges for 'Travis', 'Repostatus' 'Codecov.io' Etc in
Github Readme 
BAEssd  Bayesian Average Error approach to Sample Size Determination 
Bagidis  BAses GIving DIStances 
bagRboostR  Ensemble bagging and boosting classifiers 
BalancedSampling  Balanced and Spatially Balanced Sampling 
BaM  Functions and Datasets for Books by Jeff Gill 
bamdit  Bayesian MetaAnalysis of Diagnostic Test Data 
BAMMtools  Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees 
bandit  Functions for simple A/B split test and multiarmed bandit
analysis 
BANFF  Bayesian Network Feature Finder 
BANOVA  Hierarchical Bayesian ANOVA Models 
bapred  Batch Effect Removal and Addon Normalization (in Phenotype
Prediction using Gene Data) 
BaPreStoPro  Bayesian Prediction of Stochastic Processes 
barcode  Barcode distribution plots 
BarcodingR  Species Identification using DNA Barcodes 
Barnard  Barnard's Unconditional Test 
bartMachine  Bayesian Additive Regression Trees 
bartMachineJARs  bartMachine JARs 
BAS  Bayesian Model Averaging using Bayesian Adaptive Sampling 
base64  Base64 Encoder and Decoder 
base64enc  Tools for base64 encoding 
basefun  Infrastructure for Computing with Basis Functions 
baseline  Baseline Correction of Spectra 
basicspace  Recovering a Basic Space from Issue Scales 
BASIX  BASIX: An efficient C/C++ toolset for R 
BaSTA  AgeSpecific Survival Analysis from Incomplete
CaptureRecapture/Recovery Data 
bastah  Big Data Statistical Analysis for HighDimensional Models 
BAT  Biodiversity Assessment Tools 
batade  HTML reports and so on 
batch  Batching Routines in Parallel and Passing CommandLine Arguments
to R 
BatchExperiments  Statistical Experiments on Batch Computing Clusters 
BatchJobs  Batch Computing with R 
batchmeans  Consistent Batch Means Estimation of Monte Carlo Standard Errors 
batman  Convert Categorical Representations of Logicals to Actual
Logicals 
batteryreduction  An R Package for Data Reduction by Battery Reduction 
BayClone2  Bayesian Feature Allocation Model for Tumor Heterogeneity 
BayesBD  Bayesian Boundary Detection in Images 
BayesBinMix  Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions 
bayesbio  Miscellaneous Functions for Bioinformatics and Bayesian
Statistics 
bayesboot  An Implementation of Rubin's (1981) Bayesian Bootstrap 
BayesBridge  Bridge Regression 
BayesComm  Bayesian Community Ecology Analysis 
bayescount  Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC 
BayesCR  Bayesian Analysis of Censored Regression Models Under Scale
Mixture of Skew Normal Distributions 
BayesDA  Functions and Datasets for the book "Bayesian Data Analysis" 
bayesDccGarch  The Bayesian Dynamic Conditional Correlation GARCH Model 
bayesDem  Graphical User Interface for bayesTFR, bayesLife and bayesPop 
BayesFactor  Computation of Bayes Factors for Common Designs 
bayesGARCH  Bayesian Estimation of the GARCH(1,1) Model with Studentt
Innovations 
bayesGDS  Scalable Rejection Sampling for Bayesian Hierarchical Models 
BayesGESM  Bayesian Analysis of Generalized Elliptical SemiParametric
Models and Flexible Measurement Error Models 
BayesH  Bayesian Regression Model with Mixture of Two Scaled Inverse Chi
Square as Hyperprior 
BayesianAnimalTracker  Bayesian Melding of GPS and DR Path for Animal Tracking 
Bayesianbetareg  Bayesian Beta regression: joint mean and precision modeling 
BayesianNetwork  Bayesian Network Modeling and Analysis 
BayesLCA  Bayesian Latent Class Analysis 
bayesLife  Bayesian Projection of Life Expectancy 
BayesLogit  Logistic Regression 
bayesm  Bayesian Inference for Marketing/MicroEconometrics 
BayesMAMS  Designing Bayesian MultiArm MultiStage Studies 
bayesMCClust  MixturesofExperts Markov Chain Clustering and Dirichlet
Multinomial Clustering 
BayesMed  Default Bayesian Hypothesis Tests for Correlation, Partial
Correlation, and Mediation 
bayesmeta  Bayesian RandomEffects MetaAnalysis 
bayesmix  Bayesian Mixture Models with JAGS 
BayesMixSurv  Bayesian Mixture Survival Models using Additive
MixtureofWeibull Hazards, with Lasso Shrinkage and
Stratification 
BayesNI  BayesNI: Bayesian Testing Procedure for Noninferiority with
Binary Endpoints 
bayesPop  Probabilistic Population Projection 
bayespref  Hierarchical Bayesian analysis of ecological count data 
bayesQR  Bayesian quantile regression 
bayess  Bayesian Essentials with R 
BayesSAE  Bayesian Analysis of Small Area Estimation 
BayesSingleSub  Computation of Bayes factors for interrupted timeseries designs 
BayesSummaryStatLM  MCMC Sampling of Bayesian Linear Models via Summary Statistics 
bayesSurv  Bayesian Survival Regression with Flexible Error and Random
Effects Distributions 
bayesTFR  Bayesian Fertility Projection 
Bayesthresh  Bayesian thresholds mixedeffects models for categorical data 
BayesTree  Bayesian Additive Regression Trees 
BayesTreePrior  Bayesian Tree Prior Simulation 
BayesValidate  BayesValidate Package 
BayesVarSel  Bayes Factors, Model Choice and Variable Selection in Linear
Models 
BayesX  R Utilities Accompanying the Software Package BayesX 
BayesXsrc  R Package Distribution of the BayesX C++ Sources 
BayHap  Bayesian analysis of haplotype association using Markov Chain
Monte Carlo 
BayHaz  R Functions for Bayesian Hazard Rate Estimation 
BaylorEdPsych  R Package for Baylor University Educational Psychology
Quantitative Courses 
bayou  Bayesian Fitting of OrnsteinUhlenbeck Models to Phylogenies 
BaySIC  Bayesian Analysis of Significantly Mutated Genes in Cancer 
BAYSTAR  On Bayesian analysis of Threshold autoregressive model (BAYSTAR) 
BB  Solving and Optimizing LargeScale Nonlinear Systems 
bbefkr  Bayesian bandwidth estimation and semimetric selection for the
functional kernel regression with unknown error density 
bbemkr  Bayesian bandwidth estimation for multivariate kernel regression
with Gaussian error 
BBEST  Bayesian Estimation of Incoherent Neutron Scattering Backgrounds 
BBmisc  Miscellaneous Helper Functions for B. Bischl 
bbmle  Tools for General Maximum Likelihood Estimation 
BBMM  Brownian bridge movement model 
bbo  BiogeographyBased Optimization 
BBRecapture  Bayesian Behavioural CaptureRecapture Models 
bc3net  Gene Regulatory Network Inference with Bc3net 
BCA  Business and Customer Analytics 
BCBCSF  BiasCorrected Bayesian Classification with Selected Features 
BCDating  Business Cycle Dating and Plotting Tools 
BcDiag  Diagnostics Plots for Bicluster Data 
BCE  Bayesian composition estimator: estimating sample (taxonomic)
composition from biomarker data 
BCEA  Bayesian Cost Effectiveness Analysis 
BCEE  The Bayesian Causal Effect Estimation Algorithm 
BCEs0  Bayesian Models for CostEffectiveness Analysis in the Presence
of Structural Zero Costs 
Bchron  Radiocarbon Dating, AgeDepth Modelling, Relative Sea Level Rate
Estimation, and NonParametric Phase Modelling 
Bclim  Bayesian Palaeoclimate Reconstruction from Pollen Data 
bclust  Bayesian Hierarchical Clustering Using Spike and Slab Models 
bcp  Bayesian Analysis of Change Point Problems 
bcpa  Behavioral change point analysis of animal movement 
bcpmeta  Bayesian Multiple Changepoint Detection Using Metadata 
BCRA  Breast Cancer Risk Assessment 
bcRep  Advanced Analysis of B Cell Receptor Repertoire Data 
bcrm  Bayesian Continual Reassessment Method for Phase I
DoseEscalation Trials 
bcrypt  'Blowfish' Password Hashing Algorithm 
bcv  CrossValidation for the SVD (BiCrossValidation) 
bda  Density Estimation for Grouped Data 
bde  Bounded Density Estimation 
BDgraph  Bayesian Graph Selection Based on BirthDeath MCMC Approach 
bdots  Bootstrapped Differences of Time Series 
bdpopt  Optimisation of Bayesian Decision Problems 
bdpv  Inference and design for predictive values in binary diagnostic
tests 
bdrift  Beta Drift Analysis 
bdscale  Remove Weekends and Holidays from ggplot2 Axes 
bdsmatrix  Routines for Block Diagonal Symmetric matrices 
bdvis  Biodiversity Data Visualizations 
BDWreg  Bayesian Inference for Discrete Weibull Regression 
bdynsys  Bayesian Dynamical System Model 
beadarrayFilter  Bead filtering for Illumina bead arrays 
beadarrayMSV  Analysis of Illumina BeadArray SNP data including MSV markers 
beanplot  Visualization via Beanplots (like Boxplot/Stripchart/Violin
Plot) 
BEANSP  Bayesian Estimate of Agespecific Nest Survival Probabilities 
beanz  Bayesian Analysis of Heterogeneous Treatment Effect 
BEDASSLE  Quantifies effects of geo/eco distance on genetic
differentiation 
BEDMatrix  Matrices Backed by Binary PED Files (PLINK) 
bedr  Genomic Region Processing using Tools Such as Bedtools, Bedops
and Tabix 
beepr  Easily Play Notification Sounds on any Platform 
beeswarm  The Bee Swarm Plot, an Alternative to Stripchart 
benchden  28 benchmark densities from Berlinet/Devroye (1994) 
benchmark  Benchmark Experiments Toolbox 
Benchmarking  Benchmark and Frontier Analysis Using DEA and SFA 
benchmarkme  Crowd Sourced System Benchmarks 
benchmarkmeData  Data Set for the 'benchmarkme' Package 
benford.analysis  Benford Analysis for Data Validation and Forensic Analytics 
BenfordTests  Statistical Tests for Evaluating Conformity to Benford's Law 
bentcableAR  BentCable Regression for Independent Data or Autoregressive
Time Series 
BEQI2  Benthic Ecosystem Quality Index 2 
ber  Batch Effects Removal 
Bergm  Bayesian analysis for exponential random graph models 
berryFunctions  Function Collection Related to Plotting and Hydrology 
Bessel  Bessel – Bessel Functions Computations and Approximations 
BEST  Bayesian Estimation Supersedes the tTest 
bestglm  Best Subset GLM 
BetaBit  Mini Games from Adventures of Beta and Bit 
betafam  Detecting rare variants for quantitative traits using nuclear
families 
betalink  BetaDiversity of Species Interactions 
betapart  Partitioning beta diversity into turnover and nestedness
components 
betaper  Functions to incorporate taxonomic uncertainty on multivariate
analyses of ecological data 
betareg  Beta Regression 
betas  Standardized Beta Coefficients 
betategarch  Simulation, estimation and forecasting of BetaSkewtEGARCH
models 
bethel  Bethel's algorithm 
BeviMed  Bayesian Evaluation of Variant Involvement in Mendelian
Disorders 
bezier  Bezier Curve and Spline Toolkit 
bfa  Bayesian Factor Analysis 
bfast  Breaks For Additive Season and Trend (BFAST) 
bfork  Basic Unix Process Control 
bfp  Bayesian Fractional Polynomials 
bgeva  Binary Generalized Extreme Value Additive Models 
bglm  Bayesian Estimation in Generalized Linear Models 
BGLR  Bayesian Generalized Linear Regression 
bgmfiles  Example BGM Files for the Atlantis Ecosystem Model 
bgmm  Gaussian Mixture Modeling Algorithms And The Beliefbased
Mixture Modeling 
BGPhazard  Markov Beta and Gamma Processes for Modeling Hazard Rates 
BGSIMD  Block Gibbs Sampler with Incomplete Multinomial Distribution 
BH  Boost C++ Header Files 
Bhat  General likelihood exploration 
BHH2  Useful Functions for Box, Hunter and Hunter II 
biasbetareg  Bias correction of the parameter estimates of the beta
regression model 
BiasedUrn  Biased Urn Model Distributions 
bibliometrix  Bibliometric and CoCitation Analysis Tool 
bibliospec  Reading Mass Spectrometric Search Results 
bibtex  bibtex parser 
biclust  BiCluster Algorithms 
BiDimRegression  Calculates the bidimensional regression between two 2D
configurations 
bifactorial  Inferences for bi and trifactorial trial designs 
BIFIEsurvey  Tools for Survey Statistics in Educational Assessment 
bigalgebra  BLAS routines for native R matrices and big.matrix objects 
biganalytics  Utilities for 'big.matrix' Objects from Package 'bigmemory' 
bigdata  Big Data Analytics 
BIGDAWG  CaseControl Analysis of MultiAllelic Loci 
bigGP  Distributed Gaussian Process Calculations 
biglars  Scalable LeastAngle Regression and Lasso 
biglasso  Big Lasso: Extending Lasso Model Fitting to Big Data in R 
biglm  bounded memory linear and generalized linear models 
bigmemory  Manage Massive Matrices with Shared Memory and MemoryMapped
Files 
bigmemory.sri  A shared resource interface for Bigmemory Project packages 
bigml  Bindings for the BigML API 
bigpca  PCA, Transpose and Multicore Functionality for 'big.matrix'
Objects 
bigQueryR  Interface with Google BigQuery with Shiny Compatibility 
BigQuic  Big Quadratic Inverse Covariance Estimation 
bigReg  Generalized Linear Models (GLM) for Large Data Sets 
bigrquery  An Interface to Google's 'BigQuery' 'API' 
bigRR  Generalized Ridge Regression (with special advantage for p >> n
cases) 
bigsplines  Smoothing Splines for Large Samples 
bigtabulate  Table, Apply, and Split Functionality for Matrix and
'big.matrix' Objects 
BigTSP  Top Scoring Pair based methods for classification 
BigVAR  Dimension Reduction Methods for Multivariate Time Series 
bild  BInary Longitudinal Data 
bimetallic  Power for SNP analyses using silver standard cases 
bimixt  Estimates Mixture Models for CaseControl Data 
Binarize  Binarization of OneDimensional Data 
BinaryEMVS  Variable Selection for Binary Data Using the EM Algorithm 
BinaryEPPM  Mean and Variance Modeling of Binary Data 
binaryLogic  Binary Logic 
binda  MultiClass Discriminant Analysis using Binary Predictors 
bindata  Generation of Artificial Binary Data 
binequality  Methods for Analyzing Binned Income Data 
bingat  Binary Graph Analysis Tools 
binGroup  Evaluation and experimental design for binomial group testing 
binhf  HaarFisz functions for binomial data 
binMto  Asymptotic simultaneous confidence intervals for manytoone
comparisons of proportions 
BinNonNor  Data Generation with Binary and Continuous NonNormal Components 
BinNor  Simultaneous Generation of Multivariate Binary and Normal
Variates 
binom  Binomial Confidence Intervals For Several Parameterizations 
binomen  'Taxonomic' Specification and Parsing Methods 
binomialcftp  Generates binomial random numbers via the coupling from the past
algorithm 
binomlogit  Efficient MCMC for Binomial Logit Models 
binomSamSize  Confidence intervals and sample size determination for a
binomial proportion under simple random sampling and pooled
sampling 
binomTools  Performing diagnostics on binomial regression models 
BinOrdNonNor  Concurrent Generation of Binary, Ordinal and Continuous Data 
binr  Cut Numeric Values into Evenly Distributed Groups 
binseqtest  Exact Binary Sequential Designs and Analysis 
binst  Data Preprocessing, Binning for Classification and Regression 
bio3d  Biological Structure Analysis 
Biocomb  Feature Selection and Classification with the Embedded
Validation Procedures for Biomedical Data Analysis 
Biodem  Biodemography Functions 
BiodiversityR  Package for Community Ecology and Suitability Analysis 
BIOdry  Multilevel Modeling of Dendroclimatical Fluctuations 
BioFTF  Biodiversity Assessment Using Functional Tools 
biogas  Process Biogas Data and Predict Biogas Production 
biogeo  Point Data Quality Assessment and Coordinate Conversion 
BioGeoBEARS  BioGeography with Bayesian (and Likelihood) Evolutionary
Analysis in R Scripts 
biogram  NGram Analysis of Biological Sequences 
Biograph  Explore Life Histories 
bioinactivation  Simulation of Dynamic Microbial Inactivation 
bio.infer  Predict environmental conditions from biological observations 
biom  An interface package (beta) for the BIOM file format 
BioMark  Find Biomarkers in TwoClass Discrimination Problems 
biomartr  Functional Annotation and Biological Data Retrieval with R 
biomod2  Ensemble Platform for Species Distribution Modeling 
BIOM.utils  Utilities for the BIOM (Biological Observation Matrix) Format 
bionetdata  Biological and chemical data networks 
BioPET  Biomarker Prognostic Enrichment Tool 
BioPhysConnectoR  BioPhysConnectoR 
bioplots  Visualization of Overlapping Results with Heatmap 
bioPN  Simulation of deterministic and stochastic biochemical reaction
networks using Petri Nets 
biorxivr  Search and Download Papers from the bioRxiv Preprint Server 
bios2mds  From BIOlogical Sequences to MultiDimensional Scaling 
biosignalEMG  Tools for Electromyogram Signals (EMG) Analysis 
BioStatR  Initiation Ã la Statistique avec R 
biotic  Calculation of Freshwater Biotic Indices 
biotools  Tools for Biometry and Applied Statistics in Agricultural
Science 
bipartite  Visualising Bipartite Networks and Calculating Some (Ecological)
Indices 
biplotbootGUI  Bootstrap on Classical Biplots and Clustering Disjoint Biplot 
BiplotGUI  Interactive Biplots in R 
BIPOD  BIPOD (Bayesian Inference for Partially Observed diffusions) 
birdring  Methods to Analyse Ring ReEncounter Data 
birk  MA Birk's Functions 
bisectr  Tools to find bad commits with git bisect 
BiSEp  Toolkit to Identify Candidate Synthetic Lethality 
bisoreg  Bayesian Isotonic Regression with Bernstein Polynomials 
bit  A class for vectors of 1bit booleans 
bit64  A S3 Class for Vectors of 64bit Integers 
bitops  Bitwise Operations 
BiTrinA  Binarization and Trinarization of OneDimensional Data 
bitrugs  Bayesian Inference of Transmission Routes Using Genome Sequences 
BivarP  Estimating the Parameters of Some Bivariate Distributions 
bivarRIpower  Sample size calculations for bivariate longitudinal data 
biwavelet  Conduct Univariate and Bivariate Wavelet Analyses 
biwt  Functions to compute the biweight mean vector and covariance &
correlation matrices 
bizdays  Business Days Calculations and Utilities 
bkmr  Bayesian Kernel Machine Regression 
BKPC  Bayesian Kernel Projection Classifier 
blackbox  Black Box Optimization and Exploration of Parameter Space 
BlakerCI  Blaker's Binomial Confidence Limits 
BlandAltmanLeh  Plots (Slightly Extended) BlandAltman Plots 
blatr  Send Emails Using 'Blat' for Windows 
Blaunet  Calculate and Analyze Blau Status for Measuring Social Distance 
blavaan  Bayesian Latent Variable Analysis 
BLCOP  BlackLitterman and Copula Opinion Pooling Frameworks 
blendedLink  A New Link Function that Blends Two Specified Link Functions 
blender  Analyze biotic homogenization of landscapes 
blighty  United Kingdom coastlines 
blkergm  Fitting block ERGM given the block structure on social networks 
blm  Binomial linear and linearexpit regression 
blme  Bayesian Linear MixedEffects Models 
blmeco  Data Files and Functions Accompanying the Book "Bayesian Data
Analysis in Ecology using R, BUGS and Stan" 
blockcluster  Coclustering Package for Binary, Categorical, Contingency and
Continuous DataSets 
blockmatrix  blockmatrix: Tools to solve algebraic systems with partitioned
matrices 
BlockMessage  Creates strings that show a text message in 8 by 8 block letters 
blockmodeling  An R package for Generalized and classical blockmodeling of
valued networks 
blockmodels  Latent and Stochastic Block Model Estimation by a 'VEM'
Algorithm 
blockrand  Randomization for block random clinical trials 
blocksdesign  Nested Block Designs for Unstructured Treatments 
blockseg  Two Dimensional ChangePoints Detection 
blockTools  Block, Assign, and Diagnose Potential Interference in Randomized
Experiments 
Blossom  Statistical Comparisons with DistanceFunction Based Permutation
Tests 
BLR  Bayesian Linear Regression 
blsAPI  Request Data from the U.S. Bureau of Labor Statistics API 
blscrapeR  An API Wrapper for the Bureau of Labor Statistics (BLS) 
BMA  Bayesian Model Averaging 
bmd  Benchmark dose analysis for doseresponse data 
bmem  Mediation analysis with missing data using bootstrap 
bmeta  Bayesian MetaAnalysis and MetaRegression 
BMhyd  PCM for Hybridization 
Bmix  Bayesian Sampling for StickBreaking Mixtures 
bmk  MCMC diagnostics package 
bmlm  Bayesian Multilevel Mediation 
bmmix  Bayesian multinomial mixture 
BMN  The pseudolikelihood method for pairwise binary markov networks 
bmp  Read Windows Bitmap (BMP) images 
bmrm  Bundle Methods for Regularized Risk Minimization Package 
BMRV  Bayesian Models for Rare Variant Association Analysis 
BMS  Bayesian Model Averaging Library 
BNDataGenerator  Data Generator based on Bayesian Network Model 
bnlearn  Bayesian Network Structure Learning, Parameter Learning and
Inference 
bnnSurvival  Bagged kNearest Neighbors Survival Prediction 
bnormnlr  Bayesian Estimation for Normal Heteroscedastic Nonlinear
Regression Models 
BNPdensity  FergusonKlass Type Algorithm for Posterior Normalized Random
Measures 
bnpmr  Bayesian monotonic nonparametric regression 
BNPTSclust  A Bayesian Nonparametric Algorithm for Time Series Clustering 
BNSP  Bayesian Non and SemiParametric Model Fitting 
bnspatial  Spatial Implementation of Bayesian Networks and Mapping 
bnstruct  Bayesian Network Structure Learning from Data with Missing
Values 
boa  Bayesian Output Analysis Program (BOA) for MCMC 
BoardGames  Board Games and Tools for Building Board Games 
bodenmiller  Profilling of Peripheral Blood Mononuclear Cells using CyTOF 
BOG  Bacterium and Virus Analysis of Orthologous Groups (BOG) is a
Package for Identifying Differentially Regulated Genes in the
Light of Gene Functions 
boilerpipeR  Interface to the Boilerpipe Java Library 
BOIN  Bayesian Optimal INterval (BOIN) Design for SingleAgent and
Drug Combination Phase I Clinical Trials 
bold  Interface to Bold Systems 'API' 
Bolstad  Functions for Elementary Bayesian Inference 
Bolstad2  Bolstad functions 
BonEV  An Improved Multiple Testing Procedure for Controlling False
Discovery Rates 
bookdown  Authoring Books with R Markdown 
boolean3  Boolean Binary Response Models 
BoolNet  Construction, Simulation and Analysis of Boolean Networks 
Boom  Bayesian Object Oriented Modeling 
BoomSpikeSlab  MCMC for Spike and Slab Regression 
boostmtree  Boosted Multivariate Trees for Longitudinal Data 
boostr  A modular framework to bag or boost any estimation procedure 
boostSeq  Optimized GWAS cohort subset selection for resequencing studies 
boot  Bootstrap Functions (Originally by Angelo Canty for S) 
bootES  Bootstrap Effect Sizes 
bootLR  Bootstrapped Confidence Intervals for (Negative) Likelihood
Ratio Tests 
bootnet  Bootstrap Methods for Various Network Estimation Routines 
BootPR  Bootstrap Prediction Intervals and BiasCorrected Forecasting 
bootRes  Bootstrapped Response and Correlation Functions 
bootruin  A bootstrap test for the probability of ruin in the classical
risk process 
bootspecdens  Testing equality of spectral densities 
bootsPLS  Bootstrap Subsamplings of Sparse Partial Least Squares 
Discriminant Analysis for Classification and Signature
Identification 
bootStepAIC  Bootstrap stepAIC 
bootstrap  Functions for the Book "An Introduction to the Bootstrap" 
bootSVD  Fast, Exact Bootstrap Principal Component Analysis for High
Dimensional Data 
bootTimeInference  Robust Performance Hypothesis Testing with the Sharpe Ratio 
boottol  Bootstrap Tolerance Levels for Credit Scoring Validation
Statistics 
BootWPTOS  Test Stationarity using Bootstrap Wavelet Packet Tests 
boral  Bayesian Ordination and Regression AnaLysis 
Boruta  Wrapper Algorithm for AllRelevant Feature Selection 
BoSSA  a Bunch of Structure and Sequence Analysis 
boussinesq  Analytic Solutions for (groundwater) Boussinesq Equation 
boxplotdbl  Double Box Plot for TwoAxes Correlation 
boxr  Interface for the 'Box.com API' 
bpa  Basic Pattern Analysis 
bpca  Biplot of Multivariate Data Based on Principal Components
Analysis 
bpcp  Beta Product Confidence Procedure for Right Censored Data 
bPeaks  bPeaks: an intuitive peakcalling strategy to detect
transcription factor binding sites from ChIPseq data in small
eukaryotic genomes 
BPEC  Bayesian Phylogeographic and Ecological Clustering 
bpkde  BackProjected Kernel Density Estimation 
bqtl  Bayesian QTL Mapping Toolkit 
BradleyTerry2  BradleyTerry Models 
braidReports  Visualize Combined Action Response Surfaces and Report BRAID
Analyses 
braidrm  Fitting Dose Response with the BRAID Combined Action Model 
BrailleR  Improved Access for Blind Users 
brainGraph  Graph Theory Analysis of Brain MRI Data 
brainR  Helper functions to misc3d and rgl packages for brain imaging 
brainwaver  Basic wavelet analysis of multivariate time series with a
visualisation and parametrisation using graph theory 
Branching  Simulation and Estimation for Branching Processes 
braQCA  Bootstrapped Robustness Assessment for Qualitative Comparative
Analysis 
breakage  SICM pipette tip geometry estimation 
breakaway  Species Richness Estimation and Modeling 
breakpoint  An R Package for Multiple BreakPoint Detection via the
CrossEntropy Method 
bReeze  Functions for wind resource assessment 
brew  Templating Framework for Report Generation 
brewdata  Extracting Usable Data from the Grad Cafe Results Search 
brglm  Bias reduction in binomialresponse generalized linear models 
bride  Brier score decomposition of probabilistic forecasts for binary
events 
bridgedist  An Implementation of the Bridge Distribution with LogitLink as
in Wang and Louis (2003) 
brms  Bayesian Regression Models using Stan 
brnn  Bayesian Regularization for FeedForward Neural Networks 
Brobdingnag  Very large numbers in R 
broman  Karl Broman's R Code 
broom  Convert Statistical Analysis Objects into Tidy Data Frames 
brotli  A Compression Format Optimized for the Web 
brr  Bayesian Inference on the Ratio of Two Poisson Rates 
brranching  Fetch 'Phylogenies' from Many Sources 
BRugs  Interface to the 'OpenBUGS' MCMC Software 
BSagri  Statistical methods for safety assessment in agricultural field
trials 
BSDA  Basic Statistics and Data Analysis 
BSGS  Bayesian Sparse Group Selection 
BSGW  Bayesian Survival Model with Lasso Shrinkage Using Generalized
Weibull Regression 
bshazard  Nonparametric Smoothing of the Hazard Function 
BsMD  Bayes Screening and Model Discrimination 
bspec  Bayesian Spectral Inference 
bspmma  bspmma: Bayesian Semiparametric Models for MetaAnalysis 
BSquare  Bayesian Simultaneous Quantile Regression 
BSSasymp  Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates 
bssn  BirnbaumSaunders Model Based on SkewNormal Distribution 
bst  Gradient Boosting 
bsts  Bayesian Structural Time Series 
btergm  Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood 
btf  Estimates univariate function via Bayesian trend filtering 
BTLLasso  Modelling Heterogeneity in Paired Comparison Data 
BTR  Training and Analysing Asynchronous Boolean Models 
BTSPAS  Bayesian TimeStrat. Population Analysis 
BTYD  Implementing Buy 'Til You Die Models 
bujar  BuckleyJames Regression for Survival Data with HighDimensional
Covariates 
bunchr  Analyze Bunching in a Kink or Notch Setting 
burnr  Advanced Fire History Analysis in R 
BurStFin  Burns Statistics Financial 
BurStMisc  Burns Statistics miscellaneous 
bursts  Markov model for bursty behavior in streams 
bvarsv  Bayesian Analysis of a Vector Autoregressive Model with
Stochastic Volatility and TimeVarying Parameters 
bvenn  A Simple alternative to proportional Venn diagrams 
bvls  The StarkParker algorithm for boundedvariable least squares 
bvpSolve  Solvers for Boundary Value Problems of Differential Equations 
BVS  Bayesian Variant Selection: Bayesian Model Uncertainty
Techniques for Genetic Association Studies 
bWGR  Bagging WholeGenome Regression 
BWStest  Baumgartner Weiss Schindler Test of Equal Distributions 

c060  Extended Inference for Lasso and ElasticNet Regularized Cox and
Generalized Linear Models 
c3net  Infering largescale gene networks with C3NET 
C50  C5.0 Decision Trees and RuleBased Models 
ca  Simple, Multiple and Joint Correspondence Analysis 
cabootcrs  Bootstrap Confidence Regions for Correspondence Analysis 
cacIRT  Classification Accuracy and Consistency under Item Response
Theory 
CaDENCE  Conditional Density Estimation Network Construction and
Evaluation 
CADFtest  This package performs the CADF unit root test proposed in Hansen
(1995) 
cAIC4  Conditional Akaike information criterion for lme4 
Cairo  R graphics device using cairo graphics library for creating
highquality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output 
cairoDevice  Embeddable Cairo Graphics Device Driver 
calACS  Calculations for All Common Subsequences 
Calculator.LR.FNs  Calculator for LR Fuzzy Numbers 
CALF  Coarse Approximation Linear Function 
CALIBERrfimpute  Multiple imputation using MICE and Random Forest 
calibrar  Automated Parameter Estimation for Complex (Ecological) Models 
calibrate  Calibration of Scatterplot and Biplot Axes 
CalibrateSSB  Weighting and Estimation for Panel Data with NonResponse 
calibrator  Bayesian calibration of complex computer codes 
callr  Call R from R 
calmate  Improved AlleleSpecific Copy Number of SNP Microarrays for
Downstream Segmentation 
CAM  Causal Additive Model (CAM) 
CAMAN  Finite Mixture Models and MetaAnalysis Tools  Based on C.A.MAN 
camel  Calibrated Machine Learning 
camtrapR  Camera Trap Data Management and Preparation of Occupancy and
Spatial CaptureRecapture Analyses 
cancerGI  Analyses of Cancer Gene Interaction 
cancerTiming  Estimation of Temporal Ordering of Cancer Abnormalities 
candisc  Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis 
Canopy  Accessing IntraTumor Heterogeneity and Tracking Longitudinal
and Spatial Clonal Evolutionary History by NextGeneration
Sequencing 
CANSIM2R  Directly Extracts Complete CANSIM Data Tables 
cape  Combined Analysis of Pleiotropy and Epistasis 
caper  Comparative Analyses of Phylogenetics and Evolution in R 
capm  Companion Animal Population Management 
captioner  Numbers Figures and Creates Simple Captions 
captr  Client for the Captricity API 
capushe  CAlibrating Penalities Using Slope HEuristics 
capwire  Estimates population size from noninvasive sampling 
car  Companion to Applied Regression 
CARBayes  Spatial Generalised Linear Mixed Models for Areal Unit Data 
CARBayesdata  Data Used in the Vignettes Accompanying the CARBayes and
CARBayesST Packages 
CARBayesST  SpatioTemporal Generalised Linear Mixed Models for Areal Unit
Data 
carcass  Estimation of the Number of Fatalities from Carcass Searches 
cardidates  Identification of Cardinal Dates in Ecological Time Series 
cardioModel  Cardiovascular Safety ExposureResponse Modeling in EarlyPhase
Clinical Studies 
care  HighDimensional Regression and CAR Score Variable Selection 
CARE1  Statistical package for population size estimation in
capturerecapture models 
caret  Classification and Regression Training 
caretEnsemble  Ensembles of Caret Models 
caribou  Estimation of caribou abundance based on large scale
aggregations monitored by radio telemetry 
CarletonStats  Functions for Statistics Classes at Carleton College 
CARLIT  Ecological Quality Ratios Calculation and Plot 
caroline  A Collection of Database, Data Structure, Visualization, and
Utility Functions for R 
caRpools  CRISPR AnalyzeR for Pooled CRISPR Screens 
CARrampsOcl  Reparameterized and marginalized posterior sampling for
conditional autoregressive models, OpenCL implementation 
cartography  Thematic Cartography 
carx  Censored Autoregressive Model with Exogenous Covariates 
caschrono  SÃ©ries temporelles avec R  MÃ©thodes et cas 
caseMatch  Identify Similar Cases for Qualitative Case Studies 
cat  Analysis of categoricalvariable datasets with missing values 
catdap  Categorical Data Analysis Program Package 
catdata  Categorical Data 
CatDyn  Fishery Stock Assessment by Generalized Depletion Models 
cate  High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation 
catenary  Fits a Catenary to Given Points 
CateSelection  Categorical Variable Selection Methods 
cati  Community Assembly by Traits: Individuals and Beyond 
catIrt  An R Package for Simulating IRTBased Computerized Adaptive
Tests 
catnet  Categorical Bayesian Network Inference 
caTools  Tools: moving window statistics, GIF, Base64, ROC AUC, etc 
catR  Procedures to Generate Patterns under Computerized Adaptive
Testing 
catspec  Special models for categorical variables 
causaldrf  Tools for Estimating Causal Dose Response Functions 
causaleffect  Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models 
CausalFX  Methods for Estimating Causal Effects from Observational Data 
CausalGAM  Estimation of Causal Effects with Generalized Additive Models 
causalsens  Selection Bias Approach to Sensitivity Analysis for Causal
Effects 
Causata  Analysis utilities for binary classification and Causata users 
CAvariants  Correspondence Analysis Variants 
cba  Clustering for Business Analytics 
CBPS  Covariate Balancing Propensity Score 
cbsodataR  Statistics Netherlands (CBS) Open Data API Client 
CCA  Canonical correlation analysis 
CCAGFA  Bayesian Canonical Correlation Analysis and Group Factor
Analysis 
ccaPP  (Robust) Canonical Correlation Analysis via Projection Pursuit 
cccd  Class Cover Catch Digraphs 
ccChooser  Developing a core collections 
cccp  Cone Constrained Convex Problems 
cccrm  Concordance Correlation Coefficient for Repeated (and
NonRepeated) Measures 
ccda  Combined Cluster and Discriminant Analysis 
ccgarch  Conditional Correlation GARCH models 
cchs  Cox Model for CaseCohort Data with Stratified
SubcohortSelection 
cclust  Convex Clustering Methods and Clustering Indexes 
CCM  Correlation classification method (CCM) 
CCMnet  Simulate Congruence Class Model for Networks 
CCP  Significance Tests for Canonical Correlation Analysis (CCA) 
CCpop  One and two locus GWAS of binary phenotype with
casecontrolpopulation design 
CCTpack  Cultural Consensus Theory applications to data 
cda  Coupled dipole approximation of light scattering by clusters of
nanoparticles 
cdb  Reading and Writing Constant DataBases 
cdcfluview  Retrieve U.S. Flu Season Data from the CDC FluView Portal 
cdcsis  Conditional Distance Correlation and Its Related Feature
Screening Method 
cdfquantreg  Quantile Regression for Random Variables on the Unit Interval 
CDFt  Statistical downscaling through CDFtransform 
CDLasso  Coordinate Descent Algorithms for Lasso Penalized L1, L2, and
Logistic Regression 
CDM  Cognitive Diagnosis Modeling 
CDNmoney  Components of Canadian Monetary and Credit Aggregates 
cdom  R Functions to Model CDOM Spectra 
CDROM  Phylogenetically Classifies Retention Mechanisms of Duplicate
Genes from Gene Expression Data 
cds  Constrained Dual Scaling for Detecting Response Styles 
CDVine  Statistical Inference of C And DVine Copulas 
CEC  CrossEntropy Clustering 
cec2005benchmark  Benchmark for the CEC 2005 Special Session on RealParameter
Optimization 
cec2013  Benchmark functions for the Special Session and Competition on
RealParameter Single Objective Optimization at CEC2013 
CEGO  Combinatorial Efficient Global Optimization 
celestial  Collection of Common Astronomical Conversion Routines and
Functions 
cellranger  Translate Spreadsheet Cell Ranges to Rows and Columns 
CellularAutomaton  OneDimensional Cellular Automata 
cellVolumeDist  Functions to fit cell volume distributions and thereby estimate
cell growth rates and division times 
cem  Coarsened Exact Matching 
cems  Conditional Expectation Manifolds 
CensMixReg  Censored Linear Mixture Regression Models 
censNID  censored NID samples 
censorcopula  Estimate Parameter of Bivariate Copula 
censReg  Censored Regression (Tobit) Models 
CensRegMod  Fits Normal and Studentt Censored Regression Model 
censusr  Collect Data from the Census API 
cents  Censored time series 
CEoptim  CrossEntropy R Package for Optimization 
CePa  Centralitybased pathway enrichment 
CepLDA  Discriminant Analysis of Time Series in the Presence of
WithinGroup Spectral Variability 
cepp  Context Driven Exploratory Projection Pursuit 
CerioliOutlierDetection  Outlier Detection Using the Iterated RMCD Method of Cerioli
(2010) 
cernn  Covariance Estimation Regularized by Nuclear Norm Penalties 
CFC  CauseSpecific Framework for CompetingRisk Analysis 
CfEstimateQuantiles  Estimate quantiles using any order CornishFisher expansion 
cffdrs  Canadian Forest Fire Danger Rating System 
cg  Compare Groups, Analytically and Graphically 
cgam  Constrained Generalized Additive Model 
cgAUC  Calculate AUCtype measure when gold standard is continuous and
the corresponding optimal linear combination of variables with
respect to it 
cgdsr  RBased API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS) 
cggd  Continuous Generalized Gradient Descent 
cgh  Microarray CGH analysis using the SmithWaterman algorithm 
cghFLasso  Detecting hot spot on CGH array data with fused lasso
regression 
cghseg  Segmentation Methods for Array CGH Analysis 
CGP  Composite Gaussian process models 
cgwtools  Miscellaneous Tools 
ChainLadder  Statistical Methods and Models for Claims Reserving in General
Insurance 
changepoint  Methods for Changepoint Detection 
changepoint.np  Methods for Nonparametric Changepoint Detection 
ChangepointTesting  Change Point Estimation for Clustered Signals 
ChannelAttribution  Markov Model for the Online MultiChannel Attribution Problem 
ChannelAttributionApp  Shiny Web Application for the Multichannel Attribution Problem 
Chaos01  01 Test for Chaos 
ChaosGame  Chaos Game 
ChargeTransport  Charge Transfer Rates and Charge Carrier Mobilities 
CHAT  Clonal Heterogeneity Analysis Tool 
CHCN  Canadian Historical Climate Network 
cheb  Discrete Linear Chebyshev Approximation 
chebpol  Multivariate Chebyshev Interpolation 
CheckDigit  Calculate and verify check digits 
checkmate  Fast and Versatile Argument Checks 
checkpoint  Install Packages from Snapshots on the Checkpoint Server for
Reproducibility 
cheddar  Analysis and Visualisation of Ecological Communities 
chemCal  Calibration Functions for Analytical Chemistry 
chemometrics  Multivariate Statistical Analysis in Chemometrics 
ChemometricsWithR  Chemometrics with R  Multivariate Data Analysis in the Natural
Sciences and Life Sciences 
ChemometricsWithRData  Data for package ChemometricsWithR 
ChemoSpec  Exploratory Chemometrics for Spectroscopy 
cherry  Multiple Testing Methods for Exploratory Research 
CHFF  Closest History Flow Field Forecasting for Bivariate Time Series 
chi  The Chi Distribution 
childsds  Calculation of standard deviation scores adduced from different
growth standards 
chillR  Statistical Methods for Phenology Analysis in Temperate Fruit
Trees 
chipPCR  Toolkit of Helper Functions to PreProcess Amplification Data 
ChIPtest  Nonparametric Methods for Identifying Differential Enrichment
Regions with ChIPSeq Data 
chngpt  Change Point Regression 
CHNOSZ  Chemical Thermodynamics and Activity Diagrams 
choiceDes  Design Functions for Choice Studies 
ChoiceModelR  Choice Modeling in R 
choplump  Choplump tests 
chopthin  The Chopthin Resampler 
chords  Estimation in respondent driven samples 
choroplethr  Simplify the Creation of Choropleth Maps in R 
choroplethrAdmin1  Contains an AdministrativeLevel1 Map of the World 
choroplethrMaps  Contains maps used by the choroplethr package 
chromer  Interface to Chromosome Counts Database API 
chromoR  Analysis of chromosomal interactions data (correction,
segmentation and comparison) 
chron  Chronological Objects which can Handle Dates and Times 
CHsharp  Choi and Hall Style Data Sharpening 
chunked  Chunkwise TextFile Processing for 'dplyr' 
CIDnetworks  Generative Models for Complex Networks with Conditionally
Independent Dyadic Structure 
CIFsmry  Weighted summary of cumulative incidence functions 
cin  Causal Inference for Neuroscience 
CINID  Curculionidae INstar IDentification 
CINOEDV  CoInformation based NOrder Epistasis Detector and Visualizer 
CircE  Circumplex models Estimation 
circlize  Circular Visualization 
CircNNTSR  Statistical Analysis of Circular Data using Nonnegative
Trigonometric Sums (NNTS) Models 
CircOutlier  Detection of Outliers in CircularCircular Regression 
CircStats  Circular Statistics, from "Topics in circular Statistics" (2001) 
circular  Circular Statistics 
cIRT  Choice Item Response Theory 
cit  Causal Inference Test 
CITAN  CITation ANalysis Toolpack 
citbcmst  CIT Breast Cancer Molecular SubTypes Prediction 
citccmst  CIT Colon Cancer Molecular SubTypes Prediction 
Cite  An RStudio Addin to Insert BibTex Citation in Rmarkdown
Documents 
CityPlot  Visualization of structure and contents of a database 
cjoint  AMCE Estimator for Conjoint Experiments 
ckanr  Client for the Comprehensive Knowledge Archive Network ('CKAN')
'API' 
Ckmeans.1d.dp  Optimal and Fast Univariate kMeans Clustering 
cladoRcpp  C++ implementations of phylogenetic cladogenesis calculations 
ClamR  Time Series Modeling for Climate Change Proxies 
clarifai  Access to Clarifai API 
class  Functions for Classification 
classGraph  Construct Graphs of S4 Class Hierarchies 
classifly  Explore classification models in high dimensions 
classify  Classification Accuracy and Consistency under IRT models 
classInt  Choose Univariate Class Intervals 
classyfire  Robust multivariate classification using highly optimised SVM
ensembles 
cleangeo  Cleaning Geometries from Spatial Objects 
clere  Simultaneous Variables Clustering and Regression 
clhs  Conditioned Latin Hypercube Sampling 
ClickClust  ModelBased Clustering of Categorical Sequences 
clickstream  Analyzes Clickstreams Based on Markov Chains 
clifro  Easily Download and Visualise Climate Data from CliFlo 
clikcorr  Censoring Data and LikelihoodBased Correlation Estimation 
ClimClass  Climate Classification According to Several Indices 
climdex.pcic  PCIC Implementation of Climdex Routines 
clime  Constrained L1minimization for Inverse (covariance) Matrix
Estimation 
climtrends  Statistical Methods for Climate Sciences 
climwin  Climate Window Analysis 
clinfun  Clinical Trial Design and Data Analysis Functions 
clinsig  Clinical Significance Functions 
clinUtiDNA  Clinical Utility of DNA Testing 
clipr  Read and Write from the System Clipboard 
clisymbols  Unicode Symbols at the R Prompt 
CLME  Constrained Inference for Linear Mixed Effects Models 
clogitboost  Boosting Conditional Logit Model 
clogitL1  Fitting exact conditional logistic regression with lasso and
elastic net penalties 
cloudUtil  Cloud Utilization Plots 
clpAPI  R Interface to C API of COINOR Clp 
CLSOCP  A smoothing Newton method SOCP solver 
clttools  Central Limit Theorem Experiments (Theoretical and Simulation) 
clubSandwich  ClusterRobust (Sandwich) Variance Estimators with SmallSample
Corrections 
clue  Cluster Ensembles 
ClueR  CLUster Evaluation (CLUE) 
clues  Clustering Method Based on Local Shrinking 
CluMix  Clustering and Visualization of MixedType Data 
clusrank  Wilcoxon Rank Sum Test for Clustered Data 
cluster  "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al. 
clusterCrit  Clustering Indices 
cluster.datasets  Cluster Analysis Data Sets 
ClusteredMutations  Location and Visualization of Clustered Somatic Mutations 
clusterfly  Explore clustering interactively using R and GGobi 
clusterGeneration  Random Cluster Generation (with Specified Degree of Separation) 
clusterGenomics  Identifying clusters in genomics data by recursive partitioning 
clusterhap  Clustering Genotypes in Haplotypes 
clustering.sc.dp  Optimal DistanceBased Clustering for Multidimensional Data with
Sequential Constraint 
clusterPower  Power calculations for clusterrandomized and clusterrandomized
crossover trials 
ClusterRankTest  Rank Tests for Clustered Data 
clusterRepro  Reproducibility of gene expression clusters 
clusterSEs  Calculate ClusterRobust pValues and Confidence Intervals 
clusterSim  Searching for Optimal Clustering Procedure for a Data Set 
ClusterStability  Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions 
clustertend  Check the Clustering Tendency 
clusteval  Evaluation of Clustering Algorithms 
ClustGeo  Clustering of Observations with Geographical Constraints 
clustMD  Model Based Clustering for Mixed Data 
clustMixType  kPrototypes Clustering for Mixed VariableType Data 
ClustMMDD  Variable Selection in Clustering by Mixture Models for Discrete
Data 
ClustOfVar  Clustering of variables 
clustrd  Methods for joint dimension reduction and clustering 
clustsig  Significant Cluster Analysis 
ClustVarLV  Clustering of Variables Around Latent Variables 
clustvarsel  Variable Selection for ModelBased Clustering 
clv  Cluster Validation Techniques 
clValid  Validation of Clustering Results 
cmaes  Covariance Matrix Adapting Evolutionary Strategy 
cmaesr  Covariance Matrix Adaptation Evolution Strategy 
CMC  CronbachMesbah Curve 
CMF  Collective matrix factorization 
cmm  Categorical Marginal Models 
cmna  Computational Methods for Numerical Analysis 
CMPControl  Control Charts for ConwayMaxwellPoisson Distribution 
CMplot  Circle Manhattan Plot 
cmprsk  Subdistribution Analysis of Competing Risks 
cmprskQR  Analysis of Competing Risks Using Quantile Regressions 
cmrutils  Misc Functions of the Center for the Mathematical Research 
cmsaf  Tools for CM SAF Netcdf Data 
cmvnorm  The Complex Multivariate Gaussian Distribution 
cna  A Package for Coincidence Analysis (CNA) 
cncaGUI  Canonical NonSymmetrical Correspondence Analysis in R 
cnmlcd  Maximum Likelihood Estimation of a LogConcave Density Function 
CNOGpro  Copy Numbers of Genes in prokaryotes 
CNprep  Preprocess DNA Copy Number (CN) Data for Detection of CN Events 
CNVassoc  Association Analysis of CNV Data and Imputed SNPs 
CNVassocData  Example data sets for association analysis of CNV data 
coala  A Framework for Coalescent Simulation 
coalescentMCMC  MCMC Algorithms for the Coalescent 
coarseDataTools  A Collection of Functions to Help with Analysis of Coarsely
Observed Data 
cobalt  Covariate Balance Tables and Plots 
COBRA  Nonlinear Aggregation of Predictors 
cobs  COnstrained BSplines (Sparse Matrix Based) 
CoClust  Copula Based Cluster Analysis 
COCONUT  COmbat CONormalization Using conTrols (COCONUT) 
cocor  Comparing Correlations 
cocoreg  Extracts Shared Variation in Collections of Datasets Using
Regression Models 
cocorresp  CoCorrespondence Analysis Methods 
cocron  Statistical Comparisons of Two or more Alpha Coefficients 
coda  Output Analysis and Diagnostics for MCMC 
codadiags  Markov chain Monte Carlo burnin based on "bridge" statistics 
cOde  Automated C Code Generation for Use with the 'deSolve' and
'bvpSolve' Packages 
codep  Multiscale Codependence Analysis 
codetools  Code Analysis Tools for R 
codingMatrices  Alternative Factor Coding Matrices for Linear Model Formulae 
codyn  Community Dynamics Metrics 
coefficientalpha  Robust Coefficient Alpha and Omega with Missing and NonNormal
Data 
coefplot  Plots Coefficients from Fitted Models 
coenocliner  Coenocline Simulation 
coenoflex  GradientBased Coenospace Vegetation Simulator 
coexist  Species coexistence modeling and analysis 
cofeatureR  Generate Cofeature Matrices 
CoImp  Copula based imputation method 
coin  Conditional Inference Procedures in a Permutation Test Framework 
CoinMinD  Simultaneous Confidence Interval for Multinomial Proportion 
cointmonitoR  Consistent Monitoring of Stationarity and Cointegrating
Relationships 
cointReg  Parameter Estimation and Inference in a Cointegrating Regression 
cold  Count Longitudinal Data 
CollapsABEL  Generalized CDH (GCDH) Analysis 
CollocInfer  Collocation Inference for Dynamic Systems 
collUtils  Auxiliary Package for Package 'CollapsABEL' 
coloc  Colocalisation tests of two genetic traits 
coloredICA  Implementation of Colored Independent Component Analysis and
Spatial Colored Independent Component Analysis 
colorfulVennPlot  Plot and add custom coloring to Venn diagrams for 2dimensional,
3dimensional and 4dimensional data 
colorhcplot  Colorful Hierarchical Clustering Dendrograms 
ColorPalette  Color Palettes Generator 
colorRamps  Builds color tables 
colorscience  Color Science Methods and Data 
colorspace  Color Space Manipulation 
colorSpec  Color Calculations with Emphasis on Spectral Data 
colortools  Tools for colors in a HueSaturationValue (HSV) color model 
colourlovers  R Client for the COLOURlovers API 
comato  Analysis of Concept Maps 
COMBIA  Synergy/Antagonism Analyses of Drug Combinations 
combinat  combinatorics utilities 
Combine  GameTheoretic Probability Combination 
CombinePortfolio  Estimation of Optimal Portfolio Weights by Combining Simple
Portfolio Strategies 
CombinePValue  Combine a Vector of Correlated pvalues 
CombinS  Construction Methods of some Series of PBIB Designs 
CombMSC  Combined Model Selection Criteria 
comclim  Community climate statistics 
cometExactTest  Exact Test from the Combinations of Mutually Exclusive
Alterations (CoMEt) Algorithm 
comf  Functions for Thermal Comfort Research 
ComICS  Computational Methods for Immune CellType Subsets 
commandr  Command pattern in R 
commentr  Print Nicely Formatted Comments for Use in Script Files 
CommonJavaJars  Useful libraries for building a Java based GUI under R 
commonmark  Bindings to the CommonMark Reference Implementation 
CommonTrend  Extract and plot common trends from a cointegration system.
Calculate Pvalue for Johansen Statistics 
CommT  Comparative Phylogeographic Analysis using the Community Tree
Framework 
COMMUNAL  Robust Selection of Cluster Number K 
CommunityCorrelogram  Ecological Community Correlogram 
Comp2ROC  Compare Two ROC Curves that Intersect 
compactr  Creates empty plots with compact axis notation 
compare  Comparing Objects for Differences 
compareC  Compare Two Correlated C Indices with Rightcensored Survival
Outcome 
CompareCausalNetworks  Interface to Diverse Estimation Methods of Causal Networks 
compareDF  Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure 
compareGroups  Descriptive Analysis by Groups 
compareODM  comparison of medical forms in CDISC ODM format 
CompareTests  Correct for Verification Bias in Diagnostic Accuracy & Agreement 
comparison  Multivariate likelihood ratio calculation and evaluation 
compeir  Eventspecific incidence rates for competing risks data 
compendiumdb  Tools for Retrieval and Storage of Functional Genomics Data 
compete  Analyzing Social Hierarchies 
CompGLM  ConwayMaxwellPoisson GLM and distribution functions 
compHclust  Complementary Hierarchical Clustering 
Compind  Composite Indicators Functions 
ComplexAnalysis  Numerically Evaluate Integrals and Derivatives (also Higher
Order) of Vector And ComplexValued Functions 
complmrob  Robust Linear Regression with Compositional Data as Covariates 
CompLognormal  Functions for actuarial scientists 
compoisson  ConwayMaxwellPoisson Distribution 
COMPoissonReg  ConwayMaxwell Poisson (COMPoisson) Regression 
Compositional  Compositional Data Analysis 
compositions  Compositional Data Analysis 
compound.Cox  Regression Estimation Based on the Compound Covariate Method
Under the Cox Proportional Hazard Model 
Compounding  Computing Continuous Distributions 
CompQuadForm  Distribution function of quadratic forms in normal variables 
CompR  Paired Comparison Data Analysis 
CompRandFld  CompositeLikelihood Based Analysis of Random Fields 
compute.es  Compute Effect Sizes 
Conake  Continuous Associated Kernel Estimation 
concatenate  HumanFriendly Text from Unknown Strings 
conclust  Pairwise Constraints Clustering 
ConConPiWiFun  Optimisation with Continuous Convex Piecewise (Linear and
Quadratic) Functions 
concor  Concordance 
concordance  Product Concordance 
concreg  Concordance regression 
cond  Approximate conditional inference for logistic and loglinear
models 
condformat  Conditional Formatting in Data Frames 
condGEE  Parameter estimation in conditional GEE for recurrent event gap
times 
condmixt  Conditional Density Estimation with Neural Network Conditional
Mixtures 
condMVNorm  Conditional Multivariate Normal Distribution 
CONDOP  ConditionDependent Operon Predictions 
CondReg  Condition Number Regularized Covariance Estimation 
condSURV  Estimation of the Conditional Survival Function for Ordered
Multivariate Failure Time Data 
condvis  Conditional Visualization for Statistical Models 
coneproj  Primal or Dual Cone Projections with Routines for Constrained
Regression 
conf.design  Construction of factorial designs 
confidence  Confidence Estimation of Environmental State Classifications 
config  Manage Environment Specific Configuration Values 
conformal  Conformal Prediction for Regression and Classification 
confreq  Configural Frequencies Analysis Using LogLinear Modeling 
conicfit  Algorithms for Fitting Circles, Ellipses and Conics Based on the
Work by Prof. Nikolai Chernov 
conics  Plot Conics 
Conigrave  Flexible Tools for Multiple Imputation 
conjoint  Conjoint analysis package 
ConjointChecks  A package to check the cancellation axioms of conjoint
measurement 
connect3  A Tool for Reproducible Research by Converting 'LaTeX' Files
Generated by R Sweave to Rich Text Format Files 
ConnMatTools  Tools for working with connectivity matrices 
conover.test  ConoverIman Test of Multiple Comparisons Using Rank Sums 
ConSpline  Partial Linear LeastSquares Regression using Constrained
Splines 
ConsRank  Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach 
constrainedKriging  Constrained, CovarianceMatching Constrained and Universal Point
or Block Kriging 
ContaminatedMixt  ModelBased Clustering and Classification with the Multivariate
Contaminated Normal Distribution 
contfrac  Continued Fractions 
conting  Bayesian Analysis of Contingency Tables 
contoureR  Contouring of NonRegular ThreeDimensional Data 
contrast  A collection of contrast methods 
controlTest  Median Comparison for TwoSample RightCensored Survival Data 
ConvCalendar  Converts dates between calendars 
ConvergenceConcepts  Seeing convergence concepts in action 
convertGraph  Convert Graphical Files Format 
convevol  Quantifies and assesses the significance of convergent evolution 
convey  Income Concentration Analysis with Complex Survey Samples 
convoSPAT  ConvolutionBased Nonstationary Spatial Modeling 
cooccur  Probabilistic Species CoOccurrence Analysis in R 
coop  CoOperation: Fast Covariance, Correlation, and Cosine
Similarity Operations 
cooptrees  Cooperative aspects of optimal trees in weighted graphs 
copBasic  General Bivariate Copula Theory and Many Utility Functions 
copCAR  Fitting the copCAR Regression Model for Discrete Areal Data 
cope  Coverage Probability Excursion (CoPE) Sets 
copula  Multivariate Dependence with Copulas 
CopulaDTA  Copula Based Bivariate BetaBinomial Model for Diagnostic Test
Accuracy Studies 
copulaedas  Estimation of Distribution Algorithms Based on Copulas 
Copula.Markov  Estimation and Statistical Process Control Under CopulaBased
Time Series Models 
CopulaRegression  Bivariate Copula Based Regression Models 
CopulaREMADA  Copula Mixed Effect Models for Bivariate and Trivariate
MetaAnalysis of Diagnostic Test Accuracy Studies 
CopyDetect  Computing Statistical Indices to Detect Answer Copying on
MultipleChoice Tests 
CopyNumber450kCancer  Baseline Correction for Copy Number Data from Cancer Samples 
Corbi  Collection of Rudimentary Bioinformatics Tools 
corclass  Correlational Class Analysis 
corcounts  Generate correlated count random variables 
cord  Community Estimation in GModels via CORD 
CORE  Cores of Recurrent Events 
CORElearn  Classification, Regression and Feature Evaluation 
coreNLP  Wrappers Around Stanford CoreNLP Tools 
coreSim  Core Functionality for Simulating Quantities of Interest from
Generalised Linear Models 
coreTDT  TDT for compound heterozygous and recessive models 
corHMM  Analysis of Binary Character Evolution 
corkscrew  Preprocessor for Data Modeling 
CORM  The Clustering of Regression Models Method 
corpcor  Efficient Estimation of Covariance and (Partial) Correlation 
corpora  Statistics and data sets for corpus frequency data 
corr2D  Implementation of 2D Correlation Analysis 
CorrBin  Nonparametrics with Clustered Binary and Multinomial Data 
correctedAUC  Correcting AUC for Measurement Error 
CorrectOverloadedPeaks  Correct Overloaded Peaks from GCAPCIMS Data 
CorReg  Linear Regression Based on Linear Structure Between Covariates 
corregp  Functions and Methods for Correspondence Regression 
Correlplot  A collection of functions for graphing correlation matrices 
corrgram  Plot a Correlogram 
CorrMixed  Estimate Correlations Between Repeatedly Measured Endpoints
(E.g., Reliability) Based on Linear MixedEffects Models 
corrplot  Visualization of a Correlation Matrix 
corrr  Correlations in R 
corrsieve  CorrSieve 
CorrToolBox  Modeling Correlational Magnitude Transformations in
Discretization Contexts 
corTools  Tools for processing data after a Genome Wide Association Study 
COSINE  COndition SpecIfic subNEtwork 
cosinor  Tools for estimating and predicting the cosinor model 
cosmoFns  Functions for cosmological distances, times, luminosities, etc 
CosmoPhotoz  Photometric redshift estimation using generalized linear models 
cosmosR  cosmosR 
cosso  Fit Regularized Nonparametric Regression Models Using COSSO
Penalty 
costat  Time series costationarity determination 
CosW  The CosW Distribution 
cotrend  Consistant Cotrend Rank Selection 
couchDB  Connect to and Work with CouchDB Databases 
COUNT  Functions, data and code for count data 
Countr  Flexible Univariate and Bivariate Count Process Probability 
countrycode  Convert Country Names and Country Codes 
CountsEPPM  Mean and Variance Modeling of Count Data 
countytimezones  Convert from UTC to Local Time for United States Counties 
COUSCOus  A ResidueResidue Contact Detecting Method 
covafillr  Local Polynomial Regression of State Dependent Covariates in
StateSpace Models 
covBM  Brownian Motion Processes for 'nlme'Models 
covLCA  Latent Class Models with Covariate Effects on Underlying and
Measured Variables 
covmat  Covariance Matrix Estimation 
covr  Test Coverage for Packages 
covreg  A simultaneous regression model for the mean and covariance 
covRobust  Robust Covariance Estimation via Nearest Neighbor Cleaning 
CovSel  ModelFree Covariate Selection 
CovSelHigh  ModelFree Covariate Selection in High Dimensions 
covsep  Tests for Determining if the Covariance Structure of
2Dimensional Data is Separable 
covTest  Computes covariance test for adaptive linear modelling 
cowplot  Streamlined Plot Theme and Plot Annotations for 'ggplot2' 
cowsay  Messages, Warnings, Strings with Ascii Animals 
CoxBoost  Cox models by likelihood based boosting for a single survival
endpoint or competing risks 
coxinterval  CoxType Models for IntervalCensored Data 
coxme  Mixed Effects Cox Models 
Coxnet  Regularized Cox Model 
coxphf  Cox regression with Firth's penalized likelihood 
coxphw  Weighted Estimation in Cox Regression 
CoxPlus  Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects 
CoxRidge  Cox Models with Dynamic Ridge Penalties 
coxrobust  Robust Estimation in Cox Model 
coxsei  Fitting a CoxSEI Model 
CP  Conditional Power Calculations 
cp4p  Calibration Plot for Proteomics 
cpa  Confirmatory Path Analysis through the dsep tests 
cpca  Methods to perform Common Principal Component Analysis (CPCA) 
CPE  Concordance Probability Estimates in Survival Analysis 
CpGassoc  Association Between Methylation and a Phenotype of Interest 
cpgen  Parallelized Genomic Prediction and GWAS 
CpGFilter  CpG Filtering Method Based on Intraclass Correlation
Coefficients 
CPHshape  Find the maximum likelihood estimator of the shape constrained
hazard baseline and the effect parameters in the Cox
proportional hazards model 
cpk  Clinical Pharmacokinetics 
cplexAPI  R Interface to C API of IBM ILOG CPLEX 
cplm  Compound Poisson Linear Models 
cpm  Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods 
CPMCGLM  Correction of the pvalue after multiple coding 
Cprob  Conditional probability function of a competing event 
cqrReg  Quantile, Composite Quantile Regression and Regularized Versions 
cquad  Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data 
CR  Power Calculation for Weighted LogRank Tests in Cure Rate
Models 
CRAC  Cosmology R Analysis Code 
crackR  Probabilistic damage tolerance analysis for fatigue cracking of
metallic aerospace structures 
cramer  Multivariate nonparametric CramerTest for the
twosampleproblem 
crandatapkgs  Find DataOnly Packages on CRAN 
crank  Completing Ranks 
cranlogs  Download Logs from the 'RStudio' 'CRAN' Mirror 
crantastic  Various R tools for http://crantastic.org/ 
crawl  Fit ContinuousTime Correlated Random Walk Models to Animal
Movement Data 
crayon  Colored Terminal Output 
crblocks  Categorical Randomized Block Data Analysis 
crch  Censored Regression with Conditional Heteroscedasticity 
CreditMetrics  Functions for calculating the CreditMetrics risk model 
creditr  Credit Default Swaps in R 
credule  Credit Default Swap Functions 
CRF  Conditional Random Fields 
cricketr  Analyze Cricketers Based on ESPN Cricinfo Statsguru 
crimCV  GroupBased Modelling of Longitudinal Data 
crimelinkage  Statistical Methods for Crime Series Linkage 
CRM  Continual Reassessment Method (CRM) for Phase I Clinical Trials 
crmn  CCMN and other noRMalizatioN methods for metabolomics data 
crmPack  ObjectOriented Implementation of CRM Designs 
crn  Downloads and Builds datasets for Climate Reference Network 
crop  Graphics Cropping Tool 
CrossClustering  A Partial Clustering Algorithm with Automatic Estimation of the
Number of Clusters and Identification of Outliers 
crossdes  Construction of Crossover Designs 
crossmatch  The Crossmatch Test 
Crossover  Analysis and Search of Crossover Designs 
crossReg  Confidence intervals for crossover points of two simple
regression lines 
crossval  Generic Functions for Cross Validation 
crp.CSFP  CreditRisk+ Portfolio Model 
crqa  CrossRecurrence Quantification Analysis for Categorical and
Continuous TimeSeries 
crrp  Penalized Variable Selection in Competing Risks Regression 
crrSC  Competing risks regression for Stratified and Clustered data 
crrstep  Stepwise Covariate Selection for the Fine & Gray Competing Risks
Regression Model 
crs  Categorical Regression Splines 
crskdiag  Diagnostics for Fine and Gray Model 
crsnls  Nonlinear Regression Parameters Estimation by 'CRS4HC' and
'CRS4HCe' 
crtests  Classification and Regression Tests 
CRTgeeDR  Doubly Robust Inverse Probability Weighted Augmented GEE
Estimator 
CRTSize  Sample Size Estimation Functions for Cluster Randomized Trials 
crunch  Crunch.io Data Tools 
cruts  Interface to Climatic Research Unit TimeSeries Version 3.21
Data 
CrypticIBDcheck  Identifying cryptic relatedness in genetic association studies 
CryptRndTest  Statistical Tests for Cryptographic Randomness 
csampling  Functions for Conditional Simulation in RegressionScale Models 
cSFM  Covariateadjusted Skewed Functional Model (cSFM) 
cshapes  CShapes Dataset and Utilities 
cslogistic  Conditionally Specified Logistic Regression 
csn  Closed SkewNormal Distribution 
csp  Correlates of State Policy Data Set in R 
csrplus  Methods to Test Hypotheses on the Distribution of Spatial Point
Processes 
csSAM  csSAM  cellspecific Significance Analysis of Microarrays 
cssTools  Cognitive Social Structure Tools 
cstar  Substantive significance testing for regression estimates and
marginal effects 
csvread  Fast Specialized CSV File Loader 
ctmcmove  Modeling Animal Movement with ContinuousTime DiscreteSpace
Markov Chains 
ctmm  ContinuousTime Movement Modeling 
cts  Continuous Time Autoregressive Models 
ctsem  Continuous Time Structural Equation Modelling 
CTT  Classical Test Theory Functions 
CTTShiny  Classical Test Theory via Shiny 
ctv  CRAN Task Views 
CUB  A Class of Mixture Models for Ordinal Data 
cubature  Adaptive multivariate integration over hypercubes 
cubfits  Codon Usage Bias Fits 
Cubist  Rule and InstanceBased Regression Modeling 
cudaBayesreg  CUDA Parallel Implementation of a Bayesian Multilevel Model for
fMRI Data Analysis 
cudaBayesregData  Data sets for the examples used in the package "cudaBayesreg" 
cudia  CUDIA Crosslevel Imputation 
CUFF  Charles's Utility Function using Formula 
CUMP  Analyze Multivariate Phenotypes by Combining Univariate results 
cumplyr  Extends ddply to allow calculation of cumulative quantities 
cumSeg  Change point detection in genomic sequences 
curl  A Modern and Flexible Web Client for R 
curlconverter  Tools to Transform 'cURL' CommandLine Calls to 'httr' Requests 
currentSurvival  Estimation of CCI and CLFS Functions 
curvetest  The package will formally test two curves represented by
discrete data sets to be statistically equal or not when the
errors of the two curves were assumed either equal or not using
the tube formula to calculate the tail probabilities 
curvHDR  Filtering of Flow Cytometry Samples 
cusp  CuspCatastrophe Model Fitting Using Maximum Likelihood 
customizedTraining  Customized Training for Lasso and ElasticNet Regularized
Generalized Linear Models 
CUSUMdesign  Compute Decision Interval and Average Run Length for CUSUM
Charts 
cutoffR  CUTOFF: A Spatiotemporal Imputation Method 
cuttlefish.model  An R package to perform LPUE standardization and stock
assessment of the English Channel cuttlefish stock using a
twostage biomass model 
cvAUC  CrossValidated Area Under the ROC Curve Confidence Intervals 
CVcalibration  Estimation of the Calibration Equation with Errorin
Observations 
cvplogistic  Penalized Logistic Regression Model using Majorization
Minimization by Coordinate Descent (MMCD) Algorithm 
cvq2  Calculate the predictive squared correlation coefficient 
CVST  Fast CrossValidation via Sequential Testing 
CVThresh  LevelDependent CrossValidation Thresholding 
cvTools  Crossvalidation tools for regression models 
CVTuningCov  Regularized Estimators of Covariance Matrices with CV Tuning 
cvxbiclustr  Convex Biclustering Algorithm 
cvxclustr  Splitting methods for convex clustering 
cwhmisc  Miscellaneous Functions for Math, Plotting, Printing,
Statistics, Strings, and Tools 
cwm  Cluster Weighted Models by EM algorithm 
cxxfunplus  extend cxxfunction by saving the dynamic shared objects 
cycleRtools  Tools for Cycling Data Analysis 
cyclocomp  Cyclomatic Complexity of R Code 
cycloids  cycloids 
cymruservices  Query 'Team Cymru' 'IP' Address, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware'
Hash Data Services 
cyphid  Cycle and Phase Identification for mastication data 
cystiSim  AgentBased Model for Taenia_solium Transmission and Control 
cytoDiv  Cytometric diversity indices 

D2C  Predicting Causal Direction from Dependency Features 
d3heatmap  Interactive Heat Maps Using 'htmlwidgets' and 'D3.js' 
D3M  Two Sample Test with Wasserstein Metric 
d3Network  Tools for creating D3 JavaScript network, tree, dendrogram, and
Sankey graphs from R 
DAAG  Data Analysis and Graphics Data and Functions 
DAAGbio  Data Sets and Functions, for demonstrations with expression
arrays and gene sequences 
DAAGxtras  Data Sets and Functions, supplementary to DAAG 
dad  ThreeWay Data Analysis Through Densities 
dae  Functions Useful in the Design and ANOVA of Experiments 
daewr  Design and Analysis of Experiments with R 
daff  Diff, Patch and Merge for Data.frames 
dafs  Data analysis for forensic scientists 
dagbag  Learning directed acyclic graphs (DAGs) through bootstrap
aggregating 
DAGGER  Consensus genetic maps 
dagitty  Graphical Analysis of Structural Causal Models 
dagR  R functions for directed acyclic graphs 
Daim  Diagnostic accuracy of classification models 
DAISIE  Dynamical Assembly of Islands by Speciation, Immigration and
Extinction 
DAKS  Data Analysis and Knowledge Spaces 
DALY  DALY Calculator  A GUI for stochastic DALY calculation in R 
dam  Data Analysis Metabolomics 
DAMisc  Dave Armstrong's Miscellaneous Functions 
DAMOCLES  Dynamic Assembly Model of Colonization, Local Extinction and
Speciation 
dams  Dams in the United States from the National Inventory of Dams
(NID) 
DandEFA  Dandelion Plot for RMode Exploratory Factor Analysis 
darch  Package for Deep Architectures and Restricted Boltzmann Machines 
Dark  The Analysis of Dark Adaptation Data 
darts  Statistical Tools to Analyze Your Darts Game 
dashboard  Interactive Data Visualization with D3.js 
DatABEL  FileBased Access to Large Matrices Stored on HDD in Binary
Format 
datacheck  Tools for Checking Data Consistency 
datacheckr  Data Checking 
DataClean  Data Cleaning 
DataCombine  Tools for Easily Combining and Cleaning Data Sets 
datadr  Divide and Recombine for Large, Complex Data 
DataExplorer  Data Explorer 
dataframes2xls  dataframes2xls writes data frames to xls files 
datafsm  Estimating Finite State Machine Models from Data 
DataLoader  Import Multiple File Types 
datamap  A system for mapping foreign objects to R variables and
environments 
datamart  Unified access to your data sources 
dataonderivatives  Easily Source Publicly Available Data on Derivatives 
dataone  R Interface to the DataONE REST API 
datapack  A Flexible Container to Transport and Manipulate Data and
Associated Resources 
dataQualityR  Performs variable level data quality checks and generates
summary statistics 
dataRetrieval  Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data 
datarobot  DataRobot Predictive Modeling API 
datastepr  An Implementation of a SASStyle Data Step 
data.table  Extension of Data.frame 
data.tree  General Purpose Hierarchical Data Structure 
datautils  Support functions for packages VBmix, semisupKernelPCA, and
patchPlot 
dataview  Data and Workspace Browser for Terminals 
date  Functions for handling dates 
DATforDCEMRI  Deconvolution Analysis Tool for Dynamic Contrast Enhanced MRI 
dave  Functions for "Data Analysis in Vegetation Ecology" 
Davies  The Davies Quantile Function 
dawai  Discriminant Analysis with Additional Information 
dbarts  Discrete Bayesian Additive Regression Trees Sampler 
dbConnect  Provides a graphical user interface to connect with databases
that use MySQL 
dbEmpLikeGOF  Goodnessoffit and two sample comparison tests using sample
entropy 
dbEmpLikeNorm  Test for joint assessment of normality 
DBEST  Detecting Breakpoints and Estimating Segments in Trend 
DBGSA  methods of distancebased gene set functional enrichment
analysis 
DBI  R Database Interface 
DBItest  Testing 'DBI' Back Ends 
DBKGrad  Discrete Beta Kernel Graduation of Mortality Data 
dblcens  Compute the NPMLE of distribution from doubly censored data 
dbmss  DistanceBased Measures of Spatial Structures 
dbscan  Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms 
dbstats  DistanceBased Statistics 
DCchoice  Analyzing Dichotomous Choice Contingent Valuation Data 
dcemriS4  A Package for Image Analysis of DCEMRI (S4 Implementation) 
DCG  Data Cloud Geometry (DCG): Using Random Walks to Find Community
Structure in Social Network Analysis 
DCGL  Differential Coexpression Analysis and Differential Regulation
Analysis of Gene Expression Microarray Data 
dcGOR  Analysis of Ontologies and Protein Domain Annotations 
dChipIO  Methods for Reading dChip Files 
DCL  Claims Reserving under the Double Chain Ladder Model 
dclone  Data Cloning and MCMC Tools for Maximum Likelihood Methods 
DCluster  Functions for the Detection of Spatial Clusters of Diseases 
dcmle  Hierarchical Models Made Easy with Data Cloning 
dcmr  Attribute profile estimation using Diagnostic Classification
Models and MCMC 
DCODE  List Linear nPeptide Constraints for Overlapping Protein
Regions 
dCovTS  Distance Covariance and Correlation for Time Series Analysis 
dcv  Conventional Crossvalidation statistics for climategrowth
model 
ddalpha  DepthBased Classification and Calculation of Data Depth 
DDD  DiversityDependent Diversification 
ddeploy  Wrapper for the Duke Deploy REST API 
DDHFm  Variance Stabilization by DataDriven HaarFisz (for
Microarrays) 
DDIwR  DDI with R 
ddpcr  Analysis and Visualization of Droplet Digital PCR in R and on
the Web 
ddR  Distributed Data Structures in R 
DDRTree  Learning Principal Graphs with DDRTree 
ddst  Data Driven Smooth Tests 
deal  Learning Bayesian Networks with Mixed Variables 
deamer  Deconvolution density estimation with adaptive methods for a
variable prone to measurement error 
debug  MVB's debugger for R 
DECIDE  DEComposition of Indirect and Direct Effects 
decision  Statistical Decision Analysis 
DecisionCurve  Calculate and Plot Decision Curves 
decisionSupport  Quantitative Support of Decision Making under Uncertainty 
decode  Differential CoExpression and Differential Expression Analysis 
decoder  Decode Coded Variables to Plain Text (and Vice Versa) 
decompr  GlobalValueChain Decomposition 
decon  Deconvolution Estimation in Measurement Error Models 
deconstructSigs  Identifies Signatures Present in a Tumor Sample 
Deducer  A Data Analysis GUI for R 
DeducerExtras  Additional dialogs and functions for Deducer 
DeducerPlugInExample  Deducer Plugin Example 
DeducerPlugInScaling  Reliability and factor analysis plugin 
DeducerSpatial  Deducer for spatial data analysis 
DeducerSurvival  Add Survival Dialogue to Deducer 
DeducerText  Deducer GUI for Text Data 
deducorrect  Deductive Correction, Deductive Imputation, and Deterministic
Correction 
deductive  Data Correction and Imputation Using Deductive Methods 
deepboost  Deep Boosting Ensemble Modeling 
deeplearning  An Implementation of Deep Neural Network for Regression and
Classification 
deepnet  deep learning toolkit in R 
DEEPR  Dirichletmultinomial Evolutionary Event Profile Randomization
(DEEPR) test 
deformula  Integration of OneDimensional Functions with Double Exponential
Formulas 
degenes  Detection of differentially expressed genes 
degreenet  Models for Skewed Count Distributions Relevant to Networks 
Delaporte  Statistical Functions for the Delaporte Distribution 
deldir  Delaunay Triangulation and Dirichlet (Voronoi) Tessellation 
DeLorean  Estimates Pseudotimes for Single Cell Expression Data 
delt  Estimation of Multivariate Densities Using Adaptive Partitions 
deltaPlotR  Identification of dichotomous differential item functioning
(DIF) using Angoff's Delta Plot method 
Demerelate  Functions to Calculate Relatedness on Diploid Genetic Data 
DEMEtics  Evaluating the genetic differentiation between populations based
on Gst and D values 
demi  Differential Expression from Multiple Indicators 
deming  Deming, ThielSen and PassingBablock Regression 
demography  Forecasting mortality, fertility, migration and population data 
demoKde  Kernel Density Estimation for Demonstration Purposes 
DEMOVA  DEvelopment (of MultiLinear QSPR/QSAR) MOdels VAlidated using
Test Set 
dendextend  Extending R's Dendrogram Functionality 
dendextendRcpp  Faster Dendrogram Manipulation using 'Rcpp' 
dendroextras  Extra functions to cut, label and colour dendrogram clusters 
dendrometeR  Analyzing Dendrometer Data 
DendSer  Dendrogram seriation: ordering for visualisation 
dendsort  Modular Leaf Ordering Methods for Dendrogram Nodes 
DengueRT  Parameter Estimates and RealTime Prediction of a Single Dengue
Outbreak 
denoiseR  Regularized Low Rank Matrix Estimation 
denovolyzeR  Statistical Analyses of De Novo Genetic Variants 
denpro  Visualization of Multivariate Functions, Sets, and Data 
densityClust  Clustering by Fast Search and Find of Density Peaks 
Density.T.HoldOut  Density.T.HoldOut: Noncombinatorial Testimation HoldOut for
density estimation 
DensParcorr  DensBased Method for Partial Correlation Estimation in Large
Scale Brain Networks 
densratio  Density Ratio Estimation 
denstrip  Density strips and other methods for compactly illustrating
distributions 
DEoptim  Global Optimization by Differential Evolution 
DEoptimR  Differential Evolution Optimization in Pure R 
depend.truncation  Statistical Inference for Parametric and Semiparametric Models
Based on Dependently Truncated Data 
depmix  Dependent Mixture Models 
depmixS4  Dependent Mixture Models  Hidden Markov Models of GLMs and
Other Distributions in S4 
depth  Depth functions tools for multivariate analysis 
depth.plot  Multivariate Analogy of Quantiles 
DepthProc  Statistical Depth Functions for Multivariate Analysis 
depthTools  Depth Tools Package 
dequer  An R 'Deque' Container 
Deriv  Symbolic Differentiation 
derivmkts  Functions and R Code to Accompany Derivatives Markets 
desc  Manipulate DESCRIPTION Files 
descomponer  Seasonal Adjustment by Frequency Analysis 
descr  Descriptive Statistics 
DescribeDisplay  An Interface to the DescribeDisplay GGobi Plugin 
describer  Describe Data in R Using Common Descriptive Statistics 
DescTools  Tools for Descriptive Statistics 
deseasonalize  Optimal deseasonalization for geophysical time series using AR
fitting 
designGG  Computational tool for designing genetical genomics experiments 
designGLMM  Finding Optimal Block Designs for a Generalised Linear Mixed
Model 
designmatch  Construction of Optimally Matched Samples for Randomized
Experiments and Observational Studies that are Balanced by
Design 
desiR  Desirability Functions for Ranking, Selecting, and Integrating
Data 
desirability  Desirability Function Optimization and Ranking 
desire  Desirability functions in R 
DESnowball  Bagging with Distancebased Regression for Differential Gene
Expression Analyses 
deSolve  Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE) 
DESP  Estimation of Diagonal Elements of Sparse PrecisionMatrices 
desplot  Plotting Field Plans for Agricultural Experiments 
detect  Analyzing Wildlife Data with Detection Error 
detector  Detect Data Containing Personally Identifiable Information 
deTestSet  Testset for differential equations 
DetMCD  Implementation of the DetMCD Algorithm (Robust and Deterministic
Estimation of Location and Scatter) 
DetR  Suite of Deterministic and Robust Algorithms for Linear
Regression 
detrendeR  Start the detrendeR Graphical User Interface (GUI) 
DetSel  A computer program to detect markers responding to selection 
detzrcr  Compare Detrital Zircon Suites 
devEMF  EMF Graphics Output Device 
Devore7  Data sets from Devore's "Prob and Stat for Eng (7th ed)" 
devtools  Tools to Make Developing R Packages Easier 
df2json  Convert a dataframe to JSON 
dfcomb  Phase I/II Adaptive DoseFinding Design for Combination Studies 
dfcrm  Dosefinding by the continual reassessment method 
dfexplore  Explore data.frames by plotting NA and classes of each variable 
DFIT  Differential Functioning of Items and Tests 
dfmta  Phase I/II Adaptive DoseFinding Design for MTA 
dfoptim  DerivativeFree Optimization 
dga  CaptureRecapture Estimation using Bayesian Model Averaging 
dggridR  Discrete Global Grids for R 
dglars  Differential Geometric LARS (dgLARS) method 
dglm  Double Generalized Linear Models 
dgmb  Simulating Data for PLS Mode B Structural Models 
dgof  Discrete GoodnessofFit Tests 
dhglm  Double Hierarchical Generalized Linear Models 
dHSIC  Independence Testing via Hilbert Schmidt Independence Criterion 
diagonals  Block Diagonal Extraction or Replacement 
diagram  Functions for visualising simple graphs (networks), plotting
flow diagrams 
DiagrammeR  Create Graph Diagrams and Flowcharts Using R 
DiagrammeRsvg  Export DiagrammeR Graphviz Graphs as SVG 
DiagTest3Grp  Diagnostic test summary measures for three ordinal groups 
DiallelAnalysisR  Diallel Analysis with R 
diaplt  Beads Summary Plot of Ranges 
dice  Calculate probabilities of various dicerolling events 
DiceDesign  Designs of Computer Experiments 
DiceEval  Construction and Evaluation of Metamodels 
DiceKriging  Kriging Methods for Computer Experiments 
DiceOptim  KrigingBased Optimization for Computer Experiments 
DiceView  Plot methods for computer experiments design and surrogate 
dichromat  Color Schemes for Dichromats 
dicionariosIBGE  Dictionaries for reading microdata surveys from IBGE 
DidacticBoost  A Simple Implementation and Demonstration of Gradient Boosting 
dielectric  Defines some physical constants and dielectric functions
commonly used in optics, plasmonics 
diezeit  R Interface to the ZEIT ONLINE Content API 
DIFboost  Detection of Differential Item Functioning (DIF) in Rasch Models
by Boosting Techniques 
DiffCorr  Analyzing and Visualizing Differential Correlation Networks in
Biological Data 
diffdepprop  Calculates Confidence Intervals for two Dependent Proportions 
diffEq  Functions from the book Solving Differential Equations in R 
diffeR  Metrics of Difference for Comparing Pairs of Maps 
diffIRT  Diffusion IRT Models for Response and Response Time Data 
diffr  Display Differences Between Two Files using Codediff Library 
diffractometry  Baseline identification and peak decomposition for xray
diffractograms 
diffusionMap  Diffusion map 
DiffusionRgqd  Inference and Analysis for Generalized Quadratic Diffusions 
DiffusionRimp  Inference and Analysis for Diffusion Processes via Data
Imputation and Method of Lines 
DiffusionRjgqd  Inference and Analysis for Jump Generalized Quadratic Diffusions 
DIFlasso  A Penalty Approach to Differential Item Functioning in Rasch
Models 
difNLR  Detection of Dichotomous Differential Item Functioning (DIF) by
NonLinear Regression Function 
difR  Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF) 
DIFtree  Item Focused Trees for the Identification of Items in
Differential Item Functioning 
digest  Create Compact Hash Digests of R Objects 
Digiroo2  An application programming interface for generating null models
of social contacts based on individuals' space use 
digitalPCR  Estimate Copy Number for Digital PCR 
dils  DataInformed Link Strength. Combine multiplerelationship
networks into a single weighted network. Impute (fillin)
missing network links 
DIME  DIME (Differential Identification using Mixture Ensemble) 
dina  Bayesian Estimation of DINA Model 
dinamic  DiNAMIC A Method To Analyze Recurrent DNA Copy Number
Aberrations in Tumors 
diptest  Hartigan's Dip Test Statistic for Unimodality  Corrected 
DIRECT  Bayesian Clustering of Multivariate Data Under the
DirichletProcess Prior 
Directional  Directional Statistics 
directlabels  Direct Labels for Multicolor Plots 
directPA  Direction Analysis for Pathways and Kinases 
DirichletReg  Dirichlet Regression in R 
dirmult  Estimation in DirichletMultinomial distribution 
Disake  Discrete associated kernel estimators 
discgolf  Discourse 'API' Client 
disclap  Discrete Laplace Exponential Family 
disclapmix  Discrete Laplace Mixture Inference using the EM Algorithm 
DiscML  DiscML: An R package for estimating evolutionary rates of
discrete characters using maximum likelihood 
DiscreteInverseWeibull  Discrete Inverse Weibull Distribution 
DiscreteLaplace  Discrete Laplace Distributions 
discreteMTP  Multiple testing procedures for discrete test statistics 
discreteRV  Create and Manipulate Discrete Random Variables 
DiscreteWeibull  Discrete Weibull Distributions (Type 1 and 3) 
discretization  Data preprocessing, discretization for classification 
discrimARTs  Discrimination of Alternative Reproductive Tactics (ARTs) 
DiscriMiner  Tools of the Trade for Discriminant Analysis 
discSurv  Discrete Time Survival Analysis 
diseasemapping  Modelling Spatial Variation in Disease Risk for Areal Data 
DisimForMixed  Calculate Dissimilarity Matrix for Dataset with Mixed Attributes 
diskImageR  A Pipeline to Analyze Resistance and Tolerance from Drug Disk
Diffusion Assays 
dismo  Species Distribution Modeling 
disp2D  2D Hausdorff and Simplex Dispersion Orderings 
disparityfilter  Disparity Filter Algorithm for Weighted Networks 
displayHTS  displayHTS 
dispmod  Dispersion models 
disposables  Create Disposable R Packages for Testing 
dissUtils  Utilities for making pairwise comparisons of multivariate data 
Distance  Distance Sampling Detection Function and Abundance Estimation 
distance.sample.size  Calculates Study Size Required for Distance Sampling 
DistatisR  DiSTATIS Three Way Metric Multidimensional Scaling 
distcomp  Computations over Distributed Data without Aggregation 
distfree.cr  Distributionfree confidence region (distfree.cr) 
distillery  Method Functions for Confidence Intervals and to Distill
Information from an Object 
distory  Distance Between Phylogenetic Histories 
distr  Object Oriented Implementation of Distributions 
distrDoc  Documentation for 'distr' Family of R Packages 
distrEllipse  S4 classes for elliptically contoured distributions 
distrEx  Extensions of Package 'distr' 
DistributionUtils  Distribution Utilities 
distrMod  Object Oriented Implementation of Probability Models 
distrom  Distributed Multinomial Regression 
distrRmetrics  Distribution Classes for Distributions from Rmetrics 
distrSim  Simulation Classes Based on Package 'distr' 
distrTeach  Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School 
distrTEst  Estimation and Testing Classes Based on Package 'distr' 
divagis  Provides tools for quality checks of georeferenced plant species
accessions 
DivE  Diversity Estimator 
diveMove  Dive Analysis and Calibration 
diverse  Diversity Measures for Complex Systems 
diversitree  Comparative Phylogenetic Analyses of Diversification 
diveRsity  A Comprehensive, General Purpose Population Genetics Analysis
Package 
DiversityOccupancy  Building Diversity Models from Multiple Species Occupancy Models 
DiversitySampler  Functions for resampling a community matrix to compute
diversity indices at different sampling levels 
DivMelt  HRM Diversity Assay Analysis Tool 
divo  Tools for Analysis of Diversity and Similarity in Biological
Systems 
dixon  Nearest Neighbour Contingency Table Analysis 
DJL  Distance Measure Based Judgment and Learning 
dkDNA  Diffusion Kernels on a Set of Genotypes 
dlm  Bayesian and Likelihood Analysis of Dynamic Linear Models 
dlmap  Detection Localization Mapping for QTL 
dlmodeler  Generalized Dynamic Linear Modeler 
DLMtool  DataLimited Methods Toolkit 
dlnm  Distributed Lag NonLinear Models 
dlsem  DistributedLag Structural Equation Modelling 
dlstats  Download Stats of R Packages 
dma  Dynamic Model Averaging 
dml  Distance Metric Learning in R 
dmm  Dyadic Mixed Model for Pedigree Data 
dMod  Dynamic Modeling and Parameter Estimation in ODE Models 
DMR  Delete or Merge Regressors for linear model selection 
dmt  Dependency Modeling Toolkit 
DMwR  Functions and data for "Data Mining with R" 
dna  Differential Network Analysis 
DNAprofiles  DNA Profiling Evidence Analysis 
DNAseqtest  Generating and Testing DNA Sequences 
DNAtools  Tools for Analysing Forensic Genetic DNA Data 
dnc  Dynamic Network Clustering 
DnE  Distribution and Equation 
dnet  Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology 
DNMF  Discriminant NonNegative Matrix Factorization 
DOBAD  Analysis of Discretely Observed Linear
BirthandDeath(andImmigration) Markov Chains 
doBy  Groupwise Statistics, LSmeans, Linear Contrasts, Utilities 
docopt  CommandLine Interface Specification Language 
docopulae  Optimal Designs for Copula Models 
documair  Automatic Documentation for R packages 
docxtractr  Extract Data Tables and Comments from Microsoft Word Documents 
Dodge  Functions for Acceptance Sampling Ideas originated by H.F. Dodge 
DODR  Detection of Differential Rhythmicity 
DoE.base  Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages 
DoE.wrapper  Wrapper package for design of experiments functionality 
doFuture  Foreach Parallel Adaptor using the Future API of the 'future'
Package 
doMC  Foreach Parallel Adaptor for 'parallel' 
Dominance  ADI (Average Dominance Index), Social Network Graphs with Dual
Directions, and Music Notation Graph 
domino  R Console Bindings for the 'Domino CommandLine Client' 
doMPI  Foreach parallel adaptor for the Rmpi package 
doParallel  Foreach Parallel Adaptor for the 'parallel' Package 
doRedis  Foreach parallel adapter for the rredis package 
doRNG  Generic Reproducible Parallel Backend for foreach Loops 
DoseFinding  Planning and Analyzing Dose Finding Experiments 
doSNOW  Foreach Parallel Adaptor for the 'snow' Package 
dosresmeta  Performing Multivariate DoseResponse MetaAnalysis 
dostats  Compute Statistics Helper Functions 
DOT  Render and Export DOT Graphs in R 
DoTC  Distribution of Typicality Coefficients 
dotenv  Load Environment Variables from '.env' 
dotwhisker  DotandWhisker Plots of Regression Results 
DoubleCone  Test against parametric regression function 
DoubleExpSeq  Differential Exon Usage Test for RNASeq Data via Empirical
Bayes Shrinkage of the Dispersion Parameter 
DOvalidation  Local Linear Hazard Estimation with DoValidated and
CrossValidated Bandwidths 
Dowd  Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's
Book Measuring Market Risk 
downloader  Download Files over HTTP and HTTPS 
downscale  Downscaling Species Occupancy 
dpa  Dynamic Path Approach 
dpcR  Digital PCR Analysis 
dpglasso  Primal Graphical Lasso 
dplR  Dendrochronology Program Library in R 
dplRCon  Concordance for Dendroclimatology 
dplyr  A Grammar of Data Manipulation 
dpmixsim  Dirichlet Process Mixture model simulation for clustering and
image segmentation 
dpmr  Data Package Manager for R 
DPpackage  Bayesian nonparametric modeling in R 
dprep  Data PreProcessing and Visualization Functions for
Classification 
dr  Methods for Dimension Reduction for Regression 
drat  Drat R Archive Template 
drawExpression  Visualising R syntax through graphics 
DRaWR  Discriminative Random Walk with Restart 
DrBats  Data Representation: Bayesian Approach That's Sparse 
drc  Analysis of DoseResponse Curves 
DREGAR  Regularized Estimation of Dynamic Linear Regression in the
Presence of Autocorrelated Residuals (DREGAR) 
drfit  DoseResponse Data Evaluation 
drgee  Doubly Robust Generalized Estimating Equations 
DrillR  R Driver for Apache Drill 
DRIP  Discontinuous Regression and Image Processing 
drLumi  Multiplex Immunoassays Data Analysis 
drm  Regression and association models for repeated categorical data 
drmdel  Dual Empirical Likelihood Inference under Density Ratio Models
in the Presence of Multiple Samples 
dropR  Analyze Drop Out of an Experiment or Survey 
drsmooth  DoseResponse Modeling with Smoothing Splines 
DrugClust  Implementation of a Machine Learning Framework for Predicting
Drugs Side Effects 
ds  Descriptive Statistics 
dsample  DiscretizationBased Direct Random Sample Generation 
DSBayes  Bayesian subgroup analysis in clinical trials 
dse  Dynamic Systems Estimation (Time Series Package) 
DSL  Distributed Storage and List 
dslice  Dynamic Slicing 
dsm  Density Surface Modelling of Distance Sampling Data 
DSpat  Spatial Modelling for Distance Sampling Data 
DSsim  Distance Sampling Simulations 
dst  Using DempsterShafer Theory 
DStree  Recursive Partitioning for DiscreteTime Survival Trees 
DSviaDRM  Exploring Disease Similarity in Terms of Dysfunctional
Regulatory Mechanisms 
DT  A Wrapper of the JavaScript Library 'DataTables' 
dtables  Simplifying Descriptive Frequencies and Statistics 
DTComPair  Comparison of Binary Diagnostic Tests in a Paired Study Design 
DTDA  Doubly truncated data analysis 
dti  Analysis of Diffusion Weighted Imaging (DWI) Data 
DTK  DunnettTukeyKramer Pairwise Multiple Comparison Test Adjusted
for Unequal Variances and Unequal Sample Sizes 
DTMCPack  Suite of functions related to discretetime discretestate
Markov Chains 
dtplyr  Data Table BackEnd for 'dplyr' 
DTR  Estimation and Comparison of Dynamic Treatment Regimes 
DTRlearn  Learning Algorithms for Dynamic Treatment Regimes 
DTRreg  DTR Estimation and Inference via GEstimation, Dynamic WOLS, and
QLearning 
dtt  Discrete Trigonometric Transforms 
dtw  Dynamic Time Warping Algorithms 
dtwclust  Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance 
dtwSat  TimeWeighted Dynamic Time Warping for Satellite Image Time
Series Analysis 
dualScale  Dual Scaling Analysis of Multiple Choice Data 
dummies  Create dummy/indicator variables flexibly and efficiently 
dummy  Automatic Creation of Dummies with Support for Predictive
Modeling 
DunnettTests  Software implementation of stepdown and stepup Dunnett test
procedures 
dunn.test  Dunn's Test of Multiple Comparisons Using Rank Sums 
dupiR  Bayesian inference from count data using discrete uniform priors 
dvfBm  Discrete variations of a fractional Brownian motion 
DVHmetrics  Analyze DoseVolume Histograms and Check Constraints 
dvn  Access to Dataverse 3 APIs 
DWreg  Parametric Regression for Discrete Response 
dygraphs  Interface to 'Dygraphs' Interactive Time Series Charting Library 
DYM  Did You Mean? 
dyn  Time Series Regression 
DynamicDistribution  Dynamically visualized probability distributions and their
moments 
dynamicGraph  dynamicGraph 
dynamicTreeCut  Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms 
dynatopmodel  Implementation of the Dynamic TOPMODEL Hydrological Model 
dynaTree  Dynamic Trees for Learning and Design 
dynBiplotGUI  Full Interactive GUI for Dynamic Biplot in R 
DynClust  Denoising and clustering for dynamical image sequence (2D or
3D)+T 
dynCorr  Dynamic Correlation Package 
dynia  Fit Dynamic Intervention Model 
dynlm  Dynamic Linear Regression 
DynNom  Dynamic Nomograms for Linear, Generalized Linear and
Proportional Hazard Models 
dynpred  Companion Package to "Dynamic Prediction in Clinical Survival
Analysis" 
dynr  Dynamic Modeling in R 
dynRB  Dynamic Range Boxes 
dynsim  Dynamic Simulations of Autoregressive Relationships 
dynsurv  Dynamic Models for Survival Data 
DynTxRegime  Methods for Estimating Dynamic Treatment Regimes 
DySeq  Functions for Dyadic Sequence Analyses 

e1071  Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien 
eaf  Plots of the Empirical Attainment Function 
earlywarnings  Early Warning Signals Toolbox for Detecting Critical Transitions
in Timeseries 
earth  Multivariate Adaptive Regression Splines 
EasyABC  Efficient Approximate Bayesian Computation Sampling Schemes 
easyanova  Analysis of variance and other important complementary analyzes 
easyformatr  Tools for Building R Formats 
EasyHTMLReport  EasyHTMLReport 
EasyMARK  Utility functions for working with markrecapture data 
easynls  Easy nonlinear model 
easypackages  Easy Loading and Installing of Packages 
easypower  Sample Size Estimation for Experimental Designs 
easyPubMed  Search and Retrieve Scientific Publication Records from Pubmed 
EasyStrata  Evaluation of stratified genomewide association metaanalysis
results 
easyVerification  Ensemble Forecast Verification for Large Data Sets 
eba  EliminationbyAspects Models 
ebal  Entropy reweighting to create balanced samples 
EbayesThresh  Empirical Bayes Thresholding and Related Methods 
ebdbNet  Empirical Bayes Estimation of Dynamic Bayesian Networks 
EBEN  Empirical Bayesian Elastic Net 
ebGenotyping  Genotyping and SNP Detection using Next Generation Sequencing
Data 
EBglmnet  Empirical Bayesian Lasso and Elastic Net Methods for Generalized
Linear Models 
EBMAforecast  Ensemble BMA Forecasting 
EBS  Exact Bayesian Segmentation 
ebSNP  Genotyping and SNP calling using singlesample next generation
sequencing data 
ecb  Programmatic Access to the European Central Bank's Statistical
Data Warehouse (SDW) 
ECctmc  Simulation from EndpointConditioned Continuous Time Markov
Chains 
ecd  Elliptic Distribution and Lambda Option Pricing Model 
Ecdat  Data Sets for Econometrics 
ecespa  Functions for Spatial Point Pattern Analysis 
Ecfun  Functions for Ecdat 
ECharts2Shiny  Embedding Charts Generated with ECharts Library into Shiny
Applications 
ecipex  Efficient calculation of fine structure isotope patterns via
Fourier transforms of simplexbased elemental models 
eco  Ecological Inference in 2x2 Tables 
ecodist  Dissimilaritybased functions for ecological analysis 
ecoengine  Programmatic Interface to the API Serving UC Berkeley's Natural
History Data 
EcoGenetics  Spatial Analysis of Phenotypic, Genotypic and Environmental Data 
EcoHydRology  A community modeling foundation for EcoHydrology 
ecolMod  "A practical guide to ecological modelling  using R as a
simulation platform" 
EconDemand  General Analysis of Various Economics Demand Systems 
ecoreg  Ecological Regression using Aggregate and Individual Data 
ecoretriever  R Interface to the EcoData Retriever 
ecosim  Toolbox for Aquatic Ecosystem Modeling 
EcoSimR  Null Model Analysis for Ecological Data 
ECOSolveR  Embedded Conic Solver in R 
ecospace  Simulating Community Assembly and Ecological Diversification
Using Ecospace Frameworks 
ecospat  Spatial Ecology Miscellaneous Methods 
ecotoxicology  Methods for Ecotoxicology 
EcoTroph  EcoTroph R package 
ecoval  Procedures for Ecological Assessment of Surface Waters 
EcoVirtual  Simulation of Ecological Models 
ecp  NonParametric Multiple ChangePoint Analysis of Multivariate
Data 
edcc  Economic Design of Control Charts 
edci  Edge Detection and Clustering in Images 
edeaR  Exploratory and Descriptive EventBased Data Analysis 
edeR  Email Data Extraction Using R 
edesign  Maximum Entropy Sampling 
edf  Read Data from European Data Format (EDF and EDF+) Files 
EDFIR  Estimating Discrimination Factors 
edfReader  Reading EDF(+) and BDF(+) Files 
edgar  Platform for EDGAR Filing Management 
edgebundleR  Circle Plot with Bundled Edges 
edgeCorr  Spatial Edge Correction 
edgeRun  More Powerful Unconditional Testing of Negative Binomial Means
for Digital Gene Expression Data 
EDISON  Network Reconstruction and Changepoint Detection 
EditImputeCont  Simultaneous EditImputation for Continuous Microdata 
editrules  Parsing, Applying, and Manipulating Data Cleaning Rules 
EDR  Estimation of the effective dimension reduction (EDR) space 
edrGraphicalTools  Provides tools for dimension reduction methods 
eechidna  Exploring Election and Census Highly Informative Data Nationally
for Australia 
eegAnalysis  Tools for analysis and classification of electroencephalography
(EEG) data 
eegkit  Toolkit for Electroencephalography Data 
eegkitdata  Data for package eegkit 
eel  Extended Empirical Likelihood 
EEM  Read and Preprocess Fluorescence ExcitationEmission Matrix
(EEM) Data 
eemR  Tools for PreProcessing EmissionExcitationMatrix (EEM)
Fluorescence Data 
eeptools  Convenience Functions for Education Data 
EFDR  WaveletBased Enhanced FDR for Signal Detection in Noisy Images 
EffectLiteR  Average and Conditional Effects 
effects  Effect Displays for Linear, Generalized Linear, and Other Models 
EffectsRelBaseline  Test changes of a grouped response relative to baseline 
EffectStars  Visualization of Categorical Response Models 
EffectTreat  Prediction of Therapeutic Success 
efflog  The Causal Effects for a Causal Loglinear Model 
effsize  Efficient Effect Size Computation 
efreadr  Read European Fluxes CSV Files 
ega  Error Grid Analysis 
egcm  EngleGranger Cointegration Models 
eggCounts  Hierarchical Modelling of Faecal Egg Counts 
egonet  Tool for egocentric measures in Social Network Analysis 
EGRET  Exploration and Graphics for RivEr Trends (EGRET) 
EGRETci  Exploration and Graphics for RivEr Trends (EGRET) Confidence
Intervals 
eha  Event History Analysis 
eHOF  Extended HOF (HuismanOlffFresco) Models 
ei  Ecological Inference 
EIAdata  R Wrapper for the Energy Information Administration (EIA) API 
eiCompare  Compares EI, Goodman, RxC Estimates 
eigeninv  Generates (dense) matrices that have a given set of eigenvalues 
eigenmodel  Semiparametric factor and regression models for symmetric
relational data 
eigenprcomp  Computes confidence intervals for principal components 
EILA  Efficient Inference of Local Ancestry 
eiPack  eiPack: Ecological Inference and HigherDimension Data
Management 
eive  An algorithm for reducing errorsinvariable bias in simple
linear regression 
eiwild  Ecological Inference with individual and aggregate data 
EL  Twosample Empirical Likelihood 
elasso  Enhanced Least Absolute Shrinkage and Selection Operator
Regression Model 
elastic  General Purpose Interface to 'Elasticsearch' 
elasticnet  ElasticNet for Sparse Estimation and Sparse PCA 
elec  Collection of functions for statistical election audits 
elec.strat  Functions for election audits using stratified random samples 
ElemStatLearn  Data Sets, Functions and Examples from the Book: "The Elements
of Statistical Learning, Data Mining, Inference, and
Prediction" by Trevor Hastie, Robert Tibshirani and Jerome
Friedman 
elexr  Load Associated Press Election Results with Elex 
elliplot  Ellipse Summary Plot of Quantiles 
ellipse  Functions for drawing ellipses and ellipselike confidence
regions 
elliptic  Elliptic Functions 
elmNN  Implementation of ELM (Extreme Learning Machine ) algorithm for
SLFN ( Single Hidden Layer Feedforward Neural Networks ) 
ELMR  Extreme Machine Learning (ELM) 
EloChoice  Preference Rating for Visual Stimuli Based on Elo Ratings 
EloRating  Animal Dominance Hierarchies by Elo Rating 
elrm  Exact Logistic Regression via MCMC 
ElstonStewart  ElstonStewart Algorithm 
ELT  Experience Life Tables 
ELYP  Empirical Likelihood Analysis for the Cox Model and
YangPrentice (2005) Model 
EMA  Easy Microarray data Analysis 
EMbC  ExpectationMaximization Binary Clustering 
embryogrowth  Tools to Analyze the Thermal Reaction Norm of Embryo Growth 
EMC  Evolutionary Monte Carlo (EMC) algorithm 
EMCluster  EM Algorithm for ModelBased Clustering of Finite Mixture
Gaussian Distribution 
EMD  Empirical Mode Decomposition and Hilbert Spectral Analysis 
emdbook  Support Functions and Data for "Ecological Models and Data" 
emdist  Earth Mover's Distance 
emg  Exponentially Modified Gaussian (EMG) Distribution 
emil  Evaluation of Modeling without Information Leakage 
emIRT  EM Algorithms for Estimating Item Response Theory Models 
EmiStatR  Estimation of Wastewater Emissions in Combined Sewer Systems 
emma  Evolutionary modelbased multiresponse approach 
EMMAgeo  EndMember Modelling of GrainSize Data 
emme2  Read and Write to an EMME/2 databank 
EMMIXcontrasts  Contrasts in mixed effects for EMMIX model with random effects 
EMMIXskew  The EM Algorithm and Skew Mixture Distribution 
EMMIXuskew  Fitting Unrestricted Multivariate Skew t Mixture Models 
EMMLi  A Maximum Likelihood Approach to the Analysis of Modularity 
EMMREML  Fitting Mixed Models with Known Covariance Structures 
emoa  Evolutionary Multiobjective Optimization Algorithms 
emojifont  Emoji Fonts for using in R 
emov  Eye Movement Analysis Package for Fixation and Saccade Detection 
EMP  Expected Maximum Profit Classification Performance Measure 
EmpiricalCalibration  Routines for Performing Empirical Calibration of Observational
Study Estimates 
empiricalFDR.DESeq2  SimulationBased False Discovery Rate in RNASeq 
emplik  Empirical Likelihood Ratio for Censored/Truncated Data 
emplik2  Empirical Likelihood Ratio Test for Two Samples with Censored
Data 
EMSC  Extended Multiplicative Signal Correction 
EMT  Exact Multinomial Test: GoodnessofFit Test for Discrete
Multivariate data 
emulator  Bayesian emulation of computer programs 
emuR  Main Package of the EMU Speech Database Management System 
EMVC  Entropy Minimization over Variable Clusters (EMVC) 
enaR  Tools for Ecological Network Analysis 
endogMNP  R Package for Fitting Multinomial Probit Models with Endogenous
Selection 
endorse  R Package for Analyzing Endorsement Experiments 
energy  Estatistics (energy statistics) 
energyr  Data Published by the United States Federal Energy Regulatory
Commission 
english  Translate integers into English 
EngrExpt  Data sets from "Introductory Statistics for Engineering
Experimentation" 
engsoccerdata  English and European Soccer Results 18712016 
enigma  Client for the 'Enigma' 'API' 
ENiRG  Ecological Niche in R and GRASS 
ENMeval  Automated Runs and Evaluations of Ecological Niche Models 
ENmisc  Neuwirth miscellaneous 
enpls  Ensemble Partial Least Squares Regression 
EnQuireR  A package dedicated to questionnaires 
enRich  An R Package for the Analysis of Multiple ChIPSeq Data 
enrichvs  Enrichment assessment of virtual screening approaches 
EnsembleBase  Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling 
ensembleBMA  Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging 
EnsembleCV  Extensible Package for CrossValidationBased Integration of
Base Learners 
ensembleMOS  Ensemble Model Output Statistics 
EnsemblePCReg  Extensible Package for PrincipalComponentRegressionBased
Heterogeneous Ensemble MetaLearning 
EnsemblePenReg  Extensible Classes and Methods for PenalizedRegressionbased
Integration of Base Learners 
ensurer  Ensure Values at Runtime 
entropart  Entropy Partitioning to Measure Diversity 
entropy  Estimation of Entropy, Mutual Information and Related Quantities 
EntropyEstimation  Estimation of Entropy and Related Quantities 
EntropyExplorer  Tools for Exploring Differential Shannon Entropy, Differential
Coefficient of Variation and Differential Expression 
enveomics.R  Various R Functions from the Kostas Lab 
enviPat  Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry 
enviPick  Peak Picking for High Resolution Mass Spectrometry Data 
EnviroStat  Statistical Analysis of Environmental SpaceTime Processes 
envlpaster  Enveloping the Aster Model 
EnvNicheR  Niche Estimation 
EnvStats  Package for Environmental Statistics, Including US EPA Guidance 
epade  Easy Plots 
epandist  Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution 
epanetReader  Read Epanet Files into R 
EPGLM  Gaussian Approximation of Bayesian Binary Regression Models 
Epi  A Package for Statistical Analysis in Epidemiology 
epibasix  Elementary Epidemiological Functions for Epidemiology and
Biostatistics 
EpiBayes  Implements Hierarchical Bayesian Models for Epidemiological
Applications 
EpiContactTrace  Epidemiological Tool for Contact Tracing 
epiDisplay  Epidemiological Data Display Package 
EpiDynamics  Dynamic Models in Epidemiology 
EpiEstim  EpiEstim: a package to estimate time varying reproduction
numbers from epidemic curves 
epifit  Flexible Modelling Functions for Epidemiological Data Analysis 
EpiModel  Mathematical Modeling of Infectious Disease 
epinet  Epidemic/NetworkRelated Tools 
epiR  Tools for the Analysis of Epidemiological Data 
episensr  Basic Sensitivity Analysis of Epidemiological Results 
episplineDensity  Density Estimation with Soft Information by Exponential
Episplines 
epitools  Epidemiology Tools 
EpiWeek  Conversion Between Epidemiological Weeks and Calendar Dates 
Eplot  Plotting longitudinal series 
epoc  EPoC (Endogenous Perturbation analysis of Cancer) 
epr  Easy polynomial regression 
EQL  ExtendedQuasiLikelihoodFunction (EQL) 
eqs2lavaan  EQS Output Conversion to lavaan Functions 
eqtl  Tools for analyzing eQTL experiments: A complementary to Karl
Broman's 'qtl' package for genomewide analysis 
equate  ObservedScore Linking and Equating 
equateIRT  Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods 
equivalence  Provides Tests and Graphics for Assessing Tests of Equivalence 
erah  Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MSBased Untargeted Metabolomics 
erboost  Nonparametric Multiple Expectile Regression via ERBoost 
erer  Empirical Research in Economics with R 
ergm  Fit, Simulate and Diagnose ExponentialFamily Models for
Networks 
ergm.count  Fit, Simulate and Diagnose ExponentialFamily Models for
Networks with Count Edges 
ergm.ego  Fit, Simulate and Diagnose ExponentialFamily Random Graph
Models to Egocentrically Sampled Network Data 
ergm.graphlets  ERG Modeling Based on Graphlet Properties 
ergmharris  Local Health Department network data set 
ergm.rank  Fit, Simulate and Diagnose ExponentialFamily Models for
RankOrder Relational Data 
ergm.userterms  Userspecified terms for the statnet suite of packages 
eRm  Extended Rasch Modeling 
ERP  Significance Analysis of EventRelated Potentials Data 
erp.easy  EventRelated Potential (ERP) Data Exploration Made Easy 
erpR  Eventrelated potentials (ERP) analysis, graphics and utility
functions 
errint  Build Error Intervals 
ES  Edge Selection 
esaBcv  Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis 
esc  Effect Size Computation for Meta Analysis 
ESEA  ESEA: Discovering the Dysregulated Pathways based on Edge Set
Enrichment Analysis 
ESG  ESG  A package for asset projection 
ESGtoolkit  Toolkit for the simulation of financial assets and interest
rates models 
ESKNN  Ensemble of Subset of KNearest Neighbours Classifiers for
Classification and Class Membership Probability Estimation 
estatapi  R Interface to eStat API 
EstCRM  Calibrating Parameters for the Samejima's Continuous IRT Model 
EstHer  Estimation of Heritability in High Dimensional Sparse Linear
Mixed Models using Variable Selection 
estimability  Tools for Assessing Estimability of Linear Predictions 
estout  Estimates Output 
EstSimPDMP  Estimation and Simulation for PDMPs 
etable  Easy Table 
ETAS  Modeling Earthquake Data Using ETAS Model 
etasFLP  Mixed FLP and ML Estimation of ETAS SpaceTime Point Processes 
ETC  Equivalence to control 
etl  ExtractTransferLoad Framework for Medium Data 
ETLUtils  Utility Functions to Execute Standard Extract/Transform/Load
Operations (using Package 'ff') on Large Data 
etm  Empirical Transition Matrix 
etma  Epistasis Test in MetaAnalysis 
etrunct  Computes Moments of Univariate Truncated t Distribution 
eulerian  eulerian: A package to find eulerian paths from graphs 
euroMix  Calculations for DNA Mixtures 
europepmc  R Interface to the Europe PubMed Central RESTful Web Service 
EurosarcBayes  Bayesian Single Arm Sample Size Calculation Software 
eurostat  Tools for Eurostat Open Data 
eva  Extreme Value Analysis with GoodnessofFit Testing 
EvalEst  Dynamic Systems Estimation  Extensions 
evaluate  Parsing and Evaluation Tools that Provide More Details than the
Default 
Evapotranspiration  Modelling Actual, Potential and Reference Crop
Evapotranspiration 
evclass  Evidential DistanceBased Classification 
evclust  Evidential Clustering 
EvCombR  Evidence Combination in R 
evd  Functions for Extreme Value Distributions 
evdbayes  Bayesian Analysis in Extreme Value Theory 
eVenn  A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams 
eventInterval  Sequential Event Interval Analysis 
events  Store and manipulate event data 
eventstudies  Event study and extreme event analysis 
evir  Extreme Values in R 
evmix  Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation 
evobiR  Comparative and Population Genetic Analyses 
evolqg  Tools for Evolutionary Quantitative Genetics 
evolvability  Calculation of Evolvability Parameters 
Evomorph  Evolutionary Morphometric Simulation 
evoper  Evolutionary Parameter Estimation for 'Repast Simphony' Models 
EvoRAG  Evolutionary Rates Across Gradients 
evt0  Mean of order p, peaks over random threshold Hill and high
quantile estimates 
evtree  Evolutionary Learning of Globally Optimal Trees 
EW  Edgeworth Expansion 
EWGoF  GoodnessofFit Tests for the Exponential and TwoParameter
Weibull Distributions 
Exact  Unconditional Exact Test 
exact2x2  Exact Conditional Tests and Confidence Intervals for 2x2 tables 
exactci  Exact PValues and Matching Confidence Intervals for Simple
Discrete Parametric Cases 
ExactCIdiff  Inductive Confidence Intervals for the difference between two
proportions 
exactLoglinTest  Monte Carlo Exact Tests for Loglinear models 
exactmeta  Exact fixed effect meta analysis 
ExactPath  Exact solution paths for regularized LASSO regressions with L_1
penalty 
exactRankTests  Exact Distributions for Rank and Permutation Tests 
exams  Automatic Generation of Exams in R 
ExceedanceTools  Confidence regions for exceedance sets and contour lines 
excel.link  Convenient Data Exchange with Microsoft Excel 
exCon  Interactive Exploration of Contour Data 
excursions  Excursion Sets and Contour Credibility Regions for Random Fields 
exif  Read EXIF Metadata from JPEGs 
exifr  EXIF Image Data in R 
ExomeDepth  Calls Copy Number Variants from Targeted Sequence Data 
expands  Expanding Ploidy and AlleleFrequency on Nested Subpopulations 
ExpDE  Modular Differential Evolution for Experimenting with Operators 
ExpDes  Experimental Designs package 
ExpDes.pt  Pacote Experimental Designs (Portuguese) 
expectreg  Expectile and Quantile Regression 
experiment  experiment: R package for designing and analyzing randomized
experiments 
expert  Modeling without data using expert opinion 
ExplainPrediction  Explanation of Predictions for Classification and Regression
Models 
explor  Interactive Interfaces for Results Exploration 
exploreR  Tools for Quickly Exploring Data 
expm  Matrix Exponential 
expoRkit  Expokit in R 
ExPosition  Exploratory analysis with the singular value decomposition 
expoTree  Calculate density dependent likelihood of a phylogenetic tree 
expp  Spatial analysis of extrapair paternity 
expsmooth  Data Sets from "Forecasting with Exponential Smoothing" 
expss  Some Useful Functions from Spreadsheets and 'SPSS' Statistics 
exptest  Tests for Exponentiality 
exreport  Fast, Reliable and Elegant Reproducible Research 
EXRQ  Extreme Regression of Quantiles 
exsic  Convenience Functions for Botanists to Create Specimens Indices 
ExtDist  Extending the Range of Functions for Probability Distributions 
extfunnel  Additional Funnel Plot Augmentations 
extlasso  Maximum penalized likelihood estimation with extended lasso
penalty 
extraBinomial  Extrabinomial approach for pooled sequencing data 
extracat  Categorical Data Analysis and Visualization 
extraDistr  Additional Univariate and Multivariate Distributions 
extrafont  Tools for using fonts 
extrafontdb  Package for holding the database for the extrafont package 
extraTrees  Extremely Randomized Trees (ExtraTrees) Method for
Classification and Regression 
ExtremeBounds  Extreme Bounds Analysis (EBA) 
extremefit  Estimation of Extreme Conditional Quantiles and Probabilities 
extRemes  Extreme Value Analysis 
extremeStat  Extreme Value Statistics and Quantile Estimation 
extremevalues  Univariate Outlier Detection 
extremogram  Estimation of Extreme Value Dependence for Time Series Data 
extWeibQuant  Estimate Lower Extreme Quantile with the Censored Weibull MLE
and Censored Weibull Mixture 
eyelinker  Load Raw Data from Eyelink Eye Trackers 
eyetracking  Eyetracking Helper Functions 
eyetrackingR  EyeTracking Data Analysis 
ez  Easy Analysis and Visualization of Factorial Experiments 
ezec  Easy Interface to Effective Concentration Calculations 
ezglm  selects significant nonadditive interaction between two
variables using fast GLM implementation 
ezknitr  Avoid the Typical Working Directory Pain When Using 'knitr' 
ezsim  provide an easy to use framework to conduct simulation 
ezsummary  Generate Data Summary in a Tidy Format 

face  Fast Covariance Estimation for Sparse Functional Data 
FacPad  Bayesian Sparse Factor Analysis model for the inference of
pathways responsive to drug treatment 
FactMixtAnalysis  Factor Mixture Analysis with covariates 
FACTMLE  Maximum Likelihood Factor Analysis 
FactoClass  Combination of Factorial Methods and Cluster Analysis 
factoextra  Extract and Visualize the Results of Multivariate Data Analyses 
FactoMineR  Multivariate Exploratory Data Analysis and Data Mining 
factorplot  Graphical Presentation of Simple Contrasts 
factorQR  Bayesian quantile regression factor models 
Factoshiny  Perform Factorial Analysis from 'FactoMineR' with a Shiny
Application 
FACTscorer  Scores the FACT and FACIT Family of PatientReported Outcome
Measures 
factualR  thin wrapper for the Factual.com server API 
FADA  Variable Selection for Supervised Classification in High
Dimension 
FAdist  Distributions that are Sometimes Used in Hydrology 
Fahrmeir  Data from the Book "Multivariate Statistical Modelling Based on
Generalized Linear Models", First Edition, by Ludwig Fahrmeir
and Gerhard Tutz 
fail  File Abstraction Interface Layer (FAIL) 
FAiR  Factor Analysis in R 
faisalconjoint  Faisal Conjoint Model: A New Approach to Conjoint Analysis 
fakeR  Simulates Data from a Data Frame of Different Variable Types 
falcon  Finding AlleleSpecific Copy Number in NextGeneration
Sequencing Data 
falconx  Finding AlleleSpecific Copy Number in WholeExome Sequencing
Data 
fame  Interface for FAME Time Series Database 
FamEvent  Simulation of TimetoEvent Family Data and Penetrance
Estimation 
Familias  Probabilities for Pedigrees Given DNA Data 
FAMILY  A Convex Formulation for Modeling Interactions with Strong
Heredity 
FAmle  Maximum Likelihood and Bayesian Estimation of Univariate
Probability Distributions 
FAMT  Factor Analysis for Multiple Testing (FAMT) : simultaneous tests
under dependence in highdimensional data 
fanc  Penalized Likelihood Factor Analysis via Nonconvex Penalty 
fANCOVA  Nonparametric Analysis of Covariance 
fancycut  A Fancy Version of 'base::cut' 
fanovaGraph  Building Kriging Models from FANOVA Graphs 
fanplot  Visualisation of Sequential Probability Distributions Using Fan
Charts 
FAOSTAT  Download Data from the FAOSTAT Database of the Food and
Agricultural Organization (FAO) of the United Nations 
faoutlier  Influential Case Detection Methods for Factor Analysis and
Structural Equation Models 
far  Modelization for Functional AutoRegressive Processes 
faraway  Functions and Datasets for Books by Julian Faraway 
fArma  ARMA Time Series Modelling 
farsi  Translate integers into persian 
fAsianOptions  EBM and Asian Option Valuation 
fAssets  Rmetrics  Analysing and Modelling Financial Assets 
fast  Implementation of the Fourier Amplitude Sensitivity Test (FAST) 
fastAdaboost  a Fast Implementation of Adaboost 
FastBandChol  Fast Estimation of a Covariance Matrix by Banding the Cholesky
Factor 
fastclime  A Fast Solver for Parameterized LP Problems, Constrained L1
Minimization Approach to Sparse Precision Matrix Estimation and
Dantzig Selector 
fastcluster  Fast Hierarchical Clustering Routines for R and Python 
fastcox  Lasso and elasticnet penalized Cox's regression in high
dimensions models using the cocktail algorithm 
fastdigest  Fast, Low MemoryFootprint Digests of R Objects 
fasteraster  Raster Image Processing and Vector Recognition 
fastGHQuad  Fast Rcpp implementation of GaussHermite quadrature 
FastGP  Efficiently Using Gaussian Processes with Rcpp and RcppEigen 
fastGraph  Fast Drawing and Shading of Graphs of Statistical Distributions 
FastHCS  Robust Algorithm for Principal Component Analysis 
fastHICA  Hierarchical Independent Component Analysis: a MultiScale
Sparse NonOrthogonal DataDriven Basis 
fastICA  FastICA Algorithms to perform ICA and Projection Pursuit 
FastImputation  Learn from Training Data then Quickly Fill in Missing Data 
FastKM  A Fast MultipleKernel Method Based on a LowRank Approximation 
FastKNN  Fast kNearest Neighbors 
fastM  Fast Computation of Multivariate Mestimators 
fastmatch  Fast match() function 
FastPCS  FastPCS Robust Fit of Multivariate Location and Scatter 
fastpseudo  Fast Pseudo Observations 
fastR  Foundations and Applications of Statistics Using R 
FastRCS  Fits the FastRCS Robust Multivariable Linear Regression Model 
FastRWeb  Fast Interactive Framework for Web Scripting Using R 
fastSOM  Fast Calculation of Spillover Measures 
fasttime  Fast Utility Function for Time Parsing and Conversion 
fat2Lpoly  TwoLocus FamilyBased Association Test with Polytomic Outcome 
FatTailsR  Kiener Distributions and Fat Tails in Finance 
favnums  A Dataset of Favourite Numbers 
FAwR  Functions and Datasets for "Forest Analytics with R" 
fBasics  Rmetrics  Markets and Basic Statistics 
fbati  Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families 
FBFsearch  Algorithm for searching the space of Gaussian directed acyclic
graphical models through moment fractional Bayes factors 
FBN  FISH Based Normalization and Copy Number inference of SNP
microarray data 
fBonds  Bonds and Interest Rate Models 
fbRads  Analyzing and Managing Facebook Ads from R 
fbRanks  Association Football (Soccer) Ranking via Poisson Regression 
fbroc  Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves 
fcd  Fused Community Detection 
fCertificates  Basics of Certificates and Structured Products Valuation 
FCGR  Fatigue Crack Growth in Reliability 
fclust  Fuzzy Clustering 
FCMapper  Fuzzy Cognitive Mapping 
FCNN4R  Fast Compressed Neural Networks for R 
fCopulae  Rmetrics  Bivariate Dependence Structures with Copulae 
fcros  A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations 
FD  Measuring functional diversity (FD) from multiple traits, and
other tools for functional ecology 
fda  Functional Data Analysis 
fdakma  Functional Data Analysis: KMean Alignment 
fdaMixed  Functional data analysis in a mixed model framework 
fdapace  Functional Data Analysis and Empirical Dynamics 
fdaPDE  Functional Data Analysis and Partial Differential Equations;
Statistical Analysis of Functional and Spatial Data, Based on
Regression with Partial Differential Regularizations 
fdasrvf  Elastic Functional Data Analysis 
fdatest  Interval Testing Procedure for Functional Data 
fda.usc  Functional Data Analysis and Utilities for Statistical Computing 
FDboost  Boosting Functional Regression Models 
fdcov  Analysis of Covariance Operators 
FDGcopulas  Multivariate Dependence with FDG Copulas 
fdrci  Permutationbased FDR Point and Confidence Interval Estimation 
fdrDiscreteNull  False Discovery Rate Procedure Under Discrete Null Distributions 
FDRreg  False discovery rate regression 
FDRsampsize  Compute Sample Size that Meets Requirements for Average Power
and FDR 
fdrtool  Estimation of (Local) False Discovery Rates and Higher Criticism 
fds  Functional data sets 
fdth  Frequency Distribution Tables, Histograms and Polygons 
FeaLect  Scores Features for Feature Selection 
feather  R Bindings to the Feather 'API' 
feature  Local Inferential Feature Significance for Multivariate Kernel
Density Estimation 
FeatureHashing  Creates a Model Matrix via Feature Hashing with a Formula
Interface 
features  Feature Extraction for DiscretelySampled Functional Data 
fechner  Fechnerian Scaling of Discrete Object Sets 
FedData  Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources 
federalregister  Client Package for the U.S. Federal Register API 
FeedbackTS  Analysis of Feedback in Time Series 
FENmlm  Fixed Effects Nonlinear Maximum Likelihood Models 
fermicatsR  Fermi Large Area Telescope Catalogs 
fExoticOptions  Exotic Option Valuation 
fExpressCertificates  fExpressCertificates  Structured Products Valuation for
ExpressCertificates/Autocallables 
fExtremes  Rmetrics  Extreme Financial Market Data 
ff  memoryefficient storage of large data on disk and fast access
functions 
ffbase  Basic Statistical Functions for Package 'ff' 
FFD  Freedom from Disease 
FField  Force field simulation for a set of points 
ffmanova  Fiftyfifty MANOVA 
FFTrees  Generate, Visualise, and Compare Fast and Frugal Decision Trees 
fftw  Fast FFT and DCT based on FFTW 
fftwtools  Wrapper for FFTW3: Includes 1D, Univariate and Multivariate,
and 2D Transform 
fgac  Generalized Archimedean Copula 
FGalgorithm  Flury and Gautschi algorithms 
fGarch  Rmetrics  Autoregressive Conditional Heteroskedastic Modelling 
Fgmutils  Forest Growth Model Utilities 
FGN  Fractional Gaussian Noise and power law decay time series model
fitting 
fgof  Fast Goodnessoffit Test 
fgpt  Floating Grid Permutation Technique 
FGSG  Feature Grouping and Selection Over an Undirected Graph 
fgui  Function GUI 
fheatmap  Fantastic Heatmap 
FHtest  Tests for Right and IntervalCensored Survival Data Based on the
FlemingHarrington Class 
FI  Provide functions for forest inventory calculations 
FIACH  Retrospective Noise Control for fMRI 
fICA  Classical, Reloaded and Adaptive FastICA Algorithms 
fields  Tools for Spatial Data 
FieldSim  Random Fields (and Bridges) Simulations 
fiery  A Lightweight and Flexible Web Framework 
fifer  A collection of miscellaneous functions 
filehash  Simple KeyValue Database 
filehashSQLite  Simple keyvalue database using SQLite 
filematrix  FileBacked Matrix Class with Convenient Read and Write Access 
filenamer  Easy Management of File Names 
fImport  Rmetrics  Economic and Financial Data Import 
financial  Solving financial problems in R 
FinancialInstrument  Financial Instrument Model Infrastructure for R 
FinAsym  Classifies implicit trading activity from market quotes and
computes the probability of informed trading 
FinCal  Time Value of Money, Time Series Analysis and Computational
Finance 
FinCovRegularization  Covariance Matrix Estimation and Regularization for Finance 
FindAllRoots  Find all root(s) of the equation and Find root(s) of the
equation by dichotomy 
FindIt  Finding Heterogeneous Treatment Effects 
FindMinIC  Find Models with Minimum IC 
findpython  Python tools to find an acceptable python binary 
fingerprint  Functions to operate on binary fingerprint data 
finiteruinprob  Computation of the probability of ruin within a finite time
horizon 
finreportr  Financial Data from U.S. Securities and Exchange Commission 
FinTS  Companion to Tsay (2005) Analysis of Financial Time Series 
FisherEM  The FisherEM algorithm 
fisheyeR  Fisheye and Hyperbolicspacealike Interactive Visualization
Tools in R 
FisHiCal  Iterative FISHbased Calibration of HiC Data 
fishmethods  Fishery Science Methods and Models in R 
fishMod  Fits PoissonsumofGammas GLMs, Tweedie GLMs, and delta
lognormal mdoels 
fishmove  Prediction of Fish Movement Parameters 
FIT  Transcriptomic Dynamics Models in Field Conditions 
fit4NM  NONMEM platform 
FitAR  Subset AR Model Fitting 
FitARMA  FitARMA: Fit ARMA or ARIMA using fast MLE algorithm 
fitbitScraper  Scrapes Data from Fitbit 
fitcoach  Personalized Coach for Fitbit and R API 
fitdistrplus  Help to Fit of a Parametric Distribution to NonCensored or
Censored Data 
fitDRC  Fitting Density Ratio Classes 
fit.models  fit.models 
FITSio  FITS (Flexible Image Transport System) utilities 
fitTetra  fitTetra is an R package for assigning tetraploid genotype
scores 
FKF  Fast Kalman Filter 
flacco  FeatureBased Landscape Analysis of Continuous and Constraint
Optimization Problems 
flam  Fits Piecewise Constant Models with DataAdaptive Knots 
flan  FLuctuation ANalysis on Mutation Models 
flare  Family of Lasso Regression 
flars  Functional LARS 
flashClust  Implementation of optimal hierarchical clustering 
flexclust  Flexible Cluster Algorithms 
flexCWM  Flexible ClusterWeighted Modeling 
flexdashboard  R Markdown Format for Flexible Dashboards 
flexmix  Flexible Mixture Modeling 
FlexParamCurve  Tools to Fit Flexible Parametric Curves 
flexPM  Flexible Parametric Models for Censored and Truncated Data 
flexrsurv  Flexible Relative Survival 
flexsurv  Flexible Parametric Survival and MultiState Models 
FLIM  Farewellâ€™s Linear Increments Model 
flip  Multivariate Permutation Tests 
FLLat  Fused Lasso Latent Feature Model 
flora  Tools for Interacting with the Brazilian Flora 2020 
flowDiv  Cytometric Diversity Indices from 'FlowJo' Workspaces 
flower  Tools for characterizing flowering traits 
flowfield  Forecasts future values of a univariate time series 
flowr  Streamlining Design and Deployment of Complex Workflows 
flows  Flow Selection and Analysis 
FlowScreen  Daily Streamflow Trend and Change Point Screening 
FLR  Fuzzy Logic Rule Classifier 
flsa  Path algorithm for the general Fused Lasso Signal Approximator 
FLSSS  Multithreaded Fixed Size Subset Sum with Bounded Error in
Multidimensional Real Domain 
Flury  Data Sets from Flury, 1997 
flux  Flux rate calculation from dynamic closed chamber measurements 
fma  Data Sets from "Forecasting: Methods and Applications" by
Makridakis, Wheelwright & Hyndman (1998) 
FME  A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability, Monte Carlo Analysis 
FMP  Filtered Monotonic Polynomial IRT Models 
fmri  Analysis of fMRI experiments 
fmrs  Variable Selection in Finite Mixture of AFT Regression and FMR 
fmsb  Functions for Medical Statistics Book with some Demographic Data 
FMsmsnReg  Regression Models with Finite Mixtures of Skew HeavyTailed
Errors 
FMStable  Finite Moment Stable Distributions 
fmt  Variance estimation of FMT method (Fully Moderated tstatistic) 
fMultivar  Rmetrics  Analysing and Modeling Multivariate Financial Return
Distributions 
FNN  Fast Nearest Neighbor Search Algorithms and Applications 
fNonlinear  Nonlinear and Chaotic Time Series Modelling 
foba  greedy variable selection 
fontcm  Computer Modern font for use with extrafont package 
foodweb  visualisation and analysis of food web networks 
fOptions  Rmetrics  Pricing and Evaluating Basic Options 
forams  Foraminifera and Community Ecology Analyses 
foreach  Provides Foreach Looping Construct for R 
ForeCA  Forecastable Component Analysis 
forecast  Forecasting Functions for Time Series and Linear Models 
ForecastCombinations  Forecast Combinations 
forecastHybrid  Convenient Functions for Ensemble Time Series Forecasts 
forecTheta  Forecasting Time Series by Theta Models 
forega  FloatingPoint Genetic Algorithms with Statistical Forecast
Based Inheritance Operator 
foreign  Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ... 
forensic  Statistical Methods in Forensic Genetics 
forensim  Statistical tools for the interpretation of forensic DNA
mixtures 
forestFloor  Visualizes Random Forests with Feature Contributions 
forestinventory  DesignBased Global and SmallArea Estimations for Multiphase
Forest Inventories 
forestmodel  Forest Plots from Regression Models 
forestplot  Advanced Forest Plot Using 'grid' Graphics 
ForImp  Imputation of Missing Values Through a Forward Imputation
Algorithm 
ForIT  Functions from the 2nd Italian Forest Inventory (INFC) 
FormalSeries  Elementary arithemtic in formal series rings 
formatR  Format R Code Automatically 
formattable  Formattable Data Structures 
Formula  Extended Model Formulas 
formula.tools  Utilities for Formulas, Expressions, Calls and Other Objects 
fortunes  R Fortunes 
forward  Forward search 
ForwardSearch  Forward Search using asymptotic theory 
fossil  Palaeoecological and Palaeogeographical Analysis Tools 
fourierin  Computes Numeric Fourier Integrals 
fourPNO  Bayesian 4 Parameter Item Response Model 
FourScores  FourScores  A game for two players 
fpc  Flexible Procedures for Clustering 
fpca  Restricted MLE for Functional Principal Components Analysis 
fpCompare  Reliable Comparison of Floating Point Numbers 
FPDclustering  PDClustering and Factor PDClustering 
fPortfolio  Rmetrics  Portfolio Selection and Optimization 
fpow  Computing the noncentrality parameter of the noncentral F
distribution 
fpp  Data for "Forecasting: principles and practice" 
fptdApprox  Approximation of FirstPassageTime Densities for Diffusion
Processes 
fracdiff  Fractionally differenced ARIMA aka ARFIMA(p,d,q) models 
fracprolif  Fraction Proliferation via a Quiescent Growth Model 
fractal  Fractal Time Series Modeling and Analysis 
fractaldim  Estimation of fractal dimensions 
FractalParameterEstimation  Estimation of Parameters p and q for Randomized Sierpinski
Carpet for [pppq]Model 
fractalrock  Generate fractal time series with nonnormal returns
distribution 
FRACTION  Numeric number into fraction 
fractional  Vulgar Fractions in R 
Fragman  Fragment Analysis in R 
frailtyHL  Frailty Models via Hlikelihood 
frailtypack  General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction 
frailtySurv  General Semiparametric Shared Frailty Model 
frair  Tools for Functional Response Analysis 
Frames2  Estimation in Dual Frame Surveys 
franc  Detect the Language of Text 
FRAPO  Financial Risk Modelling and Portfolio Optimisation with R 
FRB  Fast and Robust Bootstrap 
frbs  Fuzzy RuleBased Systems for Classification and Regression Tasks 
FRCC  Fast Regularized Canonical Correlation Analysis 
freeknotsplines  FreeKnot Splines 
FreeSortR  Free Sorting Data Analysis 
freestats  Statistical algorithms used in common data mining course 
FREGAT  Family REGional Association Tests 
fRegression  Rmetrics  Regression Based Decision and Prediction 
FREQ  FREQ: Estimate population size from capture frequencies 
freqdom  Frequency Domain Analysis for Multivariate Time Series 
freqMAP  Frequency Moving Average Plots (MAP) of Multinomial Data by a
Continuous Covariate 
freqparcoord  Novel Methods for Parallel Coordinates 
FreqProf  Frequency Profiles Computing and Plotting 
freqweights  Working with Frequency Tables 
FRESA.CAD  Feature Selection Algorithms for Computer Aided Diagnosis 
FrF2  Fractional Factorial designs with 2level factors 
FrF2.catlg128  Catalogues of resolution IV 128 run 2level fractional
factorials up to 33 factors that do have 5letter words 
frm  Regression Analysis of Fractional Responses 
frmhet  Regression Analysis of Fractional Responses Under Unobserved
Heterogeneity 
frmpd  Regression Analysis of Panel Fractional Responses 
frmqa  The Generalized Hyperbolic Distribution, Related Distributions
and Their Applications in Finance 
fromo  Fast Robust Moments 
frontier  Stochastic Frontier Analysis 
frontiles  Partial Frontier Efficiency Analysis 
frt  Full Randomization Test 
FSA  Simple Fisheries Stock Assessment Methods 
FSAdata  Data to Support Fish Stock Assessment (FSA) Package 
fscaret  Automated Feature Selection from 'caret' 
FSelector  Selecting Attributes 
fsia  Import and Analysis of OMR Data from FormScanner 
FSInteract  Fast Searches for Interactions 
fslr  Wrapper Functions for FSL (FMRIB Software Library) from
Functional MRI of the Brain (FMRIB) 
fso  Fuzzy Set Ordination 
fSRM  Social Relations Analyses with Roles ("Family SRM") 
FTICRMS  Programs for Analyzing Fourier TransformIon Cyclotron Resonance
Mass Spectrometry Data 
ftnonpar  Features and Strings for Nonparametric Regression 
fTrading  Technical Trading Analysis 
fts  R interface to tslib (a time series library in c++) 
ftsa  Functional Time Series Analysis 
ftsspec  Spectral Density Estimation and Comparison for Functional Time
Series 
fueleconomy  EPA fuel economy data 
fugeR  FUzzy GEnetic, a machine learning algorithm to construct
prediction model based on fuzzy logic 
fullfact  Full Factorial Breeding Analysis 
fulltext  Full Text of 'Scholarly' Articles Across Many Data Sources 
fun  Use R for Fun 
FunChisq  ChiSquare and Exact Tests for NonParametric Functional
Dependencies 
FunCluster  Functional Profiling of Microarray Expression Data 
Funclustering  A package for functional data clustering 
FuncMap  Hive Plots of R Package Function Calls 
functional  Curry, Compose, and other higherorder functions 
FunctionalNetworks  An algorithm for gene and gene set network inference 
functools  Functional Programming in R 
funcy  Functional Clustering Algorithms 
funData  An S4 Class for Functional Data 
funFEM  Clustering in the Discriminative Functional Subspace 
fungible  Fungible Coefficients and Monte Carlo Functions 
funHDDC  Modelbased clustering in groupspecific functional subspaces 
fUnitRoots  Trends and Unit Roots 
funModeling  Learning Data Cleaning, Visual Analysis and Model Performance 
funr  Simple Utility Providing Terminal Access to all R Functions 
funrar  Functional Rarity Indices Computation 
funreg  funreg (Functional Regression for Irregularly Timed Data) 
FUNTA  Functional Tangential Angle PseudoDepth 
funtimes  Functions for Time Series Analysis 
FusedPCA  Community Detection via Fused Principal Component Analysis 
futile.any  A Tiny Utility Providing Polymorphic Operations 
futile.logger  A Logging Utility for R 
futile.matrix  Random Matrix Generation and Manipulation 
futile.options  Futile options management 
futile.paradigm  A framework for working in a functional programming paradigm in
R 
future  A Future API for R 
future.BatchJobs  A Future for BatchJobs 
futureheatwaves  Find, Characterize, and Explore Heat Waves in Climate
Projections 
fuzzr  FuzzTest R Functions 
FuzzyAHP  (Fuzzy) AHP Calculation 
fuzzyFDR  Exact calculation of fuzzy decision rules for multiple testing 
fuzzyforest  Fuzzy Forests 
fuzzyjoin  Join Tables Together on Inexact Matching 
FuzzyLP  Fuzzy Linear Programming 
FuzzyNumbers  Tools to Deal with Fuzzy Numbers 
fuzzyRankTests  Fuzzy Rank Tests and Confidence Intervals 
FuzzyStatProb  Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain 
FuzzyToolkitUoN  Type 1 Fuzzy Logic Toolkit 
fwdmsa  Forward search for Mokken scale analysis 
FWDselect  Selecting Variables in Regression Models 
fwi.fbp  Fire Weather Index System and Fire Behaviour Prediction System
Calculations 
fwsim  FisherWright Population Simulation 
fxregime  Exchange Rate Regime Analysis 

G1DBN  A package performing Dynamic Bayesian Network inference 
G2Sd  GrainSize Statistics and Description of Sediment 
GA  Genetic Algorithms 
GA4Stratification  A genetic algorithm approach to determine stratum boundaries and
sample sizes of each stratum in stratified sampling 
GAabbreviate  Abbreviating Items Measures using Genetic Algorithms 
GABi  Framework for Generalized Subspace Pattern Mining 
GAD  GAD: Analysis of variance from general principles 
GaDiFPT  First Passage Time Simulation for Gaussian Diffusion Processes 
gains  Gains Table Package 
GAIPE  Graphical Extension with Accuracy in Parameter Estimation
(GAIPE) 
galts  Genetic algorithms and Csteps based LTS (Least Trimmed Squares)
estimation 
gam  Generalized Additive Models 
gamair  Data for "GAMs: An Introduction with R" 
gambin  Fit the GamBin Model to Species Abundance Distributions 
GAMBoost  Generalized linear and additive models by likelihood based
boosting 
gamboostLSS  Boosting Methods for 'GAMLSS' 
gamboostMSM  Estimating multistate models using gamboost() 
gamclass  Functions and Data for a Course on Modern Regression and
Classification 
GAMens  Applies GAMbag, GAMrsm and GAMens Ensemble Classifiers for
Binary Classification 
games  Statistical Estimation of GameTheoretic Models 
GameTheory  Cooperative Game Theory 
GameTheoryAllocation  Tools for Calculating Allocations in Game Theory 
gamlr  Gamma Lasso Regression 
gamlss  Generalised Additive Models for Location Scale and Shape 
gamlss.add  Extra Additive Terms for GAMLSS Models 
gamlss.cens  Fitting an Interval Response Variable Using ‘gamlss.family’
Distributions 
gamlss.data  GAMLSS Data 
gamlss.demo  Demos for GAMLSS 
gamlss.dist  Distributions to be Used for GAMLSS Modelling 
gamlss.mx  Fitting Mixture Distributions with GAMLSS 
gamlss.nl  Fitting non linear parametric GAMLSS models 
gamlss.spatial  Spatial Terms in GAMLSS Models 
gamlss.tr  Generating and Fitting Truncated ‘gamlss.family’ Distributions 
gamlss.util  GAMLSS Utilities 
gamm4  Generalized additive mixed models using mgcv and lme4 
Gammareg  classic gamma regression: joint modeling of mean and shape
parameters 
gammSlice  Generalized additive mixed model analysis via slice sampling 
gamsel  Fit Regularization Path for Generalized Additive Models 
GANPA  Gene Association Networkbased Pathway Analysis 
GANPAdata  The GANPA Datasets Package 
gaoptim  Genetic Algorithm optimization for realbased and
permutationbased problems 
gap  Genetic Analysis Package 
gapfill  Fill Missing Values in Satellite Data 
gapmap  Functions for Drawing Gapped Cluster Heatmap with ggplot2 
gapminder  Data from Gapminder 
GAR  Authorize and Request Google Analytics Data 
gaselect  Genetic Algorithm (GA) for Variable Selection from
HighDimensional Data 
gaston  Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear and Logistic Mixed Models (AIREML
Algorithm), Association Testing 
gaussDiff  Difference measures for multivariate Gaussian probability
density functions 
gaussfacts  The Greatest Mathematician Since Antiquity 
gaussquad  Collection of functions for Gaussian quadrature 
gazepath  Parse EyeTracking Data into Fixations 
gb  Generalize Lambda Distribution and Generalized Bootstrapping 
GB2  Generalized Beta Distribution of the Second Kind: Properties,
Likelihood, Estimation 
gbm  Generalized Boosted Regression Models 
gbm2sas  Convert GBM Object Trees to SAS Code 
gbRd  Utilities for processing Rd objects and files 
gbutils  Simulation of Real and Complex Numbers and Small Programming
Utilities 
GCAI.bias  Guided Correction Approach for Inherited bias (GCAI.bias) 
gCat  Graphbased twosample tests for categorical data 
gcbd  GPU/CPU Benchmarking in Debianbased systems 
GCD  Global Charcoal Database 
gcdnet  LASSO and (adaptive) ElasticNet penalized least squares,
logistic regression, HHSVM and squared hinge loss SVM using a
fast GCD algorithm 
gcerisk  Generalized Competing Event Model 
gclus  Clustering Graphics 
gcmr  Gaussian Copula Marginal Regression 
gconcord  Concord method for Graphical Model Selection 
gcookbook  Data for "R Graphics Cookbook" 
GCPM  Generalized Credit Portfolio Model 
GDAdata  Datasets for the Book Graphical Data Analysis with R 
gdalUtils  Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities 
gdata  Various R Programming Tools for Data Manipulation 
g.data  DelayedData Packages 
GDAtools  A toolbox for the analysis of categorical data in social
sciences, and especially Geometric Data Analysis 
GDELTtools  Download, slice, and normalize GDELT data 
gdimap  Generalized Diffusion Magnetic Resonance Imaging 
gdistance  Distances and Routes on Geographical Grids 
gdm  Functions for Generalized Dissimilarity Modeling 
gds  Descriptive Statistics of Grouped Data 
gdtools  Utilities for Graphical Rendering 
gear  Geostatistical Analysis in R 
gee  Generalized Estimation Equation Solver 
GEEaSPU  Adaptive Association Tests for Multiple Phenotypes using
Generalized Estimating Equations (GEE) 
geeM  Solve Generalized Estimating Equations 
geepack  Generalized Estimating Equation Package 
geesmv  Modified Variance Estimators for Generalized Estimating
Equations 
geigen  Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack 
geiger  Analysis of Evolutionary Diversification 
gelnet  Generalized Elastic Nets 
gems  Generalized Multistate Simulation Model 
gemtc  Network MetaAnalysis Using Bayesian Methods 
gemtc.jar  GeMTC Java binary 
GenABEL  genomewide SNP association analysis 
GenABEL.data  Package contains data which is used by GenABEL example and test
functions 
genalg  R Based Genetic Algorithm 
genasis  Global ENvironmental ASsessment Information System (GENASIS)
computational tools 
GenBinomApps  ClopperPearson Confidence Interval and Generalized Binomial
Distribution 
GenCAT  Genetic Class Association Testing 
gencve  General Cross Validation Engine 
gendata  Generate and Modify Synthetic Datasets 
gender  Predict Gender from Names Using Historical Data 
genderizeR  Gender Prediction Based on First Names 
gendist  Generated Probability Distribution Models 
GENEAread  Package For Reading Binary files 
GeneCycle  Identification of Periodically Expressed Genes 
GeneF  Package for Generalized Fstatistics 
GeneFeST  Bayesian calculation of genespecific FST from genomic SNP data 
Geneland  Detection of structure from multilocus genetic data 
geneListPie  Profiling a gene list into GOslim or KEGG function pie 
genemodel  Gene Model Plotting in R 
GeneNet  Modeling and Inferring Gene Networks 
geneNetBP  Belief Propagation in GenotypePhenotype Networks 
genepi  Genetic Epidemiology Design and Inference 
generalCorr  Generalized Correlations and Initial Causal Path 
generalhoslem  HosmerLemeshow Test for Binary and Multinomial Logistic Models 
GeneralizedHyperbolic  The Generalized Hyperbolic Distribution 
GeneralOaxaca  BlinderOaxaca Decomposition for Generalized Linear Model 
generator  Generate Data Containing Fake Personally Identifiable
Information 
GeneReg  Construct time delay gene regulatory network 
geneSignatureFinder  A Genesignatures finder tools 
geneSLOPE  GenomeWide Association Study with SLOPE 
genetics  Population Genetics 
GeneticSubsetter  Identify Favorable Subsets of Germplasm Collections 
GeneticTools  Collection of Genetic Data Analysis Tools 
GeNetIt  Spatial GraphTheoretic Genetic Gravity Modelling 
GenForImp  The Forward Imputation: A Sequential DistanceBased Approach for
Imputing Missing Data 
genie  A New, Fast, and Outlier Resistant Hierarchical Clustering
Algorithm 
GenKern  Functions for generating and manipulating binned kernel density
estimates 
genlasso  Path algorithm for generalized lasso problems 
GENLIB  Genealogical Data Analysis 
genMOSS  Functions for the Bayesian Analysis of GWAS Data 
genMOSSplus  Application of MOSS algorithm to genomewide association study
(GWAS) 
genomeplot  'Plot genome wide values for all chromosomes' 
genomicper  Circular Genomic Permutation using Gwas pValues of Association 
genoPlotR  Plot PublicationGrade Gene and Genome Maps 
GenOrd  Simulation of Discrete Random Variables with Given Correlation
Matrix and Marginal Distributions 
genpathmox  Generalized PATHMOX Algorithm for PLSPM, LS and LAD Regression 
genridge  Generalized Ridge Trace Plots for Ridge Regression 
GenSA  R Functions for Generalized Simulated Annealing 
gensemble  generalized ensemble methods 
gensphere  Generalized Spherical Distributions 
genSurv  Generating MultiState Survival Data 
GenWin  Spline Based Window Boundaries for Genomic Analyses 
geo  Draw and Annotate Maps, Especially Charts of the North Atlantic 
geoaxe  Split 'Geospatial' Objects into Pieces 
geoBayes  Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods 
GeoBoxplot  Geographic Box Plot 
geocodeHERE  Wrapper for Nokia's HERE Geocoding API 
geoCount  Analysis and Modeling for Geostatistical Count Data 
GeoDE  A geometrical Approach to Differential expression and geneset
enrichment 
geoelectrics  3DVisualization of Geoelectric Resistivity Measurement Profiles 
geofd  Spatial Prediction for Function Value Data 
GeoGenetix  Quantification of the effect of geographic versus environmental
isolation on genetic differentiation 
geohash  Tools for Geohash Creation and Manipulation 
geojsonio  Convert Data from and to 'geoJSON' or 'topoJSON' 
geojsonlint  Tools for Validating 'GeoJSON' 
geoknife  WebProcessing of Large Gridded Datasets 
GeoLight  Analysis of Light Based Geolocator Data 
GEOmap  Topographic and Geologic Mapping 
geomapdata  Data for topographic and Geologic Mapping 
geometry  Mesh Generation and Surface Tesselation 
geomnet  Network Visualization in the 'ggplot2' Framework 
geomorph  Geometric Morphometric Analyses of 2D/3D Landmark Data 
geonames  Interface to www.geonames.org web service 
geoparser  Interface to the Geoparser.io API for Identifying and
Disambiguating Places Mentioned in Text 
geophys  Geophysics, Continuum Mechanics, Mogi Models, Gravity 
geoR  Analysis of Geostatistical Data 
geoRglm  A Package for Generalised Linear Spatial Models 
georob  Robust Geostatistical Analysis of Spatial Data 
geoscale  Geological Time Scale Plotting 
geospacom  Facilitate Generating of Distance Matrices Used in Package
'spacom' and Plotting Data on Maps 
geosphere  Spherical Trigonometry 
geospt  Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks 
geosptdb  SpatioTemporal; Inverse Distance Weighting and Radial Basis
Functions with DistanceBased Regression 
geostatsp  Geostatistical Modelling with Likelihood and Bayes 
geotech  Geotechnical Engineering 
geotools  Geo tools 
geotopbricks  An R Plugin for the Distributed Hydrological Model GEOtop 
GeoXp  Interactive exploratory spatial data analysis 
geozoo  Zoo of Geometric Objects 
gepaf  Google Encoded Polyline Algorithm Format 
GERGM  Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models 
gesca  Generalized Structured Component Analysis (GSCA) 
gesis  R Client for GESIS Data Catalogue (DBK) 
GESTr  Gene Expression State Transformation 
GetHFData  Download and Aggregate High Frequency Trading Data from Bovespa 
getMet  Get Meteorological Data for Hydrologic Models 
getopt  Clike getopt behavior 
GetoptLong  Parsing CommandLine Arguments and Variable Interpolation 
getPass  Masked User Input 
GetR  GetR: Calculate Guttman error trees in R 
gets  GeneraltoSpecific (GETS) Modelling and Indicator Saturation
Methods 
GetTDData  Get Data for Brazilian Bonds (Tesouro Direto) 
gettingtothebottom  Learning Optimization and Machine Learning for Statistics 
GEVcdn  GEV Conditional Density Estimation Network 
GEVStableGarch  ARMAGARCH/APARCH Models with GEV and Stable Distributions 
GExMap  A visual, intuitive, easy to use software giving access to a new
type of information buried into your microarray data 
gfcanalysis  Tools for Working with Hansen et al. Global Forest Change
Dataset 
GFD  Tests for General Factorial Designs 
GGally  Extension to 'ggplot2' 
ggalt  Extra Coordinate Systems, Geoms and Statistical Transformations
for 'ggplot2' 
ggbeeswarm  Categorical Scatter (Violin Point) Plots 
ggcorrplot  Visualization of a Correlation Matrix using 'ggplot2' 
ggdendro  Create Dendrograms and Tree Diagrams Using 'ggplot2' 
gge  Genotype Plus GenotypebyEnvironment Biplots 
GGEBiplotGUI  Interactive GGE Biplots in R 
ggenealogy  Visualization Tools for Genealogical Data 
ggExtra  Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements 
ggfortify  Data Visualization Tools for Statistical Analysis Results 
GGIR  Raw Accelerometer Data Analysis 
ggiraph  Make 'ggplot2' Graphics Interactive Using 'htmlwidgets' 
gglasso  Group Lasso Penalized Learning Using A Unified BMD Algorithm 
gglogo  Geom for Logo Sequence Plots 
ggm  Functions for graphical Markov models 
ggmap  Spatial Visualization with ggplot2 
ggmcmc  Tools for Analyzing MCMC Simulations from Bayesian Inference 
GGMridge  Gaussian Graphical Models Using Ridge Penalty Followed by
Thresholding and Reestimation 
GGMselect  Gaussian Graphs Models Selection 
ggnetwork  Geometries to Plot Networks with 'ggplot2' 
ggparallel  Variations of Parallel Coordinate Plots for Categorical Data 
ggplot2  An Implementation of the Grammar of Graphics 
ggplot2movies  Movies Data 
ggpmisc  Miscellaneous Extensions to 'ggplot2' 
ggpubr  'ggplot2' Based Publication Ready Plots 
ggRandomForests  Visually Exploring Random Forests 
ggraptR  Allows Interactive Visualization of Data Through a Web Browser
GUI 
ggrepel  Repulsive Text and Label Geoms for 'ggplot2' 
ggROC  package for roc curve plot with ggplot2 
ggsci  Scientific Journal and SciFi Themed Color Palettes for
'ggplot2' 
ggseas  'stats' for Seasonal Adjustment on the Fly with 'ggplot2' 
ggsn  North Symbols and Scale Bars for Maps Created with 'ggplot2' or
'ggmap' 
ggspectra  Extensions to 'ggplot2' for Radiation Spectra 
ggswissmaps  Offers Various Swiss Maps as ggplot2 Objects 
ggtern  An Extension to 'ggplot2', for the Creation of Ternary Diagrams 
ggThemeAssist  Addin to Customize 'ggplot2' Themes 
ggthemes  Extra Themes, Scales and Geoms for 'ggplot2' 
ggvis  Interactive Grammar of Graphics 
GHap  GenomeWide Haplotyping 
ghit  Lightweight GitHub Package Installer 
GHQp  Gauss Hermite Quadrature with pruning 
ghyp  A package on the generalized hyperbolic distribution and its
special cases 
GiANT  Gene Set Uncertainty in Enrichment Analysis 
GibbsACOV  Gibbs Sampler for OneWay MixedEffects ANOVA and ANCOVA Models 
gibbs.met  Naive Gibbs Sampling with Metropolis Steps 
GIGrvg  Random Variate Generator for the GIG Distribution 
GillespieSSA  Gillespie's Stochastic Simulation Algorithm (SSA) 
gimme  Group Iterative Multiple Model Estimation 
gimms  Download and Process GIMMS NDVI3g Data 
GiNA  High Throughput Phenotyping 
GiniWegNeg  Computing the GiniBased Coefficients for Weighted and Negative
Attributes 
gIPFrm  Generalized Iterative Proportional Fitting for Relational Models 
GiRaF  Gibbs Random Fields Analysis 
giRaph  The giRaph package for graph representation in R 
GISTools  Some further GIS capabilities for R 
gistr  Work with 'GitHub' 'Gists' 
git2r  Provides Access to Git Repositories 
githubinstall  An Easy Way to Install R Packages on GitHub 
gitlabr  Access to the Gitlab API 
gitter  Quantification of Pinned Microbial Cultures 
givitiR  The GiViTI Calibration Test and Belt 
Giza  Constructing panels of population pyramid plots based on lattice 
gjam  Generalized Joint Attribute Modeling 
GK2011  Gaines and Kuklinski (2011) Estimators for Hybrid Experiments 
gkmSVM  GappedKmer Support Vector Machine 
glamlasso  Lasso Penalization in Large Scale Generalized Linear Array
Models 
glarma  Generalized Linear Autoregressive Moving Average Models 
glasso  Graphical lasso estimation of Gaussian graphical models 
glba  General Linear Ballistic Accumulator Models 
glcm  Calculate Textures from GreyLevel CoOccurrence Matrices
(GLCMs) 
gld  Estimation and Use of the Generalised (Tukey) Lambda
Distribution 
GLDEX  Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods 
gldist  An AsymmetrySteepness Parameterization of the Generalized
Lambda Distribution 
GLDreg  Fit GLD Regression Model and GLD Quantile Regression Model to
Empirical Data 
glinternet  Learning Interactions via Hierarchical GroupLasso
Regularization 
gllm  Generalised loglinear model 
glm2  Fitting Generalized Linear Models 
glmbb  All Hierarchical or Graphical Models for Generalized Linear
Model 
glmBfp  Bayesian Fractional Polynomials for GLMs 
glmc  Fitting Generalized Linear Models Subject to Constraints 
glm.ddR  Distributed 'glm' for Big Data using 'ddR' API 
glmdm  R Code for Simulation of GLMDM 
glmgraph  GraphConstrained Regularization for Sparse Generalized Linear
Models 
glmlep  Fit GLM with LEPbased penalized maximum likelihood 
glmm  Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation 
glmmBUGS  Generalised Linear Mixed Models and Spatial Models with WinBUGS,
BRugs, or OpenBUGS 
glmmGS  GaussSeidel Generalized Linear Mixed Model solver 
glmmLasso  Variable Selection for Generalized Linear Mixed Models by
L1Penalized Estimation 
glmmML  Generalized linear models with clustering 
GLMMRR  Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data 
glmmsr  Fit a Generalized Linear Mixed Model 
glmnet  Lasso and ElasticNet Regularized Generalized Linear Models 
glmnetcr  Fit a penalized constrained continuation ratio model for
predicting an ordinal response 
glmpath  L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model 
glmpathcr  Fit a penalized continuation ratio model for predicting an
ordinal response 
glmulti  Model selection and multimodel inference made easy 
glmvsd  Variable Selection Deviation Measures and Instability Tests for
HighDimensional Generalized Linear Models 
glmx  Generalized Linear Models Extended 
globalboosttest  Testing the additional predictive value of highdimensional data 
GlobalDeviance  Global Deviance Permutation Tests 
GlobalFit  BiLevel Optimization of Metabolic Network Models 
globalGSA  Global GeneSet Analysis for Association Studies 
GlobalOptions  Generate Functions to Get or Set Global Options 
globalOptTests  Objective functions for benchmarking the performance of global
optimization algorithms 
globals  Identify Global Objects in R Expressions 
globe  Plot 2D and 3D Views of the Earth, Including Major Coastline 
glogis  Fitting and Testing Generalized Logistic Distributions 
glpkAPI  R Interface to C API of GLPK 
glrt  Generalized Logrank Tests for Intervalcensored Failure Time
Data 
GLSME  Generalized Least Squares with Measurement Error 
glycanr  Tools for Analysing NGlycan Data 
gmailr  Access the Gmail RESTful API 
gmapsdistance  Distance and Travel Time Between Two Points from Google Maps 
gmatrix  GPU Computing in R 
GMCM  Fast Estimation of Gaussian Mixture Copula Models 
gMCP  Graph Based Multiple Comparison Procedures 
GMD  Generalized Minimum Distance of distributions 
gmDatabase  Accessing a Geometallurgical Database with R 
GMDH  Short Term Forecasting via GMDHType Neural Network Algorithms 
Gmedian  Geometric Median, kMedian Clustering and Robust Median PCA 
gmeta  MetaAnalysis via a Unified Framework of Confidence Distribution 
Gmisc  Descriptive Statistics, Transition Plots, and More 
gmm  Generalized Method of Moments and Generalized Empirical
Likelihood 
GMMBoost  Likelihoodbased Boosting for Generalized mixed models 
gmnl  Multinomial Logit Models with Random Parameters 
gmodels  Various R Programming Tools for Model Fitting 
gmp  Multiple Precision Arithmetic 
gmt  Interface between GMT MapMaking Software and R 
gmum.r  GMUM Machine Learning Group Package 
gmwm  Generalized Method of Wavelet Moments 
gMWT  Generalized MannWhitney Type Tests 
GNE  Computation of Generalized Nash Equilibria 
gnm  Generalized Nonlinear Models 
gnmf  Generalized Nonnegative Matrix Factorization Based on Renyi
Divergence 
gnumeric  Read Data from Files Readable by Gnumeric 
goalprog  Weighted and lexicographical goal programming and optimization 
goeveg  Functions for Community Data and Ordinations 
gof  Modeldiagnostics based on cumulative residuals 
gofCopula  GoodnessofFit Tests for Copulae 
GoFKernel  Testing GoodnessofFit with the Kernel Density Estimator 
GofKmt  Khmaladze Martingale Transformation GoodnessofFit Test 
goft  Tests of Fit for some Probability Distributions 
goftest  Classical GoodnessofFit Tests for Univariate Distributions 
GOGANPA  GOFunctionalNetworkbased GeneSetAnalysis 
gogarch  Generalized Orthogonal GARCH (GOGARCH) models 
GoodmanKruskal  Association Analysis for Categorical Variables 
googleAnalyticsR  Google Analytics API into R 
googleAuthR  Easy Authentication with Google OAuth2 API 
googleformr  Collect Data Programmatically by POST Methods to Google Forms 
googlePublicData  Working with Google Public Data Explorer DSPL Metadata Files 
googlesheets  Manage Google Spreadsheets from R 
googleVis  R Interface to Google Charts 
googleway  Retrieves Data from Google Maps APIs 
GOplot  Visualization of Functional Analysis Data 
GORCure  Fit Generalized Odds Rate Mixture Cure Model with Interval
Censored Data 
goric  Generalized OrderRestricted Information Criterion 
govStatJPN  functions to get public survey data in Japan 
gpairs  gpairs: The Generalized Pairs Plot 
GPareto  Gaussian Processes for Pareto Front Estimation and Optimization 
GPArotation  GPA Factor Rotation 
GPC  Generalized Polynomial Chaos 
gPCA  Batch Effect Detection via Guided Principal Components Analysis 
gpclib  General Polygon Clipping Library for R 
GPCSIV  GPCSIV, Generalized Principal Component of Symbolic Interval
variables 
gpDDE  General Profiling Method for Delay Differential Equation 
gPdtest  Bootstrap goodnessoffit test for the generalized Pareto
distribution 
GPFDA  Apply Gaussian Process in Functional data analysis 
GPfit  Gaussian Processes Modeling 
gpk  100 Data Sets for Statistics Education 
gplm  Generalized partial linear models (GPLM) 
gplots  Various R Programming Tools for Plotting Data 
GPLTR  Generalized Partially Linear TreeBased Regression Model 
gpmap  Analysing and plotting genotypephenotype maps 
gpr  A Minimalistic package to apply Gaussian Process in R 
gProfileR  Interface to the 'g:Profiler' Toolkit 
GPseq  gpseq: Using the generalized Poisson distribution to model
sequence read counts from high throughput sequencing
experiments 
gptk  Gaussian Processes ToolKit 
gpuR  GPU Functions for R Objects 
gputools  A Few GPU Enabled Functions 
GPvam  Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in ValueAdded Modeling 
gquad  G Quadruplex Motif Prediction Tool 
Grace  GraphConstrained Estimation and Hypothesis Tests 
grade  Binary Grading functions for R 
GRaF  Species distribution modelling using latent Gaussian random
fields 
gRain  Graphical Independence Networks 
gramEvol  Grammatical Evolution for R 
GrammR  Graphical Representation and Modeling of Metagenomic Reads 
GRANBase  Creating Continuously Integrated Package Repositories from
Manifests 
granova  Graphical Analysis of Variance 
granovaGG  Graphical Analysis of Variance Using ggplot2 
gRapfa  Acyclic Probabilistic Finite Automata 
gRapHD  Efficient selection of undirected graphical models for
highdimensional datasets 
GrapheR  A MultiPlatform GUI for Drawing Customizable Graphs in R 
graphicalVAR  Graphical VAR for Experience Sampling Data 
graphicsQC  Quality Control for Graphics in R 
graphscan  Cluster Detection with Hypothesis Free Scan Statistic 
graphTweets  Visualise Twitter Interactions 
GrassmannOptim  Grassmann Manifold Optimization 
graticule  Meridional and Parallel Lines for Maps 
gRbase  A Package for Graphical Modelling in R 
gRc  Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries 
Greg  Regression Helper Functions 
greport  Graphical Reporting for Clinical Trials 
grex  Gene ID Mapping for GenotypeTissue Expression (GTEx) Data 
greyzoneSurv  Fit a GreyZone Model with Survival Data 
Grid2Polygons  Convert Spatial Grids to Polygons 
gridBase  Integration of base and grid graphics 
gridDebug  Debugging 'grid' Graphics 
gridExtra  Miscellaneous Functions for "Grid" Graphics 
gridGraphics  Redraw Base Graphics Using 'grid' Graphics 
gridGraphviz  Drawing Graphs with 'grid' 
gridSVG  Export 'grid' Graphics as SVG 
GriegSmith  Uses GriegSmith method on 2 dimentional spatial data 
gRim  Graphical Interaction Models 
grImport  Importing Vector Graphics 
grnn  General regression neural network 
groc  Generalized Regression on Orthogonal Components 
grofit  The package was developed to fit fit many growth curves obtained
under different conditions 
gromovlab  GromovHausdorff Type Distances for Labeled Metric Spaces 
grouped  Regression Analysis of Grouped and Coarse Data 
groupRemMap  Regularized Multivariate Regression for Identifying Master
Predictors Using the GroupRemMap Penalty 
GroupSeq  A GUIBased Program to Compute Probabilities Regarding Group
Sequential Designs 
GroupTest  Multiple Testing Procedure for Grouped Hypotheses 
growcurves  Bayesian Semi and Nonparametric Growth Curve Models that
Additionally Include Multiple Membership Random Effects 
growfunctions  Bayesian NonParametric Dependent Models for TimeIndexed
Functional Data 
growthcurver  Simple Metrics to Summarize Growth Curves 
growthmodels  Nonlinear Growth Models 
growthrate  Bayesian reconstruction of growth velocity 
growthrates  Estimate Growth Rates from Experimental Data 
grplasso  Fitting user specified models with Group Lasso penalty 
grppenalty  Concave 1norm and 2norm group penalty in linear and logistic
regression 
grpreg  Regularization Paths for Regression Models with Grouped
Covariates 
grpregOverlap  Penalized Regression Models with Overlapping Grouped Covariates 
grpSLOPE  Group Sorted L1 Penalized Estimation 
grpss  Group Screening and Selection 
grr  Alternative Implementations of Base R Functions 
grt  General Recognition Theory 
GRTo  Tools for the Analysis of GutenbergRichter Distributions of
Earthquake Magnitudes 
GSA  Gene set analysis 
GSAgm  Gene Set Analysis using the Gamma Method 
gsalib  Utility Functions For GATK 
gsarima  Two functions for Generalized SARIMA time series simulation 
gsbDesign  Group Sequential Bayes Design 
gsDesign  Group Sequential Design 
GSE  Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data 
gsEasy  Gene Set Enrichment Analysis in R 
gSeg  GraphBased ChangePoint Detection (gSegmentation) 
gSEM  SemiSupervised Generalized Structural Equation Modeling 
gset  Group Sequential Design in Equivalence Studies 
gsg  Calculation of selection coefficients 
gsheet  Download Google Sheets Using Just the URL 
GSIF  Global Soil Information Facilities 
gskat  GEE_KM 
gsl  wrapper for the Gnu Scientific Library 
GSM  Gamma Shape Mixture 
gsmoothr  Smoothing tools 
GSODR  Download, Clean and Generate New Variables from GSOD Data 
gsrc  Genome Structure Rearrangement Calling in Genomes with High
Synteny 
gss  General Smoothing Splines 
gsscopu  Copula Density and 2D Hazard Estimation using Smoothing Splines 
GSSE  GenotypeSpecific Survival Estimation 
gstat  Spatial and SpatioTemporal Geostatistical Modelling, Prediction
and Simulation 
gsubfn  Utilities for strings and function arguments 
gsw  Gibbs Sea Water Functions 
GsymPoint  Estimation of the Generalized Symmetry Point, an Optimal
Cutpoint in Continuous Diagnostic Tests 
gtable  Arrange 'Grobs' in Tables 
gtcorr  Calculate efficiencies of group testing algorithms with
correlated responses 
gte  Generalized Turnbull's Estimator 
gtools  Various R Programming Tools 
gtop  GameTheoretically OPtimal (GTOP) Reconciliation Method 
gtrendsR  R Functions to Perform and Display Google Trends Queries 
gtx  Genetics ToolboX 
GuardianR  The Guardian API Wrapper 
Guerry  Maps, data and methods related to Guerry (1833) "Moral
Statistics of France" 
guess  Adjust Estimates of Learning for Guessing 
GUIDE  GUI for DErivatives in R 
GUILDS  Implementation of Sampling Formulas for the Unified Neutral
Model of Biodiversity and Biogeography, with or without Guild
Structure 
GUIProfiler  Graphical User Interface for Rprof() 
gumbel  The GumbelHougaard Copula 
GUniFrac  Generalized UniFrac distances 
gunsales  Statistical Analysis of Monthly Background Checks of Gun
Purchases 
gutenbergr  Download and Process Public Domain Works from Project Gutenberg 
GUTS  Fast Calculation of the Likelihood of a Stochastic Survival
Model 
gvc  Global Value Chains Tools 
gvcm.cat  Regularized Categorical Effects/Categorical Effect
Modifiers/Continuous/Smooth Effects in GLMs 
gvlma  Global Validation of Linear Models Assumptions 
GWAF  GenomeWide Association/Interaction Analysis and Rare Variant
Analysis with Family Data 
GWASExactHW  Exact HardyWeinburg testing for Genome Wide Association Studies 
gwdegree  A Shiny App to Aid Interpretation of GeometricallyWeighted
Degree Estimates in Exponential Random Graph Models 
gwerAM  Controlling the genomewide type I error rate in association
mapping experiments 
GWG  Calculation of probabilities for inadequate and excessive
gestational weight gain 
gWidgets  gWidgets API for building toolkitindependent, interactive GUIs 
gWidgets2  Rewrite of gWidgets API for Simplified GUI Construction 
gWidgets2RGtk2  Implementation of gWidgets2 for the RGtk2 Package 
gWidgets2tcltk  Toolkit Implementation of gWidgets2 for tcltk 
gWidgetsRGtk2  Toolkit implementation of gWidgets for RGtk2 
gWidgetstcltk  Toolkit implementation of gWidgets for tcltk package 
GWLelast  Geographically Weighted Logistic Elastic Net Regression 
GWmodel  GeographicallyWeighted Models 
GWRM  Generalized Waring Regression Model for Count Data 
gwrr  Fits geographically weighted regression models with diagnostic
tools 
GWsignif  Estimating GenomeWide Significance for Whole Genome Sequencing
Studies, Either Single SNP Tests or RegionBased Tests 
GxM  Maximum Likelihood Estimation for GenebyMeasured Environment
Interaction Models 
gyriq  KinshipAdjusted Survival SNPSet Analysis 

h2o  R Interface for H2O 
h5  Interface to the 'HDF5' Library 
haarfisz  Software to perform Haar Fisz transforms 
HAC  Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC) 
HadoopStreaming  Utilities for using R scripts in Hadoop streaming 
hail  Read HYDRA Rainfall Data 
hamlet  Hierarchical Optimal Matching and Machine Learning Toolbox 
HandTill2001  Multiple Class Area under ROC Curve 
Hankel  Univariate nonparametric twosample test based on empirical
Hankel transforms 
hapassoc  Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm 
HapEstXXR  MultiLocus Stepwise Regression 
HAPim  HapIM 
Haplin  Analyzing CaseParent Triad and/or CaseControl Data with SNP
Haplotypes 
haplo.ccs  Estimate Haplotype Relative Risks in CaseControl Data 
HaploSim  Functions to simulate haplotypes 
haplo.stats  Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous 
haplotyper  Tool for Clustering Genotypes in Haplotypes 
haplotypes  Haplotype Inference and Statistical Analysis of Genetic
Variation 
HAP.ROR  Recursive Organizer (ROR) 
HardyWeinberg  Statistical Tests and Graphics for HardyWeinberg Equilibrium 
HarmonicRegression  Harmonic Regression to One or more Time Series 
harvestr  A Parallel Simulation Framework 
Harvest.Tree  Harvest the Classification Tree 
hash  Full feature implementation of hash/associated
arrays/dictionaries 
hashFunction  A collection of noncryptographic hash functions 
hashids  Generate Short Unique YouTubeLike IDs (Hashes) from Integers 
hashmap  The Faster Hash Map 
hashr  Hash R Objects to Integers Fast 
hasseDiagram  Drawing Hasse diagram 
haven  Import 'SPSS', 'Stata' and 'SAS' Files 
hawkes  Hawkes process simulation and calibration toolkit 
hazus  Damage functions from FEMA's HAZUS software for use in modeling
financial losses from natural disasters 
hBayesDM  Hierarchical Bayesian Modeling of DecisionMaking Tasks 
HBglm  Hierarchical Bayesian Regression for GLMs 
hbim  Hill/Bliss Independence Model for Combination Vaccines 
hbm  Hierarchical Block Matrix Analysis 
hbmem  Hierarchical Bayesian Analysis of Recognition Memory 
hbsae  Hierarchical Bayesian Small Area Estimation 
HBSTM  Hierarchical Bayesian SpaceTime models for Gaussian spacetime
data 
hcc  Hidden correlation check 
hcci  Interval estimation for the parameters of linear models with
heteroskedasticity (Wild Bootstrap) 
hcp  Change Point Estimation for Regression with Heteroscedastic Data 
hda  Heteroscedastic Discriminant Analysis 
HDclassif  High Dimensional Supervised Classification and Clustering 
HDDesign  Sample Size Calculation for High Dimensional Classification
Study 
hddplot  Use known groups in highdimensional data to derive scores for
plots 
hddtools  Hydrological Data Discovery Tools 
hdeco  Hierarchical DECOmposition of Entropy for Categorical Map
Comparisons 
HDGLM  Tests for High Dimensional Generalized Linear Models 
hdi  HighDimensional Inference 
HDInterval  Highest (Posterior) Density Intervals 
hdlm  Fitting High Dimensional Linear Models 
hdm  HighDimensional Metrics 
HDMD  Statistical Analysis Tools for High Dimension Molecular Data
(HDMD) 
hdnom  Nomograms for HighDimensional Cox Models 
HDoutliers  Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers 
HDPenReg  HighDimensional Penalized Regression 
hdr  Interface to the UNDR Human Development Report API 
hdrcde  Highest density regions and conditional density estimation 
HDtweedie  The Lasso for the Tweedie's Compound Poisson Model Using an
IRLSBMD Algorithm 
HEAT  Health Effects of Air Pollution and Temperature (HEAT) 
heatex  Heat exchange calculations during physical activity 
heatmap3  An Improved Heatmap Package 
heatmapFit  Fit Statistic for Binary Dependent Variable Models 
heatmaply  Interactive Heat Maps Using 'plotly' 
heatmap.plus  Heatmap with more sensible behavior 
heavy  Robust Estimation Using HeavyTailed Distributions 
heemod  Models for Health Economic Evaluation 
hellno  Providing 'stringsAsFactors=FALSE' Variants of 'data.frame()'
and 'as.data.frame()' 
helloJavaWorld  Hello Java World 
HelpersMG  Tools for Earth Meteorological Analysis 
helsinki  R Tools for Helsinki Open Data 
heplots  Visualizing Hypothesis Tests in Multivariate Linear Models 
hergm  Hierarchical ExponentialFamily Random Graph Models 
heritability  MarkerBased Estimation of Heritability Using Individual Plant
or Plot Data 
hermite  Generalized Hermite Distribution 
hetmeta  Heterogeneity Measures in MetaAnalysis 
hett  Heteroscedastic tregression 
het.test  White's Test for Heteroskedasticity 
heuristica  Heuristics Including Take the Best and UnitWeight Linear 
hexbin  Hexagonal Binning Routines 
hextri  Hexbin Plots with Triangles 
hexView  Viewing Binary Files 
hflights  Flights that departed Houston in 2011 
hgam  Highdimensional Additive Modelling 
hglasso  Learning graphical models with hubs 
hglm  Hierarchical Generalized Linear Models 
hglm.data  Data for The hglm Package 
hgm  Holonomic Gradient Method and Gradient Descent 
HGNChelper  Handy Functions for Working With HGNC Gene Symbols and
Affymetrix Probeset Identifiers 
HH  Statistical Analysis and Data Display: Heiberger and Holland 
HHG  HellerHellerGorfine Tests of Independence and Equality of
Distributions 
hht  The HilbertHuang Transform: Tools and Methods 
HI  Simulation from distributions supported by nested hyperplanes 
HIBPwned  Bindings for the HaveIBeenPwned.com Data Breach API 
HiCfeat  Multiple Logistic Regression for 3D Chromatin Domain Border
Analysis 
HiClimR  Hierarchical Climate Regionalization 
HiCseg  Detection of domains in HiC data 
hiddenf  The AllConfigurations, MaximumInteraction FTest for Hidden
Additivity 
HiddenMarkov  Hidden Markov Models 
HiDimDA  High Dimensional Discriminant Analysis 
HiDimMaxStable  Inference on High Dimensional MaxStable Distributions 
hierarchicalDS  Functions For Performing Hierarchical Analysis of Distance
Sampling Data 
hierarchicalSets  Set Data Visualization Using Hierarchies 
hierband  Convex Banding of the Covariance Matrix 
hierDiversity  Hierarchical Multiplicative Partitioning of Complex Phenotypes 
hierformR  Analysis of Dynamics Hierarchy Formation 
hierfstat  Estimation and Tests of Hierarchical FStatistics 
hierNet  A Lasso for Hierarchical Interactions 
HierO  A graphical user interface for calculating power and sample size
for hierarchical data 
hier.part  Hierarchical Partitioning 
hiertest  Convex Hierarchical Testing of Interactions 
HIest  Hybrid index estimation 
highcharter  A Wrapper for the 'Highcharts' Library 
highD2pop  TwoSample Tests for Equality of Means in High Dimension 
HighDimOut  Outlier Detection Algorithms for HighDimensional Data 
highfrequency  Tools For Highfrequency Data Analysis 
highlight  Syntax Highlighter 
highmean  TwoSample Tests for HighDimensional Mean Vectors 
highr  Syntax Highlighting for R Source Code 
highriskzone  Determining and Evaluating HighRisk Zones 
highSCREEN  High Throughput Screening for Plate Based Essays 
highTtest  Simultaneous Critical Values for tTests in Very High Dimensions 
hillmakeR  Perform occupancy analysis 
HiLMM  Estimation of Heritability in Linear Mixed Models 
hindexcalculator  HIndex Calculator using Data from a Web of Science (WoS)
Citation Report 
hint  Tools for hypothesis testing based on Hypergeometric
Intersection distributions 
HiPLARM  High Performance Linear Algebra in R 
hiPOD  hierarchical Pooled Optimal Design 
hisemi  Hierarchical Semiparametric Regression of Test Statistics 
hisse  Hidden State Speciation and Extinction 
HistData  Data Sets from the History of Statistics and Data Visualization 
HistDAWass  HistogramValued Data Analysis 
histmdl  A Most Informative HistogramLike Model 
histogram  Construction of regular and irregular histograms with different
options for automatic choice of bins 
HistogramTools  Utility Functions for R Histograms 
historydata  Data Sets for Historians 
hit  Hierarchical Inference Testing 
hitandrun  "Hit and Run" and "Shake and Bake" for Sampling Uniformly from
Convex Shapes 
hive  Hadoop InteractiVE 
HiveR  2D and 3D Hive Plots for R 
HIV.LifeTables  HIV calibrated model life tables for countries with generalized
HIV epidemics 
HK80  Conversion Tools for HK80 Geographical Coordinate System 
hkevp  Spatial Extreme Value Analysis with the Hierarchical Model of
Reich and Shaby (2012) 
hkex.api  API to Retrieve Data from Hong Kong Stock Exchange 
HKprocess  HurstKolmogorov Process 
HLMdiag  Diagnostic Tools for Hierarchical (Multilevel) Linear Models 
HLSM  Hierarchical Latent Space Network Model (HLSM) 
HMDHFDplus  Read HMD and HFD Data from the Web 
hmeasure  The Hmeasure and other scalar classification performance
metrics 
Hmisc  Harrell Miscellaneous 
HMM  HMM  Hidden Markov Models 
HMMCont  Hidden Markov Model for Continuous Observations Processes 
hmm.discnp  Hidden Markov Models with Discrete NonParametric Observation
Distributions 
hmmm  hierarchical multinomial marginal models 
HMMpa  Analysing accelerometer data using hidden Markov models 
HMP  Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP 
HMPTrees  Statistical Object Oriented Data Analysis of RDPBased Taxonomic
Trees from Human Microbiome Data 
HMR  Flux Estimation with Static Chamber Data 
hms  Pretty Time of Day 
HMVD  Group Association Test using a Hidden Markov Model 
hnp  HalfNormal Plots with Simulation Envelopes 
hoa  Higher Order Likelihood Inference 
hoardeR  Information Retrieval for Genetic Datasets 
holdem  Texas Holdem simulator 
Holidays  Holiday and HalfDay Data, for Use with the 'TimeWarp' Package 
homals  Gifi Methods for Optimal Scaling 
homeR  Useful Functions for Building Physics 
Homeric  Doughnut Plots 
homomorpheR  Homomorphic Computations in R 
HomoPolymer  Theoretical Model to Simulate Radical Polymerization 
homtest  Homogeneity tests for Regional Frequency Analysis 
hopbyhop  Transmissions and Receptions in a Hop by Hop Network 
hornpa  Horn's (1965) Test to Determine the Number of Components/Factors 
hot.deck  Multiple HotDeck Imputation 
HotDeckImputation  Hot Deck Imputation Methods for Missing Data 
Hotelling  Hotelling's Tsquared test and variants 
hotspot  Software Hotspot Analysis 
hotspots  Hot spots 
housingData  U.S. Housing Data from 2008 to 2016 
howmany  A lower bound for the number of correct rejections 
HPbayes  Heligman Pollard mortality model parameter estimation using
Bayesian Melding with Incremental Mixture Importance Sampling 
hpcwld  High Performance Cluster Models Based on KieferWolfowitz
Recursion 
hpoPlot  Functions for Plotting HPO Terms 
hqmisc  Miscellaneous convenience functions and dataset 
hqreg  Regularization Paths for Lasso or ElasticNet Penalized Huber
Loss Regression and Quantile Regression 
HRM  HighDimensional Repeated Measures 
hrr  Horizontal rule for the R language 
HSAR  Hierarchical Spatial Autoregressive Model (HSAR) 
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) 
hsdar  Manage, Analyse and Simulate Hyperspectral Data 
hSDM  hierarchical Bayesian species distribution models 
hsicCCA  Canonical Correlation Analysis based on Kernel Independence
Measures 
hsm  A PathBased BCD for Proximal Function of Latent Group Lasso 
hsmm  Hidden Semi Markov Models 
hsphase  Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Halfsib Families Using
SNP Data 
HSROC  MetaAnalysis of Diagnostic Test Accuracy when Reference Test is
Imperfect 
HSSVD  Biclustering with Heterogeneous Variance 
htmltab  Assemble Data Frames from HTML Tables 
htmlTable  Advanced Tables for Markdown/HTML 
htmltools  Tools for HTML 
HTMLUtils  Facilitates Automated HTML Report Creation 
htmlwidgets  HTML Widgets for R 
hts  Hierarchical and Grouped Time Series 
HTSCluster  Clustering HighThroughput Transcriptome Sequencing (HTS) Data 
httk  HighThroughput Toxicokinetics 
httpcache  Query Cache for HTTP Clients 
httpcode  'HTTP' Status Code Helper 
httping  'Ping' 'URLs' to Time 'Requests' 
httpRequest  Basic HTTP Request 
httpuv  HTTP and WebSocket Server Library 
httr  Tools for Working with URLs and HTTP 
huge  HighDimensional Undirected Graph Estimation 
HUM  compute HUM value and visualize ROC curves 
humanFormat  Humanfriendly formatting functions 
humaniformat  A Parser for Human Names 
humarray  Simplify Analysis and Annotation of Human Microarray Datasets 
humidity  An R Package for Calculating Water Vapor Measures from
Temperature and Relative Humidity 
hunspell  Morphological Analysis and Spell Checker for R 
hwde  Models and Tests for Departure from HardyWeinberg Equilibrium
and Independence Between Loci 
HWEBayes  Bayesian investigation of HardyWeinberg Equilibrium via
estimation and testing 
HWEintrinsic  Objective Bayesian Testing for the HardyWeinberg Equilibrium
Problem 
HW.pval  Testing HardyWeinberg Equilibrium for Multiallelic Genes 
hwriter  HTML Writer  Outputs R objects in HTML format 
hwriterPlus  hwriterPlus: Extending the hwriter Package 
hwwntest  Tests of White Noise using Wavelets 
HWxtest  Exact Tests for HardyWeinberg Proportions 
hybridEnsemble  Build, Deploy and Evaluate Hybrid Ensembles 
hybridHclust  Hybrid Hierarchical Clustering 
HybridMC  Implementation of the Hybrid Monte Carlo and Multipoint Hybrid
Monte Carlo sampling techniques 
hybridModels  Stochastic Hybrid Models in Dynamic Networks 
HydeNet  Hybrid Bayesian Networks Using R and JAGS 
hydroApps  Tools and models for hydrological applications 
hydrogeo  Groundwater Data Presentation and Interpretation 
hydroGOF  Goodnessoffit functions for comparison of simulated and
observed hydrological time series 
HydroMe  R codes for estimating water retention and infiltration model
parameters using experimental data 
hydroPSO  Particle Swarm Optimisation, with focus on Environmental Models 
hydrostats  Hydrologic Indices for Daily Time Series Data 
hydroTSM  Time series management, analysis and interpolation for
hydrological modelling 
hyfo  Hydrology and Climate Forecasting 
HyperbolicDist  The hyperbolic distribution 
hyperdirichlet  A generalization of the Dirichlet distribution 
hypergea  Hypergeometric Tests 
hypergeo  The Gauss Hypergeometric Function 
hyperSpec  Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...) 
hypervolume  HighDimensional Kernel Density Estimation and Geometry
Operations 
hyphenatr  Tools to Hyphenate Strings Using the 'Hunspell' Hyphenation
Library 
HyPhy  Macroevolutionary phylogentic analysis of species trees and gene
trees 
hypothesestest  Confidence Intervals and Tests of Statistical Hypotheses 
hypothesisr  Wrapper for the 'Hypothes.is' Web Annotation Service 
hysteresis  Tools for Modeling RateDependent Hysteretic Processes and
Ellipses 
hzar  Hybrid Zone Analysis using R 

IalsaSynthesis  Synthesizing Information Across Collaborating Research 
IASD  Model Selection for Index of Asymmetry Distribution 
IAT  Cleaning and Visualizing Implicit Association Test (IAT) Data 
IATscores  Implicit Association Test Scores Using Robust Statistics 
iBATCGH  Integrative Bayesian Analysis of Transcriptomic and CGH Data 
ibd  INCOMPLETE BLOCK DESIGNS 
IBDhaploRtools  Functions for the Analysis of IBD Haplo Output 
IBDLabels  Convert Between Different IBDState Labelling Schemes 
ibdreg  Regression Methods for IBD Linkage With Covariates 
IBDsim  Simulation of Chromosomal Regions Shared by Family Members 
ibeemd  Irregularlattice based ensemble empirical mode decomposition 
ibelief  Belief Function Implementation 
IBHM  Approximation using the IBHM method 
ibm  Individual Based Models in R 
ibmdbR  IBM inDatabase Analytics for R 
Iboot  Iboot: iterated bootstrap tests and confidence sets 
ibr  Iterative Bias Reduction 
IBrokers  R API to Interactive Brokers Trader Workstation 
iBUGS  An Interface to WinBUGS/OpenBUGS/JAGS by gWidgets 
iC10  A Copy Number and ExpressionBased Classifier for Breast Tumours 
iC10TrainingData  Training datasets for iC10 package 
IC2  Inequality and Concentration Indices and Curves 
ic50  Standardized highthroughput evaluation of cellbased compound
screens 
ica  Independent Component Analysis 
ICAFF  Imperialist Competitive Algorithm 
icamix  Estimation of ICA Mixture Models 
icaOcularCorrection  Independent Components Analysis (ICA) based artifact correction 
icapca  Mixed ICA/PCA 
icarus  Calibrates and Reweights Units in Samples 
ICBayes  Bayesian Semiparametric Models for IntervalCensored Data 
ICC  Facilitating Estimation of the Intraclass Correlation
Coefficient 
iccbeta  Multilevel model intraclass correlation for slope heterogeneity 
ICC.Sample.Size  Calculation of Sample Size and Power for ICC 
icd  Tools for Working with ICD9 and ICD10 Codes, and Finding
Comorbidities 
icd9  Tools for Working with ICD9 Codes, and Finding Comorbidities 
icdGLM  EM by the Method of Weights for Incomplete Categorical Data in
Generlized Linear Models 
ICE  Iterated Conditional Expectation 
ICEbox  Individual Conditional Expectation Plot Toolbox 
ICEinfer  Incremental CostEffectiveness (ICE) Statistical Inference from
Two Unbiased Samples 
icenReg  Regression Models for Interval Censored Data 
icensmis  Study Design and Data Analysis in the Presence of ErrorProne
Diagnostic Tests and SelfReported Outcomes 
icesAdvice  Functions Related to ICES Advice 
ICGE  Estimation of number of clusters and identification of atypical
units 
ICGOR  Fit Generalized Odds Rate Hazards Model with Interval Censored
Data 
ic.infer  Inequality constrained inference in linear normal situations 
iClick  A ButtonBased GUI for Financial and Economic Data Analysis 
iCluster  Integrative clustering of multiple genomic data types 
icpsrdata  Reproducible Data Retrieval from the ICPSR Archive 
icRSF  A Modified Random Survival Forest Algorithm 
ICS  Tools for Exploring Multivariate Data via ICS/ICA 
ICSNP  Tools for Multivariate Nonparametrics 
ICsurv  A package for semiparametric regression analysis of
intervalcensored data 
icsw  Inverse Compliance Score Weighting 
idbg  R debugger 
idbr  R Interface to the US Census Bureau International Data Base API 
idem  Inference in Randomized Controlled Trials with Death and
Missingness 
idendr0  Interactive Dendrograms 
identity  Jacquard Condensed Coefficients of Identity 
idm  Incremental Decomposition Methods 
IDPmisc  Utilities of Institute of Data Analyses and Process Design
(www.idp.zhaw.ch) 
IDPSurvival  Imprecise Dirichlet Process for Survival Analysis 
idr  Irreproducible discovery rate 
IDSpatialStats  Estimate Global Clustering in Infectious Disease 
IDTurtle  Identify Turtles by their Plastral Biometries 
iDynoR  R Analysis package for iDynoMiCS Simulation Results 
ie2misc  Irucka Embry's Miscellaneous USGS Functions 
ie2miscdata  Irucka Embry's Miscellaneous USGS Data Collection 
ieeeround  Functions to set and get the IEEE rounding mode 
iemisc  Irucka Embry's Miscellaneous Functions 
iemiscdata  Irucka Embry's Miscellaneous Data Collection 
ifa  Independent Factor Analysis 
iFad  An integrative factor analysis model for drugpathway
association inference 
ifaTools  Toolkit for Item Factor Analysis with OpenMx 
ifctools  Italian Fiscal Code ('Codice Fiscale') Utilities 
IFP  Identifying Functional Polymorphisms 
ifs  Iterated Function Systems 
ifultools  Insightful Research Tools 
iGasso  Statistical Tests and Utilities for Genetic Association 
IGM.MEA  IGM MEA Analysis 
IgorR  Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic'
Data) 
igraph  Network Analysis and Visualization 
igraphdata  A Collection of Network Data Sets for the 'igraph' Package 
igraphinshiny  Use 'shiny' to Demo 'igraph' 
igraphtosonia  Convert iGraph graps to SoNIA .son files 
ig.vancouver.2014.topcolour  Instagram 2014 Vancouver Top Colour Dataset 
ihs  Inverse Hyperbolic Sine Distribution 
iki.dataclim  Consistency, Homogeneity and Summary Statistics of
Climatological Data 
iLaplace  Improved Laplace Approximation for Integrals of Unimodal
Functions 
ilc  LeeCarter Mortality Models using Iterative Fitting Algorithms 
ILS  Interlaboratory Study 
IM  Orthogonal Moment Analysis 
imageData  Aids in Processing and Plotting Data from a LemnaTec
Scananalyzer 
imager  Image Processing Library Based on CImg 
IMak  Item Maker 
Imap  Interactive Mapping 
imfr  Download Data from the International Monetary Fund's Data API 
imguR  An Imgur.com API Client Package 
IMIS  Increamental Mixture Importance Sampling 
immer  Item Response Models for Multiple Ratings 
IMP  Interactive Model Performance Evaluation 
IMPACT  The Impact of Items 
ImpactIV  Identifying Causal Effect for MultiComponent Intervention Using
Instrumental Variable Method 
imPois  Imprecise Inferential Framework for Poisson Sampling Model 
import  An Import Mechanism for R 
ImportExport  Import and Export Data 
imprProbEst  Minimum distance estimation in an imprecise probability model 
imputeLCMD  A collection of methods for leftcensored missing data
imputation 
imputeMDR  The Multifactor Dimensionality Reduction (MDR) Analysis for
Incomplete Data 
imputeMissings  Impute Missing Values in a Predictive Context 
imputeMulti  Imputation Methods for Multivariate Multinomial Data 
imputePSF  Impute Missing Data in Time Series Data with PSF Based Method 
imputeTestbench  Test Bench for Missing Data Imputing Models/Methods Comparison 
imputeTS  Time Series Missing Value Imputation 
imputeYn  Imputing the Last Largest Censored Observation(s) Under Weighted
Least Squares 
in2extRemes  Into the extRemes Package 
inarmix  Mixture models for longitudinal count data 
inbreedR  Analysing Inbreeding Based on Genetic Markers 
inctools  Incidence Estimation Tools 
IncucyteDRC  Dose Response Curves from Incucyte Proliferation Assays 
IndependenceTests  Nonparametric tests of independence between random vectors 
indicspecies  Relationship Between Species and Groups of Sites 
inegiR  Integrate INEGIâ€™s (Mexican Stats Office) API with R 
ineq  Measuring Inequality, Concentration, and Poverty 
iNEXT  Interpolation and Extrapolation for Species Diversity 
InfDim  Infinedimensional model (IDM) to analyse phenotypic variation
in growth trajectories 
inference  Functions to extract inferential values of a fitted model object 
InferenceSMR  Inference about the standardized mortality ratio when evaluating
the effect of a screening program on survival 
inferference  Methods for Causal Inference with Interference 
inflection  Finds the Inflection Point of a Curve 
influence.ME  Tools for Detecting Influential Data in Mixed Effects Models 
influenceR  Software Tools to Quantify Structural Importance of Nodes in a
Network 
influence.SEM  Case Influence in Structural Equation Models 
infoDecompuTE  Information Decomposition of Twophase Experiments 
Information  Data Exploration with Information Theory (WeightofEvidence and
Information Value) 
InformationValue  Performance Analysis and Companion Functions for Binary
Classification Models 
informR  Sequence Statistics for Relational Event Models 
infotheo  InformationTheoretic Measures 
infra  An Infrastructure Proxy Function 
infuser  A Very Basic Templating Engine 
Infusion  Inference Using Simulation 
infutil  Information Utility 
ini  Read and Write '.ini' Files 
injectoR  R Dependency Injection 
INLABMA  Bayesian Model Averaging with INLA 
inline  Functions to Inline C, C++, Fortran Function Calls from R 
inlinedocs  Convert inline comments to documentation 
inpdfr  Analyse Text Documents Using Ecological Tools 
InPosition  Inference Tests for ExPosition 
insideRODE  insideRODE includes buildin functions with deSolve solver and
C/FORTRAN interfaces to nlme, together with compiled codes 
InSilicoVA  Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm 
insol  Solar Radiation 
InspectChangepoint  HighDimensional Changepoint Estimation via Sparse Projection 
install.load  Check, Install and Load CRAN & USGS GRAN Packages 
installr  Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!) 
instaR  Access to Instagram API via R 
insuranceData  A Collection of Insurance Datasets Useful in Risk Classification
in Nonlife Insurance 
intamap  procedures for automated interpolation 
intamapInteractive  procedures for automated interpolation  methods only to be used
interactively, not included in intamap package 
IntClust  Integrated Data Analysis via Clustering 
IntegrateBs  Integration for BSpline 
IntegratedJM  Joint Modelling of the GeneExpression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature 
IntegratedMRF  Integrated Prediction using Univariate and Multivariate Random
Forests 
Interact  Tests for marginal interactions in a 2 class response model 
interactionTest  Calculates Critical Test Statistics to Control False Discovery
and Familywise Error Rates in Marginal Effects Plots 
InteractiveIGraph  interactive network analysis and visualization 
interAdapt  interAdapt 
Interatrix  Compute ChiSquare Measures with Corrections 
intercure  Cure Rate Estimators for Interval Censored Data 
interferenceCI  Exact Confidence Intervals in the Presence of Interference 
intergraph  Coercion Routines for Network Data Objects 
internetarchive  An API Client for the Internet Archive 
interplot  Plot the Effects of Variables in Interaction Terms 
Interpol  Interpolation of amino acid sequences 
Interpol.T  Hourly interpolation of multiple temperature daily series 
interpretR  Binary Classifier and Regression Model Interpretation Functions 
InterSIM  Simulation of InterRelated Genomic Datasets 
InterVA4  Replicate and Analyse InterVA4 
interval  Weighted Logrank Tests and NPMLE for interval censored data 
intervals  Tools for Working with Points and Intervals 
interventionalDBN  Interventional Inference for Dynamic Bayesian Networks 
IntLik  Numerical Integration for Integrated Likelihood 
IntNMF  Integrative Clustering of Multiple Genomic Dataset 
intpoint  linear programming solver by the interior point method and
graphically (two dimensions) 
inTrees  Interpret Tree Ensembles 
intReg  Interval Regression 
intRegGOF  Integrated Regression Goodness of Fit 
introgress  methods for analyzing introgression between divergent lineages 
intsvy  International Assessment Data Manager 
intubate  Interface to Popular R Functions for Data Science Pipelines 
InvariantCausalPrediction  Invariant Causal Prediction 
InventorymodelPackage  Inventorymodel 
investr  Inverse Estimation/Calibration Functions 
invgamma  The Inverse Gamma Distribution 
invGauss  Threshold regression that fits the (randomized drift) inverse
Gaussian distribution to survival data 
invLT  Inversion of LaplaceTransformed Functions 
io  A Unified Framework for InputOutput Operations in R 
ioncopy  Calling Copy Number Alterations in Amplicon Sequencing Data 
ionflows  Calculate the Number of Required Flows for Semiconductor
Sequencing 
ionr  Test for Indifference of Indicator 
iopsych  Methods for Industrial/Organizational Psychology 
iosmooth  Functions for smoothing with infinite order flattop kernels 
iotools  I/O Tools for Streaming 
ipdmeta  Tools for subgroup analyses with multiple trial data using
aggregate statistics 
ipdw  Spatial Interpolation by Inverse Path Distance Weighting 
ipflasso  Integrative Lasso with Penalty Factors 
ipfp  Fast Implementation of the Iterative Proportional Fitting
Procedure in C 
iplots  iPlots  interactive graphics for R 
IPMpack  Builds and analyses Integral Projection Models (IPMs) 
ipred  Improved Predictors 
ips  Interfaces to Phylogenetic Software in R 
IPSUR  Introduction to Probability and Statistics Using R 
IPtoCountry  Convert IP Addresses to Country Names or Full Location with
Geoplotting 
iptools  Manipulate, Validate and Resolve 'IP' Addresses 
ipw  Estimate Inverse Probability Weights 
IQCC  Improved Quality Control Charts 
iqLearn  Interactive QLearning 
iqspr  Generate Chemical Strings (SMILES) with the Inverse QSPR Model 
irace  Iterated Racing Procedures 
iRafNet  Integrative Random Forest for Gene Regulatory Network Inference 
iRefR  iRefIndex Manager 
iRegression  Regression Methods for IntervalValued Variables 
iRepro  Reproducibility for IntervalCensored Data 
IRISMustangMetrics  Statistics and Metrics for Seismic Data 
IRISSeismic  Classes and Methods for Seismic Data Analysis 
irlba  Fast Truncated SVD, PCA and Symmetric Eigendecomposition for
Large Dense and Sparse Matrices 
irr  Various Coefficients of Interrater Reliability and Agreement 
irtDemo  Item Response Theory Demo Collection 
irtoys  Simple interface to the estimation and plotting of IRT models 
IRTpp  Estimating IRT Parameters using the IRT Methodology 
irtProb  Utilities and Probability Distributions Related to
Multidimensional Person Item Response Models 
irtrees  Estimation of TreeBased Item Response Models 
IRTShiny  Item Response Theory via Shiny 
isa2  The Iterative Signature Algorithm 
ISBF  Iterative Selection of Blocks of Features  ISBF 
isdals  Provides datasets for Introduction to Statistical Data Analysis
for the Life Sciences 
ISDA.R  interval symbolic data analysis for R 
IsingFit  Fitting Ising models using the eLasso method 
isingLenzMC  Monte Carlo for Classical Ising Model 
IsingSampler  Sampling Methods and Distribution Functions for the Ising Model 
island  Stochastic Island Biogeography Theory Made Easy 
ISLR  Data for An Introduction to Statistical Learning with
Applications in R 
ismev  An Introduction to Statistical Modeling of Extreme Values 
Iso  Functions to Perform Isotonic Regression 
IsoCI  Confidence intervals for current status data based on
transformations and bootstrap 
isocir  Isotonic Inference for Circular data 
ISOcodes  Selected ISO Codes 
IsoGene  OrderRestricted Inference for Microarray Experiments 
isopam  Isopam (Clustering) 
isopat  Calculation of isotopic pattern for a given molecular formula 
isoph  Isotonic Proportional Hazards Model 
IsoplotR  Statistical Toolbox for Radiometric Geochronology 
ISOpureR  Deconvolution of Tumour Profiles 
isotone  Active Set and Generalized PAVA for Isotone Optimization 
isotonic.pen  Penalized Isotonic Regression in one and two dimensions 
IsotopeR  Stable Isotope Mixing Model 
ISOweek  Week of the year and weekday according to ISO 8601 
isva  Independent Surrogate Variable Analysis 
ISwR  Introductory Statistics with R 
itcSegment  Individual Tree Crowns Segmentation 
ITEMAN  Classical Item Analysis 
iteRates  Parametric rate comparison 
iterators  Provides Iterator Construct for R 
iterLap  Approximate probability densities by iterated Laplace
Approximations 
iterpc  Efficient Iterator for Permutations and Combinations 
itertools  Iterator Tools 
itertools2  itertools2: Functions creating iterators for efficient looping 
itree  Tools for classification and regression trees, with an emphasis
on interpretability 
its  Irregular Time Series 
itsadug  Interpreting Time Series and Autocorrelated Data Using GAMMs 
itsmr  Time series analysis package for students 
IUPS  Incorporating Uncertainties in Propensity Scores 
ivbma  Bayesian Instrumental Variable Estimation and Model
Determination via Conditional Bayes Factors 
ivfixed  Instrumental fixed effect panel data model 
ivlewbel  Uses heteroscedasticity to estimate mismeasured and endogenous
regressor models 
ivmodel  Statistical Inference and Sensitivity Analysis for Instrumental
Variables Model 
ivpack  Instrumental Variable Estimation 
ivpanel  Instrumental Panel Data Models 
ivprobit  Instrumental variables probit model 
iWeigReg  Improved methods for causal inference and missing data problems 
iWISA  WaveletBased Index of Storm Activity 

jaatha  SimulationBased Maximum Likelihood Parameter Estimation 
jackknifeKME  Jackknife Estimates of KaplanMeier Estimators or Integrals 
jackstraw  Statistical Inference of Variables Driving Systematic Variation 
JacobiEigen  Classical Jacobi Eigensolution Algorithm 
jacpop  Jaccard Index for Population Structure Identification 
JADE  Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria 
jagsUI  A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses 
JAGUAR  Joint Analysis of Genotype and GroupSpecific Variability Using
a Novel Score Test Approach to Map Expression Quantitative
Trait Loci (eQTL) 
james.analysis  Analysis Tools for the 'JAMES' Framework 
janeaustenr  Jane Austen's Complete Novels 
JASPAR  R modules for JASPAR databases: a collection of transcription
factor DNAbinding preferences, modeled as matrices 
JavaGD  Java Graphics Device 
JBTools  Misc Small Tools and Helper Functions for Other Code of J.
Buttlar 
jetset  OnetoOne GeneProbeset Mapping for Affymetrix Human
Microarrays 
JGEE  Joint Generalized Estimating Equation Solver 
JGL  Performs the Joint Graphical Lasso for sparse inverse covariance
estimation on multiple classes 
JGR  JGR  Java GUI for R 
jiebaR  Chinese Text Segmentation 
jiebaRD  Chinese Text Segmentation Data for jiebaR Package 
JM  Joint Modeling of Longitudinal and Survival Data 
JMbayes  Joint Modeling of Longitudinal and TimetoEvent Data under a
Bayesian Approach 
jmcm  Joint MeanCovariance Models using 'Armadillo' and S4 
JMdesign  Joint Modeling of Longitudinal and Survival Data  Power
Calculation 
jmetrik  Tools for Interacting with 'jMetrik' 
Jmisc  Julian Miscellaneous Function 
jmotif  Time Series Analysis Toolkit Based on Symbolic Aggregate
Dicretization, i.e. SAX 
jmuOutlier  Permutation Tests for Nonparametric Statistics 
Johnson  Johnson Transformation 
JohnsonDistribution  Johnson Distribution 
joineR  Joint modelling of repeated measurements and timetoevent data 
joint.Cox  Penalized Likelihood Estimation and Dynamic Prediction under the
Joint FrailtyCopula Models Between Tumour Progression and
Death for MetaAnalysis 
jointDiag  Joint Approximate Diagonalization of a set of square matrices 
JointModel  Semiparametric Joint Models for Longitudinal and Counting
Processes 
jointPm  Risk estimation using the joint probability method 
JointRegBC  Joint Modelling of Mixed Correlated Binary and Continuous
Responses : A Latent Variable Approach 
jomo  Multilevel Joint Modelling Multiple Imputation 
JOP  Joint Optimization Plot 
JoSAE  Functions for some UnitLevel Small Area Estimators and their
Variances 
jose  Javascript Object Signing and Encryption 
jpeg  Read and write JPEG images 
JPEN  Covariance and Inverse Covariance Matrix Estimation Using Joint
Penalty 
JPSurv  Methods for populationbased cancer survival analysis 
jqr  Client for 'jq', a JSON Processor 
JRF  Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks 
jrich  JackKnife Support for Evolutionary Distinctiveness Indices I
and W 
jrvFinance  Basic Finance; NPV/IRR/Annuities/BondPricing; Black Scholes 
js  Tools for Working with JavaScript in R 
jSonarR  jSonar Analytics Platform API for R 
jsonlite  A Robust, High Performance JSON Parser and Generator for R 
jsonvalidate  Validate 'JSON' 
jtGWAS  Efficient JonckheereTerpstra Test Statistics 
jtrans  Johnson Transformation for Normality 
jug  Create a Simple Web API for your R Functions 
Julia  Fractal Image Data Generator 
junr  Access Open Data Through the Junar API 
jvnVaR  Value at Risk 

KANT  Package to identify and sort genes overexpressed 
kantorovich  Kantorovich Distance Between Probability Measures 
KappaGUI  GUI for Cohen's and Fleiss' Kappa 
kappalab  NonAdditive Measure and Integral Manipulation Functions 
kappaSize  Sample Size Estimation Functions for Studies of Interobserver
Agreement 
KappaV  Calculates "vectorial Kappa", an index of congruence between
patchy mosaics 
kaps  KAdaptive Partitioning for Survival data 
karaoke  Remove Vocals from a Song 
KATforDCEMRI  Kinetic analysis and visualization of DCEMRI data 
kcirt  kCube Thurstonian IRT Models 
kdecopula  Kernel Smoothing for Bivariate Copula Densities 
kdetrees  Nonparametric method for identifying discordant phylogenetic
trees 
kedd  Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives 
keep  Arrays with Better Control over Dimension Dropping 
kehra  Collect, Assemble and Model Air Pollution, Weather and Health
Data 
kelvin  Calculate Solutions to the Kelvin Differential Equation using
Bessel Functions 
Kendall  Kendall rank correlation and MannKendall trend test 
kequate  The Kernel Method of Test Equating 
kerdiest  Nonparametric kernel estimation of the distribution function.
Bandwidth selection and estimation of related functions 
KERE  Expectile Regression in Reproducing Kernel Hilbert Space 
kergp  Gaussian Process Laboratory 
kernDeepStackNet  Kernel Deep Stacking Networks 
kerndwd  Distance Weighted Discrimination (DWD) and Kernel Methods 
kernelFactory  Kernel Factory: An Ensemble of Kernel Machines 
Kernelheaping  Kernel Density Estimation for Heaped and Rounded Data 
KernelKnn  Kernel k Nearest Neighbors 
kernlab  KernelBased Machine Learning Lab 
kernscr  Kernel Machine Score Test for SemiCompeting Risks 
KernSmooth  Functions for Kernel Smoothing Supporting Wand & Jones (1995) 
KernSmoothIRT  Nonparametric Item Response Theory 
keyplayer  Locating Key Players in Social Networks 
keypress  Wait for a Key Press in a Terminal 
KFAS  Kalman Filter and Smoother for Exponential Family State Space
Models 
kfigr  Integrated Code Chunk Anchoring and Referencing for R Markdown
Documents 
KFKSDS  Kalman Filter, Smoother and Disturbance Smoother 
kimisc  Kirill's Miscellaneous Functions 
kin.cohort  Analysis of KinCohort Studies 
kineticF  Framework for the Analysis of Kinetic Visual Field Data 
kinfit  Routines for Fitting Kinetic Models to Chemical Degradation Data 
kinn  An Implementation of 'kinn' Algorithm, a Graph Based Regression
Model 
kinship2  Pedigree Functions 
kissmig  a Keep It Simple Species Migration Model 
kitagawa  Spectral response of water wells to harmonic strain and pressure 
kknn  Weighted kNearest Neighbors 
klaR  Classification and visualization 
klausuR  Multiple Choice Test Evaluation 
klin  Linear equations with Kronecker structure 
kmc  KaplanMeier Estimator with Constraints for Right Censored Data
– a Recursive Computational Algorithm 
km.ci  Confidence intervals for the KaplanMeier estimator 
kmconfband  KaplanMeier Simultaneous Confidence Band for the Survivor
Function 
KMDA  KernelBased Metabolite Differential Analysis 
kmeans.ddR  Distributed kMeans for Big Data using 'ddR' API 
kmi  KaplanMeier multiple imputation for the analysis of cumulative
incidence functions in the competing risks setting 
Kmisc  Kevin Miscellaneous 
kml  KMeans for Longitudinal Data 
kml3d  KMeans for Joint Longitudinal Data 
kmlcov  Clustering longitudinal data using the likelihood as a metric of
distance 
kmlShape  KMeans for Longitudinal Data using ShapeRespecting Distance 
kmodR  KMeans with Simultaneous Outlier Detection 
KMsurv  Data sets from Klein and Moeschberger (1997), Survival Analysis 
knitcitations  Citations for 'Knitr' Markdown Files 
knitLatex  'Knitr' Helpers  Mostly Tables 
knitr  A GeneralPurpose Package for Dynamic Report Generation in R 
knitrBootstrap  Knitr Bootstrap Framework 
knncat  Nearestneighbor Classification with Categorical Variables 
knnGarden  Multidistance based kNearest Neighbors 
knnIndep  Independence tests and benchmarks 
knockoff  Knockoff Filter for Controlling the False Discovery Rate 
kobe  Tools for the provision of scientific fisheries management
advice 
KODAMA  Knowledge discovery by accuracy maximization 
kofnGA  A Genetic Algorithm for FixedSize Subset Selection 
KOGMWU  Functional Summary and MetaAnalysis of Gene Expression Data 
kohonen  Supervised and Unsupervised SelfOrganising Maps 
kolmim  An Improved Evaluation of Kolmogorov's Distribution 
KoNLP  Korean NLP Package 
koRpus  An R Package for Text Analysis 
KoulMde  Koul's Minimum Distance Estimation in Linear Regression and
Autoregression Model 
Kpart  Cubic Spline Fitting with Knot Selection 
kpodclustr  Method for Clustering Partially Observed Data 
kriens  Continuation Passing Style Development 
kriging  Ordinary Kriging 
KrigInv  Krigingbased Inversion for Deterministic and Noisy Computer
Experiments 
KRLS  Kernelbased Regularized Least squares (KRLS) 
krm  Kernel Based Regression Models 
ks  Kernel Smoothing 
kSamples  KSample Rank Tests and their Combinations 
KScorrect  LillieforsCorrected KolmogorovSmirnoff GoodnessofFit Tests 
KSD  Kernelized Stein Discrepancy 
kselection  Selection of K in KMeans Clustering 
ksrlive  Identify Kinase Substrate Relationships Using Dynamic Data 
kst  Knowledge Space Theory 
ktsolve  Configurable function for solving families of nonlinear
equations 
ktspair  kTop Scoring Pairs for Microarray Classification 
kulife  Datasets and functions from the (now nonexisting) Faculty of
Life Sciences, University of Copenhagen 
kwb.hantush  Calculation of Groundwater Mounding Beneath an Infiltration
Basin 
kyotil  Utility Functions by Youyi, Krisz and Others 
kza  KolmogorovZurbenko Adaptive Filters 
kzft  KolmogorovZurbenko Fourier Transform and Applications 
kzs  KolmogorovZurbenko Spatial Smoothing and Applications 

l0ara  Sparse Generalized Linear Model with L0 Approximation for
Feature Selection 
L1pack  Routines for L1 Estimation 
l2boost  l2boost  Friedman's boosting algorithm for regularized linear
regression 
labdsv  Ordination and Multivariate Analysis for Ecology 
labeledLoop  Labeled Loop 
labeling  Axis Labeling 
labelled  Manipulating Labelled Data 
labelrank  Predicting Rankings of Labels 
label.switching  Relabelling MCMC Outputs of Mixture Models 
labeltodendro  Convert labels or tables to a dendrogram 
labstatR  Libreria Del Laboratorio Di Statistica Con R 
labstats  Data Sets for the Book "Experimental Design for Laboratory
Biologists" 
laeken  Estimation of indicators on social exclusion and poverty 
laercio  Duncan test, Tukey test and ScottKnott test 
LaF  Fast access to large ASCII files 
laGP  Local Approximate Gaussian Process Regression 
Lahman  Sean Lahman's Baseball Database 
LakeMetabolizer  Tools for the Analysis of Ecosystem Metabolism 
lakemorpho  Lake Morphometry Metrics in R 
laketemps  Lake Temperatures Collected by Situ and Satellite Methods from
19852009 
Lambda4  Collection of Internal Consistency Reliability Coefficients 
lambda.r  Modeling Data with Functional Programming 
lambda.tools  Tools for Modeling Data with Functional Programming 
LambertW  Probabilistic Models to Analyze and Gaussianize HeavyTailed,
Skewed Data 
lamW  LambertW Function 
LANDD  Liquid Association for Network Dynamics Detection 
landest  Landmark Estimation of Survival and Treatment Effect 
landpred  Landmark Prediction of a Survival Outcome 
landsat  Radiometric and topographic correction of satellite imagery 
landsat8  Landsat 8 Imagery Rescaled to Reflectance, Radiance and/or
Temperature 
landscapeR  Categorical Landscape Simulation Facility 
Langevin  Langevin Analysis in One and Two Dimensions 
languageR  Data sets and functions with "Analyzing Linguistic Data: A
practical introduction to statistics" 
LaplaceDeconv  Laplace Deconvolution with Noisy Discrete NonEqually Spaced
Observations on a Finite Time Interval 
LaplacesDemon  Complete Environment for Bayesian Inference 
lar  History of labour relations package 
LARF  Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects 
largeList  Serialization Interface for Large List Objects 
lars  Least Angle Regression, Lasso and Forward Stagewise 
laser  Likelihood Analysis of Speciation/Extinction Rates from
Phylogenies 
lasso2  L1 constrained estimation aka ‘lasso’ 
LassoBacktracking  Modelling Interactions in HighDimensional Data with
Backtracking 
lassoscore  HighDimensional Inference with the Penalized Score Test 
lassoshooting  L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting 
lasvmR  A Simple Wrapper for the LASVM Solver 
latdiag  Draws Diagrams Useful for Checking Latent Scales 
latentnet  Latent Position and Cluster Models for Statistical Networks 
Laterality  Functions to Calculate Common Laterality Statistics in
Primatology 
latex2exp  Use LaTeX Expressions in Plots 
lattice  Trellis Graphics for R 
latticeDensity  Density estimation and nonparametric regression on irregular
regions 
latticeExtra  Extra Graphical Utilities Based on Lattice 
LatticeKrig  Multiresolution Kriging Based on Markov Random Fields 
lava  Latent Variable Models 
lavaan  Latent Variable Analysis 
lavaan.shiny  Latent Variable Analysis with Shiny 
lavaan.survey  Complex Survey Structural Equation Modeling (SEM) 
lava.tobit  LVM with censored and binary outcomes 
lawn  Client for 'Turfjs' for 'Geospatial' Analysis 
lawstat  Tools for Biostatistics, Public Policy, and Law 
lazy  Lazy Learning for Local Regression 
lazyData  A LazyData Facility 
lazyeval  Lazy (NonStandard) Evaluation 
lazysql  Lazy SQL Programming 
lazyWeave  LaTeX Wrappers for R Users 
lba  Latent Budget Analysis for Compositional Data 
lbfgs  Limitedmemory BFGS Optimization 
lbfgsb3  Limited Memory BFGS Minimizer with Bounds on Parameters 
lbiassurv  Lengthbiased correction to survival curve estimation 
LCA  Localised CoDependency Analysis 
LCAextend  Latent Class Analysis (LCA) with familial dependence in extended
pedigrees 
lcda  Latent Class Discriminant Analysis 
LCFdata  Data sets for package “LMERConvenienceFunctions” 
LCMCR  Bayesian Nonparametric LatentClass CaptureRecapture 
lcmm  Extended Mixed Models Using Latent Classes and Latent Processes 
lcopula  Liouville Copulas 
lctools  Local Correlation, Spatial Inequalities, Geographically Weighted
Regression and Other Tools 
lda  Collapsed Gibbs Sampling Methods for Topic Models 
ldamatch  Selection of Statistically Similar Research Groups 
ldatuning  Tuning of the LDA Models Parameters 
LDAvis  Interactive Visualization of Topic Models 
ldbounds  LanDeMets Method for Group Sequential Boundaries 
LDcorSV  Linkage disequilibrium corrected by the structure and the
relatedness 
LDheatmap  Graphical display of pairwise linkage disequilibria between SNPs 
ldlasso  LD LASSO Regression for SNP Association Study 
LDOD  Finding Locally Doptimal optimal designs for some nonlinear and
generalized linear models 
LDPD  Probability of Default Calibration 
ldr  Methods for likelihoodbased dimension reduction in regression 
LDRTools  Tools for Linear Dimension Reduction 
LDtests  Exact tests for Linkage Disequilibrium and HardyWeinberg
Equilibrium 
leaderCluster  Leader Clustering Algorithm 
LeafAngle  Analysis and Visualization of Plant Leaf Angle Distributions 
LeafArea  Rapid Digital Image Analysis of Leaf Area 
leaflet  Create Interactive Web Maps with the JavaScript 'Leaflet'
Library 
leafletR  Interactive WebMaps Based on the Leaflet JavaScript Library 
LEAP  Constructing Gene CoExpression Networks for SingleCell
RNASequencing Data Using Pseudotime Ordering 
LEAPFrOG  Likelihood Estimation of Admixture in Parents From Offspring
Genotypes 
leapp  latent effect adjustment after primary projection 
leaps  regression subset selection 
LearnBayes  Functions for Learning Bayesian Inference 
learningr  Data and functions to accompany the book "Learning R" 
learNN  Examples of Neural Networks 
learnstats  An Interactive Environment for Learning Statistics 
lefse  Phylogenetic and Functional Analyses for Ecology 
leiv  Bivariate Linear ErrorsInVariables Estimation 
LeLogicielR  Functions and datasets to accompany the book "Le logiciel R:
Maitriser le langage, Effectuer des analyses statistiques"
(french) 
lessR  Less Code, More Results 
lestat  A package for LEarning STATistics 
letsR  Tools for Data Handling and Analysis in Macroecology 
lettercase  Utilities for Formatting Strings with Consistent Capitalization,
Word Breaks and White Space 
LexisPlotR  Plot Lexis Diagrams for Demographic Purposes 
lfactors  Factors with Levels 
lfda  Local Fisher Discriminant Analysis 
LFDR.MLE  Estimation of the Local False Discovery Rates by Type II Maximum
Likelihood Estimation 
lfe  Linear Group Fixed Effects 
lfl  Linguistic Fuzzy Logic 
lfstat  Calculation of Low Flow Statistics for Daily Stream Flow Data 
lga  Tools for linear grouping analysis (LGA) 
lgarch  Simulation and Estimation of LogGARCH Models 
lgcp  LogGaussian Cox Process 
LGEWIS  Tests for Genetic Association/GeneEnvironment Interaction in
Longitudinal GeneEnvironmentWide Interaction Studies 
LGRF  SetBased Tests for Genetic Association in Longitudinal Studies 
lgtdl  A set of methods for longitudinal data objects 
lhs  Latin Hypercube Samples 
libamtrack  Computational Routines for Proton and Ion Radiotherapy 
LiblineaR  Linear Predictive Models Based on the LIBLINEAR C/C++ Library 
LiblineaR.ACF  Linear Classification with Online Adaptation of Coordinate
Frequencies 
Libra  Linearized Bregman Algorithms for Generalized Linear Models 
LICORS  Light Cone Reconstruction of States  Predictive State
Estimation From SpatioTemporal Data 
LICurvature  Sensitivity Analysis for Case Weight in Normal Linear Regression 
lifecontingencies  Financial and Actuarial Mathematics for Life Contingencies 
lifecourse  Quantification of Lifecourse Fluidity 
LifeHist  Life History Models of Individuals 
LifeTables  TwoParameter HMD Model Life Table System 
lift  Compute the Top Decile Lift and Plot the Lift Curve 
liftr  Dockerize R Markdown Documents 
LightningR  Tools for Communication with LightningViz Server 
lightsout  Implementation of the 'Lights Out' Puzzle Game 
LIHNPSD  Poisson Subordinated Distribution 
likelihood  Methods for Maximum Likelihood Estimation 
likelihoodAsy  Functions for Likelihood Asymptotics 
likeLTD  Tools to Evaluate DNA Profile Evidence 
likert  Functions to Analyze and Visualize Likert Type Items 
LIM  Linear Inverse Model examples and solution methods 
limitplot  Jitter/CI Plot with Ordered Points Below the Limit of Detection 
limSolve  Solving Linear Inverse Models 
linbin  Binning and Plotting of Linearly Referenced Data 
LinCal  Static Univariate Frequentist and Bayesian Linear Calibration 
LindenmayeR  Functions to Explore LSystems (Lindenmayer Systems) 
LindleyR  The Lindley Distribution and Its Modifications 
LinearizedSVR  Linearized Support Vector Regression 
LinearRegressionMDE  Minimum Distance Estimation in Linear Regression Model 
linear.tools  Manipulate Formulas and Evaluate Marginal Effects 
linERR  Linear Excess Relative Risk Model 
lineup  Lining Up Two Sets of Measurements 
linkcomm  Tools for Generating, Visualizing, and Analysing Link
Communities in Networks 
LinkedMatrix  ColumnLinked and RowLinked Matrices 
linkim  Linkage information based genotype imputation method 
linkR  3D Lever and Linkage Mechanism Modeling 
linLIR  linear Likelihoodbased Imprecise Regression 
linprog  Linear Programming / Optimization 
LinRegInteractive  Interactive Interpretation of Linear Regression Models 
LINselect  Selection of Linear Estimators 
lint  Tools to check R code style 
lintools  Manipulation of Linear Systems of (in)Equalities 
lintr  Static R Code Analysis 
lira  LInear Regression in Astronomy 
liso  Fitting lasso penalised additive isotone models 
lisp  Listprocessing Ã la SRFI1 
lisrelToR  Import output from LISREL into R 
list  Statistical Methods for the Item Count Technique and List
Experiment 
listenv  Environments Behaving (Almost) as Lists 
LIStest  Tests of independence based on the Longest Increasing
Subsequence 
listviewer  'htmlwidget' for Interactive Views of R Lists 
listWithDefaults  List with Defaults 
littler  R at the CommandLine via 'r' 
livechatR  R Wrapper for LiveChat REST API 
ljr  Logistic Joinpoint Regression 
llama  Leveraging Learning to Automatically Manage Algorithms 
lle  Locally linear embedding 
lllcrc  Local Loglinear Models for CaptureRecapture 
LLSR  Data Analysis of LiquidLiquid Systems 
lm.beta  Add Standardized Regression Coefficients to lmObjects 
lm.br  Linear Model with Breakpoint 
lme4  Linear MixedEffects Models using 'Eigen' and S4 
lmec  Linear MixedEffects Models with Censored Responses 
lmem.gwaser  Linear Mixed Effects Models for GenomeWide Association Studies 
lmem.qtler  Linear Mixed Effects Models for QTL Mapping for Multienvironment
and Multitrait Analysis 
lmeNB  Compute the Personalized Activity Index Based on a Negative
Binomial Model 
lmeNBBayes  Compute the Personalized Activity Index Based on a Flexible
Bayesian Negative Binomial Model 
lmenssp  Linear Mixed Effects Models with NonStationary Stochastic
Processes 
LMERConvenienceFunctions  Model Selection and Posthoc Analysis for (G)LMER Models 
lmeresampler  Bootstrap Methods for Nested Linear MixedEffects Models 
lmerTest  Tests in Linear Mixed Effects Models 
lmeSplines  Add smoothing spline modelling capability to nlme 
LMest  Latent Markov Models with and without Covariates 
lmeVarComp  Testing for a subset of variance components in linear mixed
models 
lmf  Functions for estimation and inference of selection in
agestructured populations 
lmfor  Functions for Forest Biometrics 
lmm  Linear Mixed Models 
lmmlasso  Linear mixedeffects models with Lasso 
lmmot  Multiple Ordinal Tobit (MOT) Model 
lmms  Linear Mixed Effect Model Splines for Modelling and Analysis of
Time Course Data 
lmodel2  Model II Regression 
lmom  Lmoments 
lmomco  LMoments, Censored LMoments, Trimmed LMoments, LComoments,
and Many Distributions 
Lmoments  LMoments and Quantile Mixtures 
lmomRFA  Regional frequency analysis using Lmoments 
lmSupport  Support for Linear Models 
lmtest  Testing Linear Regression Models 
LncMod  Predicting Modulator and Functional/Survival Analysis 
LncPath  Identifying the Pathways Regulated by LncRNA Sets of Interest 
LncPriCNet  Prioritizing Candidate LncRNAs Based on a Composite MultiLevel
Network 
loa  Lattice Options and AddIns 
localdepth  Local Depth 
localgauss  Estimating Local Gaussian Parameters 
localsolver  R API to LocalSolver 
locfdr  Computes Local False Discovery Rates 
LocFDRPois  Functions for Performing Local FDR Estimation when Null and
Alternative are Poisson 
locfit  Local Regression, Likelihood and Density Estimation 
locits  Test of Stationarity and Localized Autocovariance 
Lock5Data  Datasets for "Statistics: UnLocking the Power of Data" 
Lock5withR  Datasets for 'Statistics: Unlocking the Power of Data' 
locpol  Kernel local polynomial regression 
lodGWAS  GenomeWide Association Analysis of a Biomarker Accounting for
Limit of Detection 
loe  Local Ordinal Embedding 
log4r  A simple logging system for R, based on log4j 
logbin  Relative Risk Regression Using the LogBinomial Model 
LogConcDEAD  Logconcave Density Estimation in Arbitrary Dimensions 
logconcens  Maximum likelihood estimation of a logconcave density based on
censored data 
logcondens  Estimate a LogConcave Probability Density from Iid Observations 
logcondens.mode  Compute MLE of LogConcave Density on R with Fixed Mode, and
Perform Inference for the Mode 
logcondiscr  Estimate a LogConcave Probability Mass Function from Discrete
i.i.d. Observations 
logconPH  CoxPH Model with Log Concave Baseline Distribution 
logging  R logging package 
LogicForest  Logic Forest 
LOGICOIL  LOGICOIL: multistate prediction of coiledcoil oligomeric
state 
LogicOpt  Truth Table Logic Optimizer 
LogicReg  Logic Regression 
logistf  Firth's bias reduced logistic regression 
LogisticDx  Diagnostic Tests for Models with a Binomial Response 
logisticPCA  Binary Dimensionality Reduction 
LOGIT  Functions, Data and Code for Binary and Binomial Data 
logitchoice  Fitting l2regularized logit choice models via generalized
gradient descent 
LogitNet  Infer network based on binary arrays using regularized logistic
regression 
logitnorm  Functions for the logitnormal distribution 
loglognorm  Double log normal distribution functions 
logmult  LogMultiplicative Models, Including Association Models 
LogrankA  Logrank Test for Aggregated Survival Data 
logspline  Logspline Density Estimation Routines 
lokern  Kernel Regression Smoothing with Local or Global Plugin
Bandwidth 
lomb  LombScargle Periodogram 
longCatEDA  Package for Plotting Categorical Longitudinal and TimeSeries
Data 
longclust  ModelBased Clustering and Classification for Longitudinal Data 
longitudinal  Analysis of Multiple Time Course Data 
longitudinalData  Longitudinal Data 
longmemo  Statistics for LongMemory Processes (Jan Beran) – Data and
Functions 
longpower  Sample Size Calculations for Longitudinal Data 
longurl  Expand Short URLs Using the 'LongURL' API 
loo  Efficient LeaveOneOut CrossValidation and WAIC for Bayesian
Models 
lookupTable  LookUp Tables using S4 
loop  loop decomposition of weighted directed graphs for life cycle
analysis, providing flexbile network plotting methods, and
analyzing food chain properties in ecology 
LoopAnalyst  A Collection of Tools to Conduct Levins' Loop Analysis 
loopr  Uses an Archive to Amend Previous Stages of a Pipe using Current
Output 
lordif  Logistic Ordinal Regression Differential Item Functioning using
IRT 
lorec  LOw Rand and sparsE Covariance matrix estimation 
LOST  Missing Morphometric Data Simulation and Estimation 
LotkasLaw  Runs Lotka's Law which is One of the Special Applications of
Zipf's Law 
LowRankQP  Low Rank Quadratic Programming 
lpbrim  LPBRIM Bipartite Modularity 
lpc  Lassoed principal components for testing significance of
features 
LPCM  Local Principal Curve Methods 
lpint  Local polynomial estimators of intensity function or its
derivatives 
LPM  Linear Parametric Models Applied to Hydrological Series 
lpme  Local Polynomial Estimator in Measurement Error Models 
LPmerge  Merging linkage maps by linear programming 
lpmodeler  Modeler for linear programs (LP) and mixed integer linear
programs (MILP) 
LPR  Lasso and Partial Ridge 
lpridge  Local Polynomial (Ridge) Regression 
LPS  Linear Predictor Score, for Binary Inference from Multiple
Continuous Variables 
lpSolve  Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs 
lpSolveAPI  R Interface to 'lp_solve' Version 5.5.2.0 
LPStimeSeries  Learned Pattern Similarity and Representation for Time Series 
LPTime  LP Nonparametric Approach to NonGaussian NonLinear Time Series
Modelling 
lqa  Penalized Likelihood Inference for GLMs 
lqmm  Linear Quantile Mixed Models 
lqr  Robust Linear Quantile Regression 
LRcontrast  Dose Response Signal Detection under Model Uncertainty 
lrequire  Sources an R "Module" with Caching & Encapsulation, Returning
Exported Vars 
lrgs  Linear Regression by Gibbs Sampling 
lrmest  Different Types of Estimators to Deal with Multicollinearity 
LRTH  A Likelihood Ratio Test Accounting for Genetic Heterogeneity 
LS2W  Locally stationary twodimensional wavelet process estimation
scheme 
LS2Wstat  A Multiscale Test of Spatial Stationarity for LS2W processes 
lsa  Latent Semantic Analysis 
LSAfun  Applied Latent Semantic Analysis (LSA) Functions 
lsbclust  LeastSquares Bilinear Clustering for ThreeWay Data 
LSC  Local Statistical Complexity  Automatic Pattern Discovery in
SpatioTemporal Data 
LSD  Lots of Superior Depictions 
LSDinterface  Reading LSD Results (.res) Files 
lsdv  Least square dummy variable regression 
lsei  Solving Least Squares Problems under Equality/Inequality
Constraints 
lsgl  Linear Sparse Group Lasso 
lshorth  The Length of the Shorth 
lsl  Latent Structure Learning 
lsmeans  LeastSquares Means 
LSMonteCarlo  American options pricing with Least Squares Monte Carlo method 
LSPFP  Lysate and Secretome Peptide Feature Plotter 
lspls  LSPLS Models 
lsr  Companion to "Learning Statistics with R" 
lss  the accelerated failure time model to right censored data based
on leastsquares principle 
LSTS  Locally Stationary Time Series 
ltbayes  SimulationBased Bayesian Inference for Latent Traits of Item
Response Models 
ltm  Latent Trait Models under IRT 
ltmle  Longitudinal Targeted Maximum Likelihood Estimation 
LTPDvar  LTPD and AOQL Plans for Acceptance Sampling Inspection by
Variables 
LTR  Perform LTR analysis on microarray data 
LTRCtrees  Survival Trees to Fit LeftTruncated and RightCensored Survival
Data 
ltsa  Linear Time Series Analysis 
ltsbase  Ridge and Liu Estimates based on LTS (Least Trimmed Squares)
Method 
ltsk  Local Time Space Kriging 
lubridate  Make Dealing with Dates a Little Easier 
luca  Likelihood inference from casecontrol data Under Covariate
Assumptions (LUCA) 
lucid  Printing Floating Point Numbers in a HumanFriendly Format 
lucr  Currency Formatting and Conversion 
lulcc  Land Use Change Modelling in R 
lumendb  Lumen Database API Client 
Luminescence  Comprehensive Luminescence Dating Data Analysis 
lunar  Lunar Phase & Distance, Seasons and Other Environmental Factors 
luzlogr  Lightweight Logging for R Scripts 
lvm4net  Latent Variable Models for Networks 
LVMMCOR  A Latent Variable Model for Mixed Continuous and Ordinal
Responses 
lvplot  Letter Value 'Boxplots' 
LW1949  An Automated Approach to Evaluating DoseEffect Experiments
Following Litchfield and Wilcoxon (1949) 
lxb  Fast LXB File Reader 
lymphclon  Accurate Estimation of Clonal Coincidences and Abundances from
Biological Replicates 

M3  Reading M3 files 
M4comp  Data from the M4 Time Series Forecasting Competition 
m4fe  Models for Financial Economics 
maboost  Binary and Multiclass Boosting Algorithms 
MAc  MetaAnalysis with Correlations 
machina  Machina Time Series Generation and Backtesting 
machQA  QA Machina Indicators 
macleish  Retrieve Data from MacLeish Field Station 
MAclinical  Class prediction based on microarray data and clinical
parameters 
MAd  MetaAnalysis with Mean Differences 
mada  MetaAnalysis of Diagnostic Accuracy 
maddison  Maddison Project Database 
madness  Automatic Differentiation of Multivariate Operations 
mads  MultiAnalysis Distance Sampling 
madsim  A Flexible Microarray Data Simulation Model 
Maeswrap  Wrapper Functions for MAESTRA/MAESPA 
magclass  Data Class and Tools for Handling SpatialTemporal Data 
magic  create and investigate magic squares 
magicaxis  Pretty Scientific Plotting with MinorTick and Log MinorTick
Support 
magick  Advanced ImageProcessing in R 
magrittr  A ForwardPipe Operator for R 
maGUI  A Graphical User Interface for Microarray Data Analysis 
mail  Sending Email Notifications from R 
mailR  A Utility to Send Emails from R 
MAINT.Data  Model and Analyse Interval Data 
MakefileR  Create 'Makefiles' Using R 
makeProject  Creates an empty package framework for the LCFD format 
MALDIquant  Quantitative Analysis of Mass Spectrometry Data 
MALDIquantForeign  Import/Export Routines for MALDIquant 
mallet  A wrapper around the Java machine learning tool MALLET 
MAMA  MetaAnalysis of MicroArray 
MAMS  Designing multiarm multistage studies 
MAMSE  Calculation of Minimum Averaged Mean Squared Error (MAMSE)
weights 
managelocalrepo  Manage a CRANStyle Local Repository 
MANCIE  Matrix Analysis and Normalization by Concordant Information
Enhancement 
mangoTraining  Mango Solutions Training Datasets 
manhattanly  Interactive QQ and Manhattan Plots Using 'plotly.js' 
manifestoR  Access and Process Data and Documents of the Manifesto Project 
manipulate  Interactive Plots for RStudio 
ManlyMix  Manly Mixture Modeling and ModelBased Clustering 
MANOVA.RM  Analysis of Multivariate Data and Repeated Measures Designs 
ManyTests  Multiple testing procedures of Cox (2011) and Wang and Cox
(2007) 
Map2NCBI  Mapping Markers to the Nearest Genomic Feature 
MAPA  Multiple Aggregation Prediction Algorithm 
mapdata  Extra Map Databases 
mapfit  A Tool for PH/MAP Parameter Estimation 
MapGAM  Mapping Smoothed Effect Estimates from IndividualLevel Data 
MAPLES  Smoothed age profile estimation 
mapmisc  Utilities for Producing Maps 
mapplots  Data Visualisation on Maps 
mapproj  Map Projections 
mapr  'Visualize' Species Occurrence Data 
maps  Draw Geographical Maps 
mapStats  Geographic Display of Survey Data Statistics 
maptools  Tools for Reading and Handling Spatial Objects 
maptpx  MAP Estimation of Topic Models 
maptree  Mapping, pruning, and graphing tree models 
mapview  Interactive Viewing of Spatial Objects in R 
mAr  Multivariate AutoRegressive analysis 
MAR1  Multivariate Autoregressive Modeling for Analysis of Community
TimeSeries Data 
mar1s  Multiplicative AR(1) with Seasonal Processes 
march  Markov Chains 
marelac  Tools for Aquatic Sciences 
MareyMap  Estimation of Meiotic Recombination Rates Using Marey Maps 
marg  Approximate marginal inference for regressionscale models 
marima  Multivariate ARIMA and ARIMAX Analysis 
markdown  'Markdown' Rendering for R 
marked  MarkRecapture Analysis for Survival and Abundance Estimation 
maRketSim  Market simulator for R 
markmyassignment  Automatic Marking of R Assignments 
markophylo  Markov Chain Models for Phylogenetic Trees 
markovchain  Easy Handling Discrete Time Markov Chains 
MarkowitzR  Statistical Significance of the Markowitz Portfolio 
marl  Multivariate Analysis Based on Relative Likelihoods 
marmap  Import, Plot and Analyze Bathymetric and Topographic Data 
marqLevAlg  An algorithm for leastsquares curve fitting 
MARSS  Multivariate Autoregressive StateSpace Modeling 
maSAE  Mandallaz' ModelAssisted Small Area Estimators 
mason  Build Data Structures for Common Statistical Analysis 
MASS  Support Functions and Datasets for Venables and Ripley's MASS 
MASSTIMATE  Body Mass Estimation Equations for Vertebrates 
MasterBayes  ML and MCMC Methods for Pedigree Reconstruction and Analysis 
MAT  Multidimensional Adaptive Testing 
MATA  ModelAveraged Tail Area Wald (MATAWald) Confidence Interval 
Matching  Multivariate and Propensity Score Matching with Balance
Optimization 
MatchingFrontier  Computation of the Balance  Sample Size Frontier in Matching
Methods for Causal Inference 
matchingMarkets  Analysis of Stable Matchings 
matchingR  Matching Algorithms in R and C++ 
MatchIt  MatchIt: Nonparametric Preprocessing for Parametric Casual
Inference 
MatchLinReg  Combining Matching and Linear Regression for Causal Inference 
matchMulti  Optimal Multilevel Matching using a Network Algorithm 
matconv  A Code Converter from the Matlab/Octave Language to R 
mateable  Tools to Assess Mating Potential in Space and Time 
mathgraph  Directed and undirected graphs 
matie  Measuring Association and Testing Independence Efficiently 
matlab  MATLAB emulation package 
matlabr  An Interface for MATLAB using System Calls 
matlib  Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics 
matpow  matrix powers 
matR  Metagenomics Analysis Tools for R 
Matrix  Sparse and Dense Matrix Classes and Methods 
matrixcalc  Collection of functions for matrix calculations 
MatrixCorrelation  Matrix Correlation Coefficients 
MatrixEQTL  Matrix eQTL: Ultra fast eQTL analysis via large matrix
operations 
matrixLaplacian  Normalized Laplacian Matrix and Laplacian Map 
MatrixModels  Modelling with Sparse And Dense Matrices 
matrixpls  MatrixBased Partial Least Squares Estimation 
matrixStats  Functions that Apply to Rows and Columns of Matrices (and to
Vectors) 
Matrix.utils  Data.frameLike Operations on Sparse and Dense Matrix Objects 
MATTOOLS  Modern Calibration Functions for the Modern Analog Technique
(MAT) 
MAVIS  Meta Analysis via Shiny 
MAVTgsa  Three methods to identify differentially expressed gene sets,
ordinary least square test, Multivariate Analysis Of Variance
test with n contrasts and Random forest 
MaXact  Exact maxtype CochranArmitage trend test(CATT) 
maxent  Lowmemory Multinomial Logistic Regression with Support for Text
Classification 
MaxentVariableSelection  Selecting the Best Set of Relevant Environmental Variables along
with the Optimal Regularization Multiplier for Maxent Niche
Modeling 
maxLik  Maximum Likelihood Estimation and Related Tools 
maxlike  Model species distributions by estimating the probability of
occurrence using presenceonly data 
MaxPro  Maximum Projection Designs 
MaxSkew  Orthogonal Data Projections with Maximal Skewness 
maxstat  Maximally Selected Rank Statistics 
MazamaSpatialUtils  Mazama Science Spatial Data Download and Utility Functions 
MBA  Multilevel Bspline Approximation 
mbbefd  Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and
Destruction Rate Modelling 
MBCluster.Seq  ModelBased Clustering for RNAseq Data 
MBESS  The MBESS R Package 
mbest  MomentBased Estimation for Hierarchical Models 
MBI  (M)ultiplesite (B)iodiversity (I)ndices Calculator 
mblm  MedianBased Linear Models 
MBmca  Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R 
mbmdr  Model Based Multifactor Dimensionality Reduction 
mboost  ModelBased Boosting 
MBTAr  Access Data from the Massachusetts Bay Transit Authority (MBTA)
Web API 
mBvs  Multivariate Bayesian Variable Selection Method Exploiting
Dependence among Outcomes 
mc2d  Tools for TwoDimensional MonteCarlo Simulations 
MC2toPath  Translates information from netcdf files with MC2 output into
interPVT transitions 
MCAPS  MCAPS data and results 
mcbiopi  Matrix Computation Based Identification Of Prime Implicants 
mcc  Moment Corrected Correlation 
mcclust  Process an MCMC Sample of Clusterings 
MCDA  Functions to Support the Multicriteria Decision Aiding Process 
MCDM  MultiCriteria Decision Making Methods 
mcemGLM  Maximum Likelihood Estimation for Generalized Linear Mixed
Models 
mcga  Machine Coded Genetic Algorithms for RealValued Optimization
Problems 
mcgibbsit  Warnes and Raftery's MCGibbsit MCMC diagnostic 
mcglm  Multivariate Covariance Generalized Linear Models 
mcGlobaloptim  Global optimization using Monte Carlo and Quasi Monte Carlo
simulation 
mcheatmaps  Multiple matrices heatmap visualization 
MChtest  Monte Carlo hypothesis tests with Sequential Stopping 
MCI  Multiplicative Competitive Interaction (MCI) Model 
mcIRT  IRT models for multiple choice items (mcIRT) 
MCL  Markov Cluster Algorithm 
mcll  Monte Carlo Local Likelihood Estimation 
mclogit  Mixed Conditional Logit 
mclust  Gaussian Mixture Modelling for ModelBased Clustering,
Classification, and Density Estimation 
mcmc  Markov Chain Monte Carlo 
MCMC4Extremes  Posterior Distribution of Extreme Value Models in R 
MCMCglmm  MCMC Generalised Linear Mixed Models 
MCMC.OTU  Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology 
MCMCpack  Markov Chain Monte Carlo (MCMC) Package 
mcmcplots  Create Plots from MCMC Output 
MCMC.qpcr  Bayesian Analysis of qRTPCR Data 
mcmcse  Monte Carlo Standard Errors for MCMC 
mco  Multiple Criteria Optimization Algorithms and Related Functions 
Mcomp  Data from the Mcompetitions 
MConjoint  Conjoint Analysis through Averaging of Multiple Analyses 
mcPAFit  Estimating Preferential Attachment from a Single Network
Snapshot by Markov Chain Monte Carlo 
MCPAN  Multiple Comparisons Using Normal Approximation 
mcparallelDo  A Simplified Interface for Running Commands on Parallel
Processes 
MCPerm  A Monte Carlo permutation method for multiple test correlation 
MCPMod  Design and Analysis of DoseFinding Studies (see also
DoseFinding package) 
mcprofile  Multiple Contrast Profiles 
mcr  Method Comparison Regression 
MCS  Model Confidence Set Procedure 
mcsm  Functions for Monte Carlo Methods with R 
McSpatial  Nonparametric spatial data analysis 
mctest  Multicollinearity Diagnostic Measures 
MCTM  Markov Chains Transition Matrices 
md  Selecting Bandwidth for Kernel Density Estimator with Minimum
Distance Method 
mda  Mixture and Flexible Discriminant Analysis 
mdatools  Multivariate Data Analysis for Chemometrics 
mded  Measuring the Difference Between Two Empirical Distributions 
mdhglm  Multivariate Double Hierarchical Generalized Linear Models 
MDimNormn  MultiDimensional MA Normalization for Plate Effect 
MDM  Multinomial Diversity Model 
MDMR  Multivariate Distance Matrix Regression 
MDplot  Visualising Molecular Dynamics Analyses 
MDPtoolbox  Markov Decision Processes toolbox 
MDR  Detect genegene interactions using multifactor dimensionality
reduction 
mdscore  Improved Score Tests for Generalized Linear Models 
mdsdt  Functions for Analysis of Data with General Recognition Theory 
MDSGUI  A GUI for interactive MDS in R 
MeanShift  Clustering via the Mean Shift Algorithm 
measurements  Tools for Units of Measurement 
measuRing  Detection and Control of TreeRing Widths on Scanned Image
Sections 
meboot  Maximum Entropy Bootstrap for Time Series 
mederrRank  Bayesian Methods for Identifying the Most Harmful Medication
Errors 
medflex  Flexible Mediation Analysis Using Natural Effect Models 
MediaK  Calculate MeDiA_K Distance 
Mediana  Clinical Trial Simulations 
mediation  Causal Mediation Analysis 
medicalrisk  Medical Risk and Comorbidity Tools for ICD9CM Data 
MedOr  Median Ordering Statistical R package 
medSTC  A maxmargin supervised Sparse Topical Coding Model 
MEET  MEET: Motif Elements Estimation Toolkit 
mefa  Multivariate Data Handling in Ecology and Biogeography 
mefa4  Multivariate Data Handling with S4 Classes and Sparse Matrices 
megaptera  MEGAPhylogeny Techniques in R 
MEGENA  Multiscale Clustering of Geometrical Network 
meifly  Interactive model exploration using GGobi 
mem  Moving Epidemic Method R Package 
memgene  Spatial pattern detection in genetic distance data using Moran's
Eigenvector Maps 
memisc  Tools for Management of Survey Data and the Presentation of
Analysis Results 
memoise  Memoisation of Functions 
MEMSS  Data sets from Mixedeffects Models in S 
memuse  Memory Estimation Utilities 
MenuCollection  Collection of Configurable GTK+ Menus 
MergeGUI  A GUI for Merging Datasets in R 
merror  Accuracy and Precision of Measurements 
merTools  Tools for Analyzing Mixed Effect Regression Models 
MESS  Miscellaneous Esoteric Statistical Scripts 
meta  General Package for MetaAnalysis 
meta4diag  MetaAnalysis for Diagnostic Test Studies 
MetABEL  Metaanalysis of genomewide SNP association results 
MetabolAnalyze  Probabilistic latent variable models for metabolomic data 
metabolomics  Analysis of Metabolomics Data 
metacom  Analysis of the 'Elements of Metacommunity Structure' 
metacor  Metaanalysis of correlation coefficients 
MetaCycle  Evaluate Periodicity in Large Scale Data 
MetaDE  MetaDE: Microarray metaanalysis for differentially expressed
gene detection 
metafolio  Metapopulation simulations for conserving salmon through
portfolio optimization 
metafor  MetaAnalysis Package for R 
metafuse  Fused Lasso Approach in Regression Coefficient Clustering 
metagear  Comprehensive Research Synthesis Tools for Systematic Reviews
and MetaAnalysis 
metagen  Inference in Meta Analysis and Meta Regression 
metaheur  Metaheuristic Optimization Framework for Preprocessing
Combinations 
MetaLandSim  Landscape and Range Expansion Simulation 
metaLik  Likelihood Inference in MetaAnalysis and MetaRegression Models 
metaMA  Metaanalysis for MicroArrays 
metamisc  Diagnostic and prognostic meta analysis (metamisc) 
metaMix  Bayesian Mixture Analysis for Metagenomic Community Profiling 
metansue  MetaAnalysis of Studies with Non StatisticallySignificant
Unreported Effects 
metap  MetaAnalysis of Significance Values 
MetaPath  Perform the MetaAnalysis for Pathway Enrichment Analysis (MAPE) 
MetaPCA  MetaPCA: Metaanalysis in the Dimension Reduction of Genomic
data 
metaplotr  Creates CrossHairs Plots for MetaAnalyses 
metaplus  Robust MetaAnalysis and MetaRegression 
MetaQC  MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic MetaAnalysis 
metaRNASeq  Metaanalysis of RNAseq data 
metaSEM  MetaAnalysis using Structural Equation Modeling 
metasens  Advanced Statistical Methods to Model and Adjust for Bias in
MetaAnalysis 
MetaSKAT  Meta Analysis for SNPSet (Sequence) Kernel Association Test 
metatest  Fit and test metaregression models 
Metatron  Metaanalysis for Classification Data and Correction to
Imperfect Reference 
meteo  SpatioTemporal Analysis and Mapping of Meteorological
Observations 
meteoForecast  Numerical Weather Predictions 
meteogRam  Tools for plotting meteograms 
meteR  Fitting and Plotting Tools for the Maximum Entropy Theory of
Ecology (METE) 
MetFns  Analysis of Visual Meteor Data 
Meth27QC  Meth27QC: sample quality analysis, and sample control analysis 
MethComp  Functions for Analysis of Agreement in Method Comparison Studies 
Methplot  Visualize the methylation patterns 
MethyBayes  Full Bayesian Partition Model for Identifying Differentially
Methylated Loci 
MethylCapSig  Detection of Differentially Methylated Regions using
MethylCapSeq Data 
MetNorm  Statistical Methods for Normalizing Metabolomics Data 
MetProc  Separate Metabolites into Likely Measurement Artifacts and True
Metabolites 
Metrics  Evaluation metrics for machine learning 
metricsgraphics  Create Interactive Charts with the JavaScript 'MetricsGraphics'
Library 
metricTester  Test Metric and Null Model Statistical Performance 
metRology  Support for metrological applications 
mets  Analysis of Multivariate Event Times 
MetSizeR  GUI Tool for Estimating Sample Sizes for Metabolomic Experiments 
MetStaT  Statistical metabolomics tools 
mev  Multivariate Extreme Value Distributions 
mewAvg  A Fixed Memeory Moving Expanding Window Average 
mexhaz  Mixed Effect Excess Hazard Models 
MExPosition  Multitable ExPosition 
MF  Mitigated Fraction 
MFAg  Multiple Factor Analysis (MFA) 
MFHD  Multivariate Functional Halfspace Depth 
mFilter  Miscellaneous time series filters 
mfp  Multivariable Fractional Polynomials 
MFPCA  Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains 
MfUSampler  MultivariatefromUnivariate (MfU) MCMC Sampler 
mfx  Marginal Effects, Odds Ratios and Incidence Rate Ratios for GLMs 
mgarchBEKK  Simulating, Estimating and Diagnosing MGARCH (BEKK and mGJR)
Processes 
mgcv  Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation 
MGGM  Structural Pursuit Over Multiple Undirected Graphs 
MGL  Module Graphical Lasso 
MGLM  Multivariate Response Generalized Linear Models 
mglmn  Model Averaging for Multivariate GLM with Null Models 
mgm  Estimating TimeVarying Mixed Graphical Models 
mgpd  mgpd: Functions for multivariate generalized Pareto distribution
(MGPD of Type II) 
mgraph  Graphing map attributes and nonmap variables in R 
MGRASTer  API Client for the MGRAST Server of the US DOE KBase 
MGSDA  MultiGroup Sparse Discriminant Analysis 
mGSZ  Gene set analysis based on GSZscoring function and asymptotic
pvalue 
MHadaptive  General Markov Chain Monte Carlo for Bayesian Inference using
adaptive MetropolisHastings sampling 
mhde  Minimum Hellinger Distance Test for Normality 
mHG  MinimumHypergeometric Test 
mhsmm  Inference for Hidden Markov and SemiMarkov Models 
mht  Multiple Hypothesis Testing for Variable Selection in
HighDimensional Linear Models 
MHTrajectoryR  Bayesian Model Selection in Logistic Regression for the
Detection of Adverse Drug Reactions 
mhurdle  Multiple hurdle Tobit models 
mi  Missing Data Imputation and Model Checking 
mice  Multivariate Imputation by Chained Equations 
miceadds  Some Additional Multiple Imputation Functions, Especially for
'mice' 
micEcon  Microeconomic Analysis and Modelling 
micEconAids  Demand Analysis with the Almost Ideal Demand System (AIDS) 
micEconCES  Analysis with the Constant Elasticity of Substitution (CES)
function 
micEconSNQP  Symmetric Normalized Quadratic Profit Function 
micompr  Multivariate Independent Comparison of Observations 
miCoPTCM  Promotion Time Cure Model with MisMeasured Covariates 
microbats  An Implementation of Bat Algorithm in R 
microbenchmark  Accurate Timing Functions 
MicroDatosEs  Utilities for Official Spanish Microdata 
micromap  Linked Micromap Plots 
micromapST  Linked Micromap Plots for U. S. States 
micropan  Microbial Pangenome Analysis 
microplot  Use R Graphics Files as Microplots (Sparklines) in Tables in
LaTeX or HTML Files, and Output Data.frames to OrgMode 
microseq  Basic Biological Sequence Analysis 
MicroStrategyR  MicroStrategyR Package 
MicSim  Performing ContinuousTime Microsimulation 
midasr  Mixed Data Sampling Regression 
midastouch  Multiple Imputation by Distance Aided Donor Selection 
midrangeMCP  Multiple Comparisons Procedures Based on Studentized Midrange
and Range Distributions 
MigClim  Implementing dispersal into species distribution models 
migest  Methods for the Indirect Estimation of Bilateral Migration 
migration.indices  Migration indices 
migui  Graphical User Interface to the 'mi' Package 
MIICD  Multiple Imputation for Interval Censored Data 
MIIVsem  Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models 
MILC  MIcrosimulation Lung Cancer (MILC) model 
milonga  Multiple Imputation for Multivariate Binary Outcome 
milr  MultipleInstance Logistic Regression with LASSO Penalty 
mime  Map Filenames to MIME Types 
MImix  Mixture summary method for multiple imputation 
MindOnStats  Data sets included in Utts and Heckard's Mind on Statistics 
minerva  Maximal InformationBased Nonparametric Exploration R Package
for Variable Analysis 
Miney  Implementation of the WellKnown Game to Clear Bombs from a
Given Field (Matrix) 
miniCRAN  Create a Mini Version of CRAN Containing Only Selected Packages 
miniGUI  tktcl quick and simple function GUI 
minimap  Create Tile Grid Maps 
minimax  Minimax distribution family 
minimaxdesign  Minimax and Minimax Projection Designs 
minimist  Parse Argument Options 
miniUI  Shiny UI Widgets for Small Screens 
minpack.lm  R Interface to the LevenbergMarquardt Nonlinear LeastSquares
Algorithm Found in MINPACK, Plus Support for Bounds 
minPtest  Gene regionlevel testing procedure for SNP data, using the min
P test resampling approach 
minqa  Derivativefree optimization algorithms by quadratic
approximation 
minque  An R Package for Linear Mixed Model Analyses 
MInt  Learn Direct Interaction Networks 
minval  MINimal VALidation for Stoichiometric Reactions 
minxent  Entropy Optimization Distributions 
mipfp  Multidimensional Iterative Proportional Fitting and Alternative
Models 
MIPHENO  Mutant Identification through Probabilistic High throughput
Enabled NOrmalization 
miRada  MicroRNA Microarray Data Analysis 
MiRSEA  'MicroRNA' Set Enrichment Analysis 
mirt  Multidimensional Item Response Theory 
mirtCAT  Computerized Adaptive Testing with Multidimensional Item
Response Theory 
miRtest  combined miRNA and mRNAtesting 
misc3d  Miscellaneous 3D Plots 
miscF  Miscellaneous Functions 
miscFuncs  Miscellaneous Useful Functions Including LaTeX Tables, Kalman
Filtering and Development Tools 
miscset  Miscellaneous Tools Set 
miscTools  Miscellaneous Tools and Utilities 
mise  Clears the Workspace (Mise en Place) 
MiSPU  Microbiome Based Sum of Powered Score (MiSPU) Tests 
missDeaths  'Correctly Analyse Disease Recurrence with Missing at Risk
Information using Population Mortality' 
missForest  Nonparametric Missing Value Imputation using Random Forest 
MissingDataGUI  A GUI for Missing Data Exploration 
missMDA  Handling Missing Values with Multivariate Data Analysis 
MissMech  Testing Homoscedasticity, Multivariate Normality, and Missing
Completely at Random 
MiST  Mixed effects Score Test for continuous outcomes 
mistat  Data Sets, Functions and Examples from the Book: "Modern
Industrial Statistics" by Kenett, Zacks and Amberti 
mistral  Methods in Structural Reliability Analysis 
MitISEM  Mixture of Student t Distributions using Importance Sampling and
Expectation Maximization 
mitml  Tools for Multiple Imputation in Multilevel Modeling 
mitools  Tools for multiple imputation of missing data 
mix  Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data 
mixAK  Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering 
MixAll  Clustering using Mixture Models 
mixcat  Mixed effects cumulative link and logistic regression models 
mixdist  Finite Mixture Distribution Models 
MixedDataImpute  Missing Data Imputation for Continuous and Categorical Data
using Nonparametric Bayesian Joint Models 
mixedMem  Tools for Discrete Multivariate Mixed Membership Models 
MixedPoisson  Mixed Poisson Models 
mixedsde  Estimation Methods for Stochastic Differential Mixed Effects
Models 
MixedTS  Mixed Tempered Stable Distribution 
mixer  Random graph clustering 
mixexp  Design and Analysis of Mixture Experiments 
MIXFIM  Evaluation of the FIM in NLMEMs using MCMC 
MixGHD  Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions 
mixlm  Mixed Model ANOVA and Statistics for Education 
MixMAP  Implements the MixMAP Algorithm 
mixOmics  Omics Data Integration Project 
mixor  MixedEffects Ordinal Regression Analysis 
mixpack  Tools to Work with Mixture Components 
mixPHM  Mixtures of Proportional Hazard Models 
mixRasch  Mixture Rasch Models with JMLE 
mixreg  Functions to fit mixtures of regressions 
MixRF  A RandomForestBased Approach for Imputing Clustered Incomplete
Data 
mixsep  Forensic Genetics DNA Mixture Separation 
MixSIAR  Bayesian Mixing Models in R 
MixSim  Simulating Data to Study Performance of Clustering Algorithms 
mixsmsn  Fitting Finite Mixture of Scale Mixture of SkewNormal
Distributions 
mixtNB  DE Analysis of RNASeq Data by Mixtures of NB 
mixtools  Tools for Analyzing Finite Mixture Models 
mixtox  Curve Fitting and Mixture Toxicity Assessment 
mixture  Mixture Models for Clustering and Classification 
MixtureInf  Inference for Finite Mixture Models 
mizer  Multispecies sIZE spectrum modelling in R 
mkde  2D and 3D movementbased kernel density estimates (MKDEs) 
mkin  Kinetic Evaluation of Chemical Degradation Data 
MKLE  Maximum kernel likelihood estimation 
MKmisc  Miscellaneous Functions from M. Kohl 
mkssd  Efficient multilevel kcirculant supersaturated designs 
mlbench  Machine Learning Benchmark Problems 
MLCIRTwithin  Latent Class Item Response Theory (LCIRT) Models under
WithinItem Multidimensionality 
MLCM  Maximum Likelihood Conjoint Measurement 
mlDNA  Machine Learningbased Differential Network Analysis of
Transcriptome Data 
mldr  Exploratory Data Analysis and Manipulation of MultiLabel Data
Sets 
mldr.datasets  R Ultimate Multilabel Dataset Repository 
MLDS  Maximum Likelihood Difference Scaling 
mlearning  Machine learning algorithms with unified interface and confusion
matrices 
MLEcens  Computation of the MLE for bivariate (interval) censored data 
mlegp  Maximum Likelihood Estimates of Gaussian Processes 
mleur  Maximum likelihood unit root test 
mlgt  MultiLocus GenoTyping 
mlica2  Independent Component Analysis using Maximum Likelihood 
mlma  Multilevel Mediation Analysis 
mlmc  MultiLevel Monte Carlo 
MLmetrics  Machine Learning Evaluation Metrics 
mlmmm  ML estimation under multivariate linear mixed models with
missing values 
mlmRev  Examples from Multilevel Modelling Software Review 
mlogit  multinomial logit model 
mlogitBMA  Bayesian Model Averaging for Multinomial Logit Models 
mlPhaser  MultiLocus Haplotype Phasing 
MLPUGS  MultiLabel Prediction Using Gibbs Sampling (and Classifier
Chains) 
mlr  Machine Learning in R 
MLRMPA  A package for Multilinear Regression Model Population Analysis 
mlsjunkgen  Use the MLS Junk Generator Algorithm to Generate a Stream of
PseudoRandom Numbers 
mlt  Most Likely Transformations 
mlt.docreg  Most Likely Transformations: Documentation and Regression Tests 
mlVAR  MultiLevel Vector Autoregression 
mlxR  Simulation of Longitudinal Data 
MM  The multiplicative multinomial distribution 
MM2S  SingleSample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines 
MM2Sdata  Gene Expression Datasets for the 'MM2S' Package 
mma  Multiple Mediation Analysis 
mmand  Mathematical Morphology in Any Number of Dimensions 
mmap  Map Pages of Memory 
mmc  Multivariate Measurement Error Correction 
mmcm  Modified Maximum Contrast Method 
mmds  Mixture Model Distance Sampling (mmds) 
mme  Multinomial Mixed Effects Models 
mmeln  Estimation of Multinormal Mixture Distribution 
mmeta  Multivariate MetaAnalysis 
mmm  an R package for analyzing multivariate longitudinal data with
multivariate marginal models 
mmm2  Multivariate marginal models with shared regression parameters 
MMMS  MultiMarker Molecular Signature for Treatmentspecific Subgroup
Identification 
mmod  Modern Measures of Population Differentiation 
mmpp  Various Similarity and Distance Metrics for Marked Point
Processes 
mmppr  Markov Modulated Poisson Process for Unsupervised Event
Detection in Time Series of Counts 
MMS  Fixed effects Selection in Linear Mixed Models 
mmtfa  ModelBased Clustering and Classification with Mixtures of
Modified t Factor Analyzers 
MMWRweek  Convert Dates to MMWR Day, Week, and Year 
mnlogit  Multinomial Logit Model 
MNM  Multivariate Nonparametric Methods. An Approach Based on Spatial
Signs and Ranks 
mnormpow  Multivariate Normal Distributions with Power Integrand 
mnormt  The Multivariate Normal and t Distributions 
MNP  R Package for Fitting the Multinomial Probit Model 
MNS  Mixed Neighbourhood Selection 
Mobilize  Mobilize plots and functions 
MOCCA  Multiobjective optimization for collecting cluster alternatives 
mod09nrt  Extraction of Bands from MODIS Surface Reflectance Product MOD09
NRT 
Modalclust  Hierarchical Modal Clustering 
modeest  Mode Estimation 
modehunt  Multiscale Analysis for Density Functions 
modelfree  Modelfree estimation of a psychometric function 
ModelGood  Validation of risk prediction models 
modellingTools  A Collection of Useful Custom Tools for D&A and Modelling 
ModelMap  Modeling and Map Production using Random Forest and Stochastic
Gradient Boosting 
modelObj  A Model Object Framework for Regression Analysis 
modeltools  Tools and Classes for Statistical Models 
modes  Find the Modes and Assess the Modality of Complex and Mixture
Distributions, Especially with Big Datasets 
modEvA  Model Evaluation and Analysis 
modiscloud  R tools for processing Level 2 Cloud Mask products from MODIS 
MODISTools  MODIS Subsetting Tools 
modMax  Community Structure Detection via Modularity Maximization 
modQR  MultipleOutput Directional Quantile Regression 
modTempEff  Modelling temperature effects using time series data 
moduleColor  Basic Module Functions 
modules  Self Contained Units of Source Code 
modygliani  MOlecular DYnamics GLobal ANalysis 
mogavs  Multiobjective Genetic Algorithm for Variable Selection in
Regression 
MOJOV  Mojo Variants: Rare Variants analysis 
mokken  Perform Mokken Scale Analysis in R 
molaR  Dental Surface Complexity Measurement Tools 
mombf  Moment and Inverse Moment Bayes Factors 
momentchi2  MomentMatching Methods for Weighted Sums of ChiSquared Random
Variables 
moments  Moments, cumulants, skewness, kurtosis and related tests 
Momocs  Morphometrics using R 
momr  Mining Metaomics Data (MetaOMineR) 
mondate  Keep track of dates in terms of months 
Mondrian  A Simple Graphical Representation of the Relative Occurrence and
CoOccurrence of Events 
MonetDBLite  InProcess Version of MonetDB for R 
MonetDB.R  Connect MonetDB to R 
mongolite  Fast and Simple MongoDB Client for R 
monitoR  Acoustic Template Detection in R 
monmlp  Monotone MultiLayer Perceptron Neural Network 
monogeneaGM  Geometric Morphometric Analysis of Monogenean Anchors 
monographaR  Taxonomic Monographs Tools 
MonoInc  Monotonic Increasing 
monomvn  Estimation for Multivariate Normal and Studentt Data with
Monotone Missingness 
MonoPhy  Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups
in a Phylogeny 
MonoPoly  Functions to Fit Monotone Polynomials 
monreg  Nonparametric Monotone Regression 
moonBook  Functions and Datasets for the Book by KeonWoong Moon 
moonsun  Basic astronomical calculations with R 
mopsocd  MOPSOCD: Multiobjective Particle Swarm Optimization with
Crowding Distance 
MOrder  Check Time Homogeneity and Markov Chain Order 
morgenstemning  Color schemes compatible with redgreen color perception
difficulties 
Morpho  Calculations and Visualisations Related to Geometric
Morphometrics 
morse  MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology 
MorseGen  Simple raw data generator based on userspecified summary
statistics 
MortalitySmooth  Smoothing and Forecasting Poisson Counts with PSplines 
mosaic  Project MOSAIC Statistics and Mathematics Teaching Utilities 
mosaicData  Project MOSAIC Data Sets 
MoTBFs  Learning Hybrid Bayesian Networks using Mixtures of Truncated
Basis Functions 
MotilityLab  Quantitative Analysis of Motion 
moult  Models for Analysing Moult in Birds 
mountainplot  Mountain Plots, Folded Empirical Cumulative Distribution Plots 
mousetrack  MouseTracking Measures from Trajectory Data 
mousetrap  Process and Analyze MouseTracking Data 
move  Visualizing and Analyzing Animal Track Data 
moveHMM  Animal Movement Modelling using Hidden Markov Models 
movMF  Mixtures of von MisesFisher Distributions 
mp  Multidimensional Projection Techniques 
mpa  CoWords Method 
MPAgenomics  MultiPatient Analysis of Genomic Markers 
mpath  Regularized Linear Models 
mpbart  Multinomial Probit Bayesian Additive Regression Trees 
MPCI  Multivariate Process Capability Indices (MPCI) 
mpcv  Multivariate Process Capability Vector 
MPDiR  Data sets and scripts for Modeling Psychophysical Data in R 
mph  Multiscale persistent homology 
MPINet  The package can implement the networkbased metabolite pathway
identification of pathways 
MPLikelihoodWB  Modified Profile Likelihood Estimation for Weibull Shape and
Regression Parameters 
mplot  Graphical Model Stability and Variable Selection Procedures 
MplusAutomation  Automating Mplus Model Estimation and Interpretation 
mpm  Multivariate Projection Methods 
mpMap  Multiparent RIL genetic analysis 
mpmcorrelogram  Multivariate Partial Mantel Correlogram 
mpmi  Mixedpair mutual information estimators 
mpoly  Symbolic Computation and More with Multivariate Polynomials 
Mposterior  Mposterior: R package for Robust and Scalable Bayes via a Median
of Subset Posterior Measures 
mppa  Statistics for analysing multiple simultaneous point processes
on the real line 
MPSEM  Modeling Phylogenetic Signals using Eigenvector Maps 
mpt  Multinomial Processing Tree Models 
MPTinR  Analyze Multinomial Processing Tree Models 
mptools  RAMAS Metapop Tools 
MPV  Data Sets from Montgomery, Peck and Vining's Book 
mQTL  Metabolomic Quantitative Trait Locus Mapping 
mra  Analysis of MarkRecapture Data 
mratios  Inferences for ratios of coefficients in the general linear
model 
MRCE  Multivariate regression with covariance estimation 
MRCV  Methods for Analyzing Multiple Response Categorical Variables
(MRCVs) 
mrds  MarkRecapture Distance Sampling 
mreg  Fits regression models when the outcome is partially missing 
MRH  MultiResolution Estimation of the Hazard Rate 
mri  Modified Rand Index (1 and 2.1 and 2.2) and Modified Adjusted
Rand Index (1 and 2.1 and 2.2) 
mritc  MRI Tissue Classification 
mRm  An R package for conditional maximum likelihood estimation in
mixed Rasch models 
mrMLM  Multilocus Random Mixed Linear Model for GenomeWide Association
Study and Linkage Analysis 
MRMR  Multivariate Regression Models for Reserving 
mRMRe  R package for parallelized mRMR ensemble feature selection 
MRQoL  Minimal Clinically Important Difference and Response Shift
Effect for HealthRelated Quality of Life 
MRS  MultiResolution Scanning for CrossSample Differences 
MRSP  Multinomial Response Models with Structured Penalties 
MRsurv  A multiplicativeregression model for relative survival 
MRwarping  Multiresolution time warping for functional data 
msap  Statistical analysis for Methylationsensitive Amplification
Polymorphism data 
msarc  Draw Diagrams (mis)Representing the Results of Mass Spec
Experiments 
msBP  Multiscale Bernstein Polynomials for Densities 
MSBVAR  MarkovSwitching, Bayesian, Vector Autoregression Models 
MSCMT  Multivariate Synthetic Control Method Using Time Series 
MScombine  Combine Data from Positive and Negative Ionization Mode Finding
Common Entities 
mscstexta4r  R Client for the Microsoft Cognitive Services Text Analytics
REST API 
mscsweblm4r  R Client for the Microsoft Cognitive Services Web Language Model
REST API 
msda  MultiClass Sparse Discriminant Analysis 
mseapca  Metabolite set enrichment analysis for factor loading in
principal component analysis 
MSeasy  Preprocessing of Gas ChromatographyMass Spectrometry (GCMS)
data 
MSeasyTkGUI  MSeasy Tcl/Tk Graphical User Interface 
MSG  Data and Functions for the Book Modern Statistical Graphics 
msgl  High Dimensional Multiclass Classification Using Sparse Group
Lasso 
msgpackR  A library to serialize or unserialize data in MessagePack format 
msgps  Degrees of freedom of elastic net, adaptive lasso and
generalized elastic net 
msir  ModelBased Sliced Inverse Regression 
MSIseq  Assess Tumor Microsatellite Instability with a Decision Tree
Classifier from Exome Somatic Mutations 
msltrend  Improved Techniques to Estimate Trend, Velocity and Acceleration
from Sea Level Records 
msm  MultiState Markov and Hidden Markov Models in Continuous Time 
msma  Multiblock Sparse Multivariable Analysis 
msme  Functions and Datasets for "Methods of Statistical Model
Estimation" 
msmtools  Building Augmented Data to Run MultiState Models with 'msm'
Package 
msos  Datasets and Functions used in Multivariate Statistics: Old
School by John Marden 
MSQC  Multivariate Statistical Quality Control 
msr  MorseSmale Approximation, Regression and Visualization 
ms.sev  Package for Calculation of ARMSS, Local MSSS and Global MSSS 
msSurv  Nonparametric Estimation for Multistate Models 
MST  Multivariate Survival Trees 
mstate  Data Preparation, Estimation and Prediction in MultiState
Models 
MSwM  Fitting Markov Switching Models 
mtconnectR  Read Data from Delimited 'MTConnect' Data Files and Perform some
Analysis 
mtk  Mexico ToolKit library (MTK) 
MTS  AllPurpose Toolkit for Analyzing Multivariate Time Series (MTS)
and Estimating Multivariate Volatility Models 
mtsdi  Multivariate time series data imputation 
MTurkR  R Client for the MTurk Requester API 
MTurkRGUI  A Graphical User Interface for MTurkR 
MUCflights  Munich FranzJosefStrauss Airport Pattern Analysis 
muckrock  Data on Freedom of Information Act Requests 
MuFiCokriging  MultiFidelity Cokriging models 
muhaz  Hazard Function Estimation in Survival Analysis 
muir  Exploring Data with Tree Data Structures 
MultAlloc  Optimal Allocation in Stratified Sampling 
multcomp  Simultaneous Inference in General Parametric Models 
multcompView  Visualizations of Paired Comparisons 
MultEq  Multiple Equivalence Tests and Simultaneous Confidence Intervals 
multgee  GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses 
multiAssetOptions  Finite Difference Method for MultiAsset Option Valuation 
multiband  Period Estimation for Multiple Bands 
multibiplotGUI  Multibiplot Analysis in R 
multic  Quantitative Linkage Analysis Tools using the Variance
Components Approach 
MultiCNVDetect  Multiple Copy Number Variation Detection 
multicon  Multivariate Constructs 
multicool  Permutations of Multisets in CoolLex Order 
multiDimBio  Multivariate Analysis and Visualization for Biological Data 
multifwf  Read Fixed Width Format Files Containing Lines of Different Type 
multigroup  Multigroup Data Analysis 
MultiLCIRT  Multidimensional Latent Class Item Response Theory Models 
multilevel  Multilevel Functions 
multilevelPSA  Multilevel Propensity Score Analysis 
multimark  CaptureMarkRecapture Analysis using Multiple NonInvasive
Marks 
MultiMeta  Metaanalysis of Multivariate Genome Wide Association Studies 
multinbmod  Regression analysis of overdispersed correlated count data 
MultinomialCI  Simultaneous confidence intervals for multinomial proportions
according to the method by Sison and Glaz 
multinomRob  Robust Estimation of Overdispersed Multinomial Regression Models 
MultiOrd  Generation of Multivariate Ordinal Variates 
multipanelfigure  Infrastructure to Assemble MultiPanel Figures (from Grobs) 
MultiPhen  A Package to Test for Pleiotropic Effects 
multiPIM  Variable Importance Analysis with Population Intervention Models 
multipleNCC  Weighted CoxRegression for Nested CaseControl Data 
multiplex  Algebraic Tools for the Analysis of Multiple Social Networks 
multiplyr  Data Manipulation with Parallelism and Shared Memory Matrices 
multipol  multivariate polynomials 
multirich  Calculate Multivariate Richness via UTC and sUTC 
MultiRR  Bias, Precision, and Power for MultiLevel Random Regressions 
multisensi  Multivariate Sensitivity Analysis 
multisom  Clustering a Dataset using MultiSOM Algorithm 
multispatialCCM  Multispatial Convergent Cross Mapping 
MultiSV  MultiSV: an R package for identification of structural
variations in multiple populations based on whole genome
resequencing 
multitaper  Multitaper Spectral Analysis Tools 
MultivariateRandomForest  Multivariate Random Forest for Linearly Related Output Features 
multivator  A multivariate emulator 
multiwave  Estimation of Multivariate LongMemory Models Parameters 
multiway  Component Models for MultiWay Data 
multiwayvcov  MultiWay Standard Error Clustering 
MultNonParam  Multivariate Nonparametric Methods 
multxpert  Common Multiple Testing Procedures and Gatekeeping Procedures 
muma  Metabolomics Univariate and Multivariate Analysis 
MuMIn  MultiModel Inference 
munfold  Metric Unfolding 
munsell  Utilities for Using Munsell Colours 
munsellinterpol  Interpolate Munsell Renotation Data from Hue/Chroma to CIE/sRGB 
muRL  Mailmerge using R, LaTeX, and the Web 
murphydiagram  Murphy Diagrams for Forecast Comparisons 
musicNMR  Conversion of Nuclear Magnetic Resonance spectrum in audio file 
muStat  Prentice Rank Sum Test and McNemar Test 
mutoss  Unified Multiple Testing Procedures 
mutossGUI  A Graphical User Interface for the MuToss Project 
MuViCP  MultiClass Visualizable Classification using Combination of
Projections 
MVA  An Introduction to Applied Multivariate Analysis with R 
mvabund  Statistical Methods for Analysing Multivariate Abundance Data 
MVar.pt  Analise multivariada (brazilian portuguese) 
MVB  Mutivariate Bernoulli loglinear model 
MvBinary  Modelling Multivariate Binary Data with Blocks of Specific
OneFactor Distribution 
mvbutils  Workspace organization, code and documentation editing, package
prep and editing, etc 
mvc  MultiView Clustering 
mvcluster  MultiView Clustering 
mvctm  Multivariate Variance Components Tests for Multilevel Data 
mvcwt  Wavelet analysis of multiple time series 
mvdalab  Multivariate Data Analysis Laboratory 
mvglmmRank  Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams 
mvinfluence  Influence Measures and Diagnostic Plots for Multivariate Linear
Models 
MVLM  Multivariate Linear Model with Analytic pValues 
mvmesh  Multivariate Meshes and Histograms in Arbitrary Dimensions 
mvmeta  Multivariate and Univariate MetaAnalysis and MetaRegression 
mvMORPH  Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data 
MVN  Multivariate Normality Tests 
mvna  NelsonAalen estimator of the cumulative hazard in multistate
models 
mvnfast  Fast Multivariate Normal Methods 
mvngGrAd  Moving Grid Adjustment in Plant Breeding Field Trials 
mvnmle  ML estimation for multivariate normal data with missing values 
mvnormtest  Normality test for multivariate variables 
mvnpermute  Generate New Multivariate Normal Samples from Permutations 
mvnTest  Goodness of Fit Tests for Multivariate Normality 
mvoutlier  Multivariate outlier detection based on robust methods 
mvPot  Multivariate PeaksoverThreshold Modelling for Spatial Extreme
Events 
mvProbit  Multivariate Probit Models 
mvprpb  Orthant Probability of the Multivariate Normal Distribution 
mvQuad  Methods for Multivariate Quadrature 
MVR  MeanVariance Regularization 
mvrtn  Mean and Variance of Truncated Normal Distribution 
mvsf  ShapiroFrancia Multivariate Normality Test 
mvShapiroTest  Generalized ShapiroWilk test for multivariate normality 
mvSLOUCH  Multivariate Stochastic Linear OrnsteinUhlenbeck Models for
Phylogenetic Comparative Hypotheses 
mvst  Bayesian Inference for the Multivariate Skewt Model 
MVT  Estimation and Testing for the Multivariate tDistribution 
mvtboost  Tree Boosting for Multivariate Outcomes 
mvtmeta  Multivariate metaanalysis 
mvtnorm  Multivariate Normal and t Distributions 
mvtsplot  Multivariate Time Series Plot 
mwa  Causal Inference in Spatiotemporal Event Data 
mwaved  Multichannel Wavelet Deconvolution with Additive Long Memory
Noise 
mxkssd  Efficient mixedlevel kcirculant supersaturated designs 
MXM  Discovering Multiple, StatisticallyEquivalent Signatures 
mycobacrvR  Integrative immunoinformatics for Mycobacterial diseases in R
platform 
mycor  Automatic Correlation and Regression Test in a Data Frame 
myepisodes  MyEpisodes RSS/API functions 
Myrrix  Interface to Myrrix. Myrrix is a complete, realtime, scalable
clustering and recommender system, evolved from Apache Mahout 
Myrrixjars  External jars required for package Myrrix 
myTAI  Perform Evolutionary Transcriptomics Studies 
mztwinreg  Regression Models for Monozygotic Twin Data 

nabor  Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low
Dimensions 
NADA  Nondetects And Data Analysis for environmental data 
nadiv  (Non)Additive Genetic Relatedness Matrices 
NAEPprimer  The NAEP Primer 
NAM  Nested Association Mapping Analysis 
namespace  Provide namespace managment functions not (yet) present in base
R 
nanop  Tools for Nanoparticle Simulation and Calculation of PDF and
Total Scattering Structure Function 
NanoStringNorm  Normalize NanoString miRNA and mRNA Data 
NAPPA  Performs the Processing and Normalisation of Nanostring miRNA
and mRNA Data 
nasadata  Interface to Various NASA API's 
nasaweather  Collection of datasets from the ASA 2006 data expo 
nat  NeuroAnatomy Toolbox for Analysis of 3D Image Data 
nat.nblast  NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron
Similarity and Clustering 
nat.templatebrains  NeuroAnatomy Toolbox ('nat') Extension for Handling Template
Brains 
naturalsort  Natural Ordering 
nat.utils  File System Utility Functions for 'NeuroAnatomy Toolbox' 
NB  Maximum Likelihood method in estimating effective population
size from genetic data 
nbc4va  Bayes Classifier for Verbal Autopsy Data 
NbClust  Determining the Best Number of Clusters in a Data Set 
nbconvertR  Vignette Engine Wrapping IPython Notebooks 
NBDdirichlet  NBDDirichlet Model of Consumer Buying Behavior for Marketing
Research 
nbpMatching  Functions for Optimal NonBipartite Matching 
NBPSeq  Negative Binomial Models for RNASequencing Data 
NCA  Necessary Condition Analysis 
nCal  Nonlinear Calibration 
ncappc  NCA Calculation and Population PK Model Diagnosis 
ncbit  retrieve and build NBCI taxonomic data 
ncdf4  Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files 
ncdf4.helpers  Helper functions for use with the ncdf4 package 
ncdf.tools  Easier 'NetCDF' File Handling 
nCDunnett  Noncentral Dunnett's Test Distribution 
ncf  Spatial Nonparametric Covariance Functions 
ncg  Computes the noncentral gamma function 
NCmisc  Miscellaneous Functions for Creating Adaptive Functions and
Scripts 
ncvreg  Regularization Paths for SCAD and MCP Penalized Regression
Models 
ndl  Naive Discriminative Learning 
ndtv  Network Dynamic Temporal Visualizations 
NEArender  Network Enrichment Analysis 
neariso  NearIsotonic Regression 
neat  Efficient Network Enrichment Analysis Test 
NeatMap  Nonclustered heatmap alternatives 
needs  Attaches and Installs Packages 
needy  needy 
NEff  Calculating Effective Sizes Based on Known Demographic
Parameters of a Population 
negenes  Estimating the Number of Essential Genes in a Genome 
neldermead  R port of the Scilab neldermead module 
neotoma  Access to the Neotoma Paleoecological Database Through R 
nephro  Biostatistics Utilities for Nephrology 
NEpiC  Network Assisted Algorithm for Epigenetic Studies Using Mean and
Variance Combined Signals 
NestedCohort  Survival Analysis for Cohorts with Missing Covariate Information 
nestedRanksTest  MannWhitneyWilcoxon Test for Nested Ranks 
netassoc  Inference of Species Associations from CoOccurrence Data 
netClass  netClass: An R Package for NetworkBased Biomarker Discovery 
NetCluster  Clustering for networks 
netcoh  Statistical Modeling with Network Cohesion 
NetComp  Network Generation and Comparison 
NetData  Network Data for McFarland's SNA R labs 
netdiffuseR  Network Analysis for Diffusion of Innovations 
netgen  Network Generator for Combinatorial Graph Problems 
netgsa  NetworkBased Gene Set Analysis 
NetIndices  Estimating network indices, including trophic structure of
foodwebs in R 
netmeta  Network MetaAnalysis using Frequentist Methods 
NetOrigin  Origin Estimation for Propagation Processes on Complex Networks 
NetPreProc  Network PreProcessing and Normalization 
nets  Network Estimation for Time Series 
NetSim  A Social Networks Simulation Tool in R 
NetSwan  Network Strengths and Weaknesses Analysis 
nettools  A Network Comparison Framework 
network  Classes for Relational Data 
networkD3  D3 JavaScript Network Graphs from R 
networkDynamic  Dynamic Extensions for Network Objects 
networkDynamicData  Dynamic (Longitudinal) Network Datasets 
networkreporting  Tools for using Network Reporting Estimators 
networksis  Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling 
networkTomography  Tools for network tomography 
neural  Neural Networks 
neuralnet  Training of neural networks 
NeuralNetTools  Visualization and Analysis Tools for Neural Networks 
neuroblastoma  Neuroblastoma copy number profiles 
neuroim  Data Structures and Handling for Neuroimaging Data 
neuRosim  Functions to Generate fMRI Data Including Activated Data, Noise
Data and Resting State Data 
Newdistns  Computes Pdf, Cdf, Quantile and Random Numbers, Measures of
Inference for 19 General Families of Distributions 
nFactors  Parallel Analysis and Non Graphical Solutions to the Cattell
Scree Test 
nFCA  Numerical Formal Concept Analysis for Systematic Clustering 
ngram  Fast nGram 'Tokenization' 
ngramrr  A Simple General Purpose NGram Tokenizer 
ngspatial  Fitting the centered autologistic and sparse spatial generalized
linear mixed models for areal data 
NHANES  Data from the US National Health and Nutrition Examination Study 
nhanesA  NHANES Data Retrieval 
NHEMOtree  Nonhierarchical evolutionary multiobjective tree learner to
perform costsensitive classification 
nhlscrapr  Compiling the NHL Real Time Scoring System Database for easy use
in R 
NHMM  Bayesian NHMM Modeling (Multiple Time Series) 
NHMSAR  NonHomogeneous Markov Switching Autoregressive Models 
NHPoisson  Modelling and Validation of Non Homogeneous Poisson Processes 
nice  Get or Set UNIX Niceness 
nicheROVER  (Niche) (R)egion and Niche (Over)lap Metrics for
Multidimensional Ecological Niches 
NightDay  Night and Day Boundary Plot Funtion 
nima  Nima Hejazi's Miscellaneous R Code 
Nippon  Japanese Utility Functions and Data 
NIPTeR  Fast and Accurate Trisomy Prediction in NonInvasive Prenatal
Testing 
NISTnls  Nonlinear least squares examples from NIST 
NISTunits  Fundamental Physical Constants and Unit Conversions from NIST 
nivm  Noninferiority Tests with Variable Margins 
NlcOptim  Solve Nonlinear Optimization with Nonlinear Constraints 
nleqslv  Solve Systems of Nonlinear Equations 
nlme  Linear and Nonlinear Mixed Effects Models 
nlmeODE  Nonlinear mixedeffects modelling in nlme using differential
equations 
nlmeU  Datasets and utility functions enhancing functionality of nlme
package 
nlmrt  Functions for Nonlinear Least Squares Solutions 
nlnet  Nonlinear Network Reconstruction and Clustering Based on DCOL
(Distance Based on Conditional Ordered List) 
nloptr  R interface to NLopt 
NLP  Natural Language Processing Infrastructure 
NLPutils  Natural Language Processing Utilities 
nlreg  Higher Order Inference for Nonlinear Heteroscedastic Models 
NLRoot  searching for the root of equation 
nlrr  NonLinear Relative Risk Estimation and Plotting 
nls2  Nonlinear regression with brute force 
nlsem  Fitting Structural Equation Mixture Models 
nlshrink  NonLinear Shrinkage Estimation of Population Eigenvalues and
Covariance Matrices 
nlsMicrobio  Nonlinear regression in predictive microbiology 
nlsmsn  Fitting nonlinear models with scale mixture of skewnormal
distributions 
nlstools  Tools for Nonlinear Regression Analysis 
NlsyLinks  Utilities and Kinship Information for Research with the NLSY 
nlt  A nondecimated lifting transform for signal denoising 
nlts  (non)linear time series analysis 
nLTT  Calculate the 'nLTT' Statistic 
nlWaldTest  Wald Test of Nonlinear Restrictions and Nonlinear CI 
nmcdr  Nonparametric Multiple Changepoints Detection 
NMF  Algorithms and Framework for Nonnegative Matrix Factorization
(NMF) 
nmfgpu4R  NonNegative Matrix Factorization (NMF) using CUDA 
NMFN  Nonnegative Matrix Factorization 
NMOF  Numerical Methods and Optimization in Finance 
nnet  FeedForward Neural Networks and Multinomial LogLinear Models 
nnetpredint  Prediction Intervals of MultiLayer Neural Networks 
nnlasso  NonNegative Lasso and Elastic Net Penalized Generalized Linear
Models 
NNLM  Fast and Versatile NonNegative Matrix Factorization 
nnls  The LawsonHanson algorithm for nonnegative least squares
(NNLS) 
NNS  Nonlinear Nonparametric Statistics 
NNTbiomarker  Calculate Design Parameters for Biomarker Validation Studies 
nodeHarvest  Node Harvest for Regression and Classification 
nodiv  Compares the Distribution of Sister Clades Through a Phylogeny 
noia  Implementation of the Natural and Orthogonal InterAction (NOIA)
model 
NoiseFiltersR  Label Noise Filters for Data Preprocessing in Classification 
nomadlist  Interface to the Nomad List API 
nomclust  Hierarchical Nominal Clustering Package 
NominalLogisticBiplot  Biplot representations of categorical data 
noncensus  U.S. Census Regional and Demographic Data 
noncompliance  Causal Inference in the Presence of Treatment Noncompliance
Under the Binary Instrumental Variable Model 
nonlinearTseries  Nonlinear Time Series Analysis 
nonmem2R  Loading NONMEM Output Files and Simulate with Parameter
Uncertainty 
nonnest2  Tests of NonNested Models 
nonparaeff  Nonparametric Methods for Measuring Efficiency and Productivity 
NonpModelCheck  Model Checking and Variable Selection in Nonparametric
Regression 
nonrandom  Stratification and matching by the propensity score 
nontarget  Detecting Isotope, Adduct and Homologue Relations in LCMS Data 
nontargetData  Quantized simulation data of isotope pattern centroids 
nopp  Nash Optimal Party Positions 
nor1mix  Normal (1d) Mixture Models (S3 Classes and Methods) 
nordklimdata1  Dataset for Climate Analysis with Data from the Nordic Region 
norm  Analysis of multivariate normal datasets with missing values 
norm2  Analysis of Incomplete Multivariate Data under a Normal Model 
NormalGamma  Normalgamma convolution model 
NormalLaplace  The Normal Laplace Distribution 
normalp  Routines for Exponential Power Distribution 
NormPsy  Normalisation of Psychometric Tests 
NORMT3  Evaluates complex erf, erfc, Faddeeva, and density of sum of
Gaussian and Student's t 
normtest  Tests for Normality 
normwhn.test  Normality and White Noise Testing 
NORRRM  Geochemical Toolkit for R 
NORTARA  Generation of Multivariate Data with Arbitrary Marginals 
nortest  Tests for Normality 
nortestARMA  Neyman Smooth Tests of Normality for the Errors of ARMA Models 
nose  nose Package for R 
NostalgiR  Advanced TextBased Plots 
notifyR  Send push notifications to your smartphone via pushover.net
(ACCOUNT REQUIRED!) 
novelist  NOVEL Integration of the Sample and Thresholded (NOVELIST)
Correlation and Covariance Estimators 
noweb  Noweb system for R 
Nozzle.R1  Nozzle Reports 
np  Nonparametric kernel smoothing methods for mixed data types 
nparACT  NonParametric Measures of Actigraphy Data 
nparcomp  Multiple Comparisons and Simultaneous Confidence Intervals 
nparLD  Nonparametric Analysis of Longitudinal Data in Factorial
Experiments 
NPBayesImpute  NonParametric Bayesian Multiple Imputation for Categorical Data 
npbr  Nonparametric Boundary Regression 
NPC  Nonparametric Combination of Hypothesis Tests 
NPCD  Nonparametric Methods for Cognitive Diagnosis 
NPCirc  Nonparametric Circular Methods 
npcp  Some Nonparametric Tests for ChangePoint Detection in Possibly
Multivariate Observations 
npde  Normalised prediction distribution errors for nonlinear
mixedeffect models 
NPflow  Bayesian Nonparametrics for Automatic Gating of FlowCytometry
Data 
NPHMC  Sample Size Calculation for the Proportional Hazards Mixture
Cure Model 
npIntFactRep  Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures 
nplplot  Plotting linkage and association results 
nplr  NParameter Logistic Regression 
NPMLEcmprsk  TypeSpecific Failure Rate and Hazard Rate on Competing Risks
Data 
npmlreg  Nonparametric maximum likelihood estimation for random effect
models 
NPMPM  tertiary probabilistic model in predictive microbiology for use
in food manufacture 
npmr  Nuclear Penalized Multinomial Regression 
npmv  Nonparametric Comparison of Multivariate Samples 
NPMVCP  Nonparametric Multivariate Change Point Model 
nppbib  Nonparametric PartiallyBalanced Incomplete Block Design
Analysis 
npregfast  Nonparametric Estimation of Regression Models with
FactorbyCurve Interactions 
nproc  NeymanPearson Receiver Operator Curve 
npROCRegression  KernelBased Nonparametric ROC Regression Modelling 
NPS  Convenience Functions and Tests for Working With the Net
Promoter Score (NPS) 
npsf  Nonparametric and Stochastic Efficiency and Productivity
Analysis 
NPsimex  Nonparametric Smoothing for contaminated data using
SimulationExtrapolation 
npsm  Package for Nonparametric Statistical Methods using R 
npsp  Nonparametric spatial (geo)statistics 
npst  Generalization of Hewitt's Seasonality Test 
npsurv  NonParametric Survival Analysis 
NSA  Postnormalization of total copy numbers 
nscancor  NonNegative and Sparse CCA 
NScluster  Simulation and Estimation of the NeymanScott Type Spatial
Cluster Models 
nsga2R  Elitist Nondominated Sorting Genetic Algorithm based on R 
nsgp  NonStationary Gaussian Process Regression 
NSM3  Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken  Nonparametric Statistical Methods, Third Edition 
nsprcomp  NonNegative and Sparse PCA 
nsRFA  Nonsupervised Regional Frequency Analysis 
NSUM  Network Scale Up Method 
NUCOMBog  NUtrient Cycling and COMpetition Model Undisturbed Open Bog
Ecosystems in a Temperate to SubBoreal Climate 
nullabor  Tools for Graphical Inference 
numbers  NumberTheoretic Functions 
numDeriv  Accurate Numerical Derivatives 
numOSL  Numeric Routines for Optically Stimulated Luminescence Dating 
nutshell  Data for "R in a Nutshell" 
nutshell.audioscrobbler  Audioscrobbler data for "R in a Nutshell" 
nutshell.bbdb  Baseball Database for "R in a Nutshell" 
nws  R functions for NetWorkSpaces and Sleigh 
nycflights13  Flights that Departed NYC in 2013 
nzelect  New Zealand Election Results 

oaColors  OpenAnalytics Colors Package 
oai  General Purpose 'OaiPMH' Services Client 
OAIHarvester  Harvest Metadata Using OAIPMH v2.0 
oapackage  Orthogonal Array Package 
oaPlots  OpenAnalytics Plots Package 
Oarray  Arrays with arbitrary offsets 
oasis  Multiple Sclerosis Lesion Segmentation using Magnetic Resonance
Imaging (MRI) 
OasisR  Outright Tool for the Analysis of Spatial Inequalities and
Segregation 
oaxaca  BlinderOaxaca Decomposition 
obAnalytics  Limit Order Book Analytics 
objectProperties  A factory of selfdescribing properties 
objectSignals  objectSignals 
obliclus  Clusterbased factor rotation 
obliqueRF  Oblique Random Forests from Recursive Linear Model Splits 
oblique.tree  Oblique Trees for Classification Data 
obs.agree  An R package to assess agreement between observers 
OBsMD  Objective Bayesian Model Discrimination in FollowUp Designs 
obsSens  Sensitivity analysis for Observational studies 
oc  OC Roll Call Analysis Software 
occ  Estimates PET neuroreceptor occupancies 
oce  Analysis of Oceanographic Data 
ocean  Biophysical Oceanography Tools 
OceanView  Visualisation of Oceanographic Data and Model Output 
ocedata  Oceanographic Datasets for Oce 
ocomposition  Regression for RankIndexed Compositional Data 
OData  R Helper for OData Web Services 
ODB  Open Document Databases (.odb) management 
odds.converter  Betting Odds Conversion 
odeintr  C++ ODE Solvers Compiled onDemand 
odfWeave  Sweave processing of Open Document Format (ODF) files 
odfWeave.survey  Support for odfWeave on the survey package 
ODMconverter  Tools to Convert ODM Files 
oec  The Observatory of Economic Complexity 
OECD  Search and Extract Data from the OECD 
oem  Orthogonalizing Expectation maximization 
oglmx  Estimation of Ordered Generalized Linear Models 
Ohmage  R Client for Ohmage 2 server 
OIdata  Data sets and supplements (OpenIntro) 
OIsurv  Survival analysis supplement to OpenIntro guide 
OjaNP  Multivariate Methods Based on the Oja Median and Related
Concepts 
okmesonet  Retrieve Oklahoma Mesonet climatological data 
olctools  Open Location Code Handling in R 
OligoSpecificitySystem  Oligo Specificity System 
OLScurve  OLS growth curve trajectories 
omd  filter the molecular descriptors for QSAR 
OmicKriging  PolyOmic Prediction of Complex TRaits 
omics  '–omics' Data Analysis Toolbox 
oncomodel  Maximum likelihood tree models for oncogenesis 
Oncotree  Estimating oncogenetic trees 
OneArmPhaseTwoStudy  Planing, Monitoring and Evaluating Oncological Phase 2 Studies 
onemap  Software for constructing genetic maps in experimental crosses:
fullsib, RILs, F2 and backcrosses 
OneR  One Rule Machine Learning Classification Algorithm with
Enhancements 
ONETr  Efficient Authenticated Interaction with the O*NET API 
OneTwoSamples  Deal with one and two (normal) samples 
onewaytests  OneWay Independent Groups Design 
onion  octonions and quaternions 
onlinePCA  Online Principal Component Analysis 
onls  Orthogonal Nonlinear LeastSquares Regression 
ontologyIndex  Functions for Reading Ontologies into R 
ontologyPlot  Functions for Visualising Sets of Ontological Terms 
ontologySimilarity  Functions for Calculating Ontological Similarities 
OOmisc  OzgurOzlem Miscellaneous 
OpasnetUtils  Opasnet Modelling Environment Utility Functions 
OPDOE  OPtimal Design Of Experiments 
opefimor  Option Pricing and Estimation of Financial Models in R 
openair  Tools for the Analysis of Air Pollution Data 
opencage  Interface to the OpenCage API 
OpenCL  Interface allowing R to use OpenCL 
opencpu  Embedded Scientific Computing and Reproducible Research with R 
OpenImageR  An Image Processing Toolkit 
openintro  OpenIntro data sets and supplemental functions 
OpenMPController  Control number of OpenMP threads dynamically 
OpenMx  Extended Structural Equation Modelling 
openNLP  Apache OpenNLP Tools Interface 
openNLPdata  Apache OpenNLP Jars and Basic English Language Models 
OpenRepGrid  Tools to analyse repertory grid data 
openssl  Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL 
OpenStreetMap  Access to Open Street Map Raster Images 
opentraj  Tools for Creating and Analysing Air Trajectory Data 
openVA  Automated Method for Verbal Autopsy 
openxlsx  Read, Write and Edit XLSX Files 
operators  Additional Binary Operators 
operator.tools  Utilities for Working with R's Operators 
OPI  Open Perimetry Interface 
ops  Optimal Power Space Transformation 
optAUC  Optimal Combinations of Diagnostic Tests Based on AUC 
optBiomarker  Estimation of optimal number of biomarkers for twogroup
microarray based classifications at a given error tolerance
level for various classification rules 
optCluster  Determine Optimal Clustering Algorithm and Number of Clusters 
optDesignSlopeInt  Optimal Designs for Estimating the Slope Divided by the
Intercept 
optextras  Tools to Support Optimization Methods 
OptGS  NearOptimal and Balanced GroupSequential Designs for Clinical
Trials with Continuous Outcomes 
OptHedging  Estimation of value and hedging strategy of call and put
options 
optifunset  Set Options if Unset 
optigrab  CommandLine Parsing for an R World 
OptimalCutpoints  Computing optimal cutpoints in diagnostic tests 
OptimaRegion  Confidence Regions for Optima 
optimbase  R port of the Scilab optimbase module 
optimsimplex  R port of the Scilab optimsimplex module 
optimx  A Replacement and Extension of the optim() Function 
OptInterim  Optimal Two and Three Stage Designs for SingleArm and TwoArm
Randomized Controlled Trials with a LongTerm Binary Endpoint 
OptionPricing  Option Pricing with Efficient Simulation Algorithms 
OptiQuantR  Simplifies and Automates Analyzing and Reporting OptiQuant's log
Data 
optiRum  Financial Functions & More 
optiscale  Optimal scaling 
optiSel  Optimum Contribution Selection and Pedigree Analysis 
optismixture  Optimal Mixture Weights in Multiple Importance Sampling 
optmatch  Functions for Optimal Matching 
optparse  Command Line Option Parser 
optpart  Optimal Partitioning of Similarity Relations 
optR  Optimization Toolbox for solving linear systems 
optrees  Optimal Trees in Weighted Graphs 
ora  Convenient Tools for Working with Oracle Databases 
orca  Computation of Graphlet Orbit Counts in Sparse Graphs 
ORCI  Several confidence intervals for the odds ratio 
orclus  ORCLUS subspace clustering 
ORCME  Order Restricted Clustering for Microarray Experiments 
orcutt  Estimate procedure in case of first order autocorrelation 
ordBTL  Modelling comparison data with ordinal response 
orddom  Ordinal Dominance Statistics 
ORDER2PARENT  Estimate parent distributions with data of several order
statistics 
orderbook  Orderbook visualization/Charting software 
orderedLasso  Ordered Lasso and Timelag Sparse Regression 
OrdFacReg  Least Squares, Logistic, and CoxRegression with Ordered
Predictors 
ordiBreadth  Ordinated Diet Breadth 
ordinal  Regression Models for Ordinal Data 
ordinalCont  Ordinal Regression Analysis for Continuous Scales 
ordinalgmifs  Ordinal Regression for Highdimensional Data 
OrdinalLogisticBiplot  Biplot representations of ordinal variables 
ordinalNet  Penalized Ordinal Regression 
OrdLogReg  Ordinal Logic Regression 
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 
ordPens  Selection and/or Smoothing of Ordinal Predictors 
ore  An R Interface to the Oniguruma Regular Expression Library 
ores  Connector to the Objective Revision Evaluation Service (ORES) 
OrgMassSpecR  Organic Mass Spectrometry 
orgR  Analyse Text Files Created by Emacs' Org mode 
ORIClust  Orderrestricted Information Criterionbased Clustering
Algorithm 
orientlib  Support for orientation data 
OriGen  Fast Spatial Ancestry via Flexible Allele Frequency Surfaces 
originr  Fetch Species Origin Data from the Web 
orloca  The package deals with Operations Research LOCational Analysis
models 
orloca.es  Spanish version of orloca package 
ORMDR  ORMDR 
oro.dicom  Rigorous  DICOM Input / Output 
oro.nifti  Rigorous  NIfTI + ANALYZE + AFNI : Input / Output 
oro.pet  Rigorous  Positron Emission Tomography 
orQA  Order Restricted Assessment Of Microarray Titration Experiments 
orsifronts  Southern Ocean Frontal Distributions (Orsi) 
orsk  Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information 
orthogonalsplinebasis  Orthogonal BSpline Basis Functions 
OrthoPanels  Dynamic Panel Models with Orthogonal Reparameterization of Fixed
Effects 
orthopolynom  Collection of functions for orthogonal and orthonormal
polynomials 
osc  Orthodromic Spatial Clustering 
osd  Orthogonal Signal Deconvolution for Spectra Deconvolution in
GCMS and GCxGCMS Data 
osDesign  Design and analysis of observational studies 
osi  Open Source Initiative API Connector 
osmar  OpenStreetMap and R 
osmplotr  Customisable Images of OpenStreetMap Data 
osrm  Interface Between R and the OpenStreetMapBased Routing Service
OSRM 
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 
ouch  OrnsteinUhlenbeck Models for Phylogenetic Comparative
Hypotheses 
outbreaker  Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data 
OutbreakTools  Basic Tools for the Analysis of Disease Outbreaks 
OutlierDC  Outlier Detection using quantile regression for Censored Data 
OutlierDM  Outlier Detection for Multireplicated Highthroughput Data 
outliers  Tests for outliers 
OutrankingTools  Functions for Solving Multiplecriteria Decisionmaking Problems 
OUwie  Analysis of Evolutionary Rates in an OU Framework 
overlap  Estimates of Coefficient of Overlapping for Animal Activity
Patterns 
overlapping  Estimation of Overlapping in Empirical Distributions 
OxyBS  Processing of OxyBisulfite Microarray Data 
oz  Plot the Australian Coastline and States 

P2C2M  Posterior Predictive Checks of Coalescent Models 
p2distance  Welfare's Synthetic Indicator 
p3state.msm  Analyzing survival data 
pa  Performance Attribution for Equity Portfolios 
PAactivPAL  Summarize Daily Physical Activity from 'activPAL' Accelerometer
Data 
PabonLasso  Pabon Lasso Graphs and Comparing Situations of a Unit in Two
Different Times 
PAC  PartitionAssisted Clustering 
PACBO  Clustering Online Datasets 
pacbpred  PACBayesian Estimation and Prediction in Sparse Additive
Models 
pack  Convert values to/from raw vectors 
packagetrackr  Track R Package Downloads from RStudio's CRAN Mirror 
packcircles  Circle Packing 
packClassic  Toy example of Pack Classic 
packHV  A few Useful Functions for Statisticians 
packrat  A Dependency Management System for Projects and their R Package
Dependencies 
packS4  Toy Example of S4 Package 
pacman  Package Management Tool 
paco  Procrustes Application to Cophylogenetic Analysis 
pact  Predictive Analysis of Clinical Trials 
PACVB  Variational Bayes (VB) Approximation of Gibbs Posteriors with
Hinge Losses 
Pade  PadÃ© Approximant Coefficients 
paf  Attributable Fraction Function for Censored Survival Data 
PAFit  Nonparametric Estimation of Preferential Attachment and Node
Fitness in Temporal Complex Networks 
pagenum  Put Page Numbers on Graphics 
pageviews  An API Client for Wikimedia Traffic Data 
PAGI  The package can identify the dysregulated KEGG pathways based on
global influence from the internal effect of pathways and
crosstalk between pathways 
PAGWAS  Pathway Analysis Methods for Genomewide Association Data 
pairedCI  Confidence intervals for the ratio of locations and for the
ratio of scales of two paired samples 
PairedData  Paired Data Analysis 
pairheatmap  A tool for comparing heatmaps 
pairsD3  D3 Scatterplot Matrices 
PairViz  Visualization using Eulerian tours and Hamiltonian
decompositions 
pairwise  Rasch Model Parameters by Pairwise Algorithm 
pairwiseCI  Confidence Intervals for Two Sample Comparisons 
palaeoSig  Significance Tests for Palaeoenvironmental Reconstructions 
paleobioDB  Download and Process Data from the Paleobiology Database 
paleofire  Analysis of Charcoal Records from the Global Charcoal Database 
paleoMAS  Paleoecological Analysis 
paleotree  Paleontological and Phylogenetic Analyses of Evolution 
paleoTS  Analyze Paleontological TimeSeries 
palettetown  Use Pokemon Inspired Colour Palettes 
palinsol  Insolation for Palaeoclimate Studies 
palr  Colour Palettes for Data 
pamctdp  Principal Axes Methods for Contingency Tables with Partition
Structures on Rows and Columns 
pamm  Power Analysis for Random Effects in Mixed Models 
pampe  Implementation of the Panel Data Approach Method for Program
Evaluation 
pamr  Pam: prediction analysis for microarrays 
pan  Multiple Imputation for Multivariate Panel or Clustered Data 
pAnalysis  Benchmarking and Rescaling R2 using Noise Percentile Analysis 
PANDA  Preferential Attachment Based Common Neighbor Distribution
Derived Functional Associations 
pander  An R Pandoc Writer 
pandocfilters  Pandoc Filters for R 
panelaggregation  Aggregate Longitudinal Survey Data 
panelAR  Estimation of Linear AR(1) Panel Data Models with
CrossSectional Heteroskedasticity and/or Correlation 
PanelCount  Random Effects and/or Sample Selection Models for Panel Count
Data 
Paneldata  Linear models for panel data 
pangaear  Client for the 'Pangaea' Database 
PANICr  PANIC Tests of Nonstationarity 
papayar  View Medical Research Images using the Papaya JavaScript Library 
papeR  A Toolbox for Writing Pretty Papers and Reports 
ParallelForest  Random Forest Classification with Parallel Computing 
parallelize.dynamic  Automate parallelization of function calls by means of dynamic
code analysis 
parallelMap  Unified Interface to Parallelization BackEnds 
parallelMCMCcombine  Methods for combining independent subset Markov chain Monte
Carlo (MCMC) posterior samples to estimate a posterior density
given the full data set 
parallelML  A ParallelVoting Algorithm for many Classifiers 
ParallelPC  Paralellised Versions of Constraint Based Causal Discovery
Algorithms 
parallelSVM  A ParallelVoting Version of the SupportVectorMachine
Algorithm 
ParallelTree  Parallel Tree 
paramGUI  A Shiny GUI for some Parameter Estimation Examples 
ParamHelpers  Helpers for Parameters in BlackBox Optimization, Tuning and
Machine Learning 
paramlink  Parametric Linkage Analysis in R 
params  Simplify Parameters 
paran  Horn's Test of Principal Components/Factors 
parboost  Distributed ModelBased Boosting 
parcor  Regularized estimation of partial correlation matrices 
ParDNAcopy  Parallel implementation of the "segment" function of package
"DNAcopy" 
ParentOffspring  Conduct the ParentOffspring Test Using Monomorphic SNP Markers 
ParetoPosStable  Computing, Fitting and Validating the PPS Distribution 
parfm  Parametric Frailty Models 
parfossil  Parallelized functions for palaeoecological and
palaeogeographical analysis 
parma  Portfolio Allocation and Risk Management Applications 
parmigene  Parallel Mutual Information estimation for Gene Network
reconstruction 
PARSE  ModelBased Clustering with Regularization Methods for
HighDimensional Data 
parsec  Partial Orders in SocioEconomics 
parsedate  Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats 
partDSA  Partitioning Using Deletion, Substitution, and Addition Moves 
partialAR  Partial Autoregression 
partialOR  Partial Odds Ratio 
partitionMap  Partition Maps 
partitionMetric  Compute a distance metric between two partitions of a set 
partitions  Additive Partitions of Integers 
partools  Tools for the 'Parallel' Package 
partsm  Periodic Autoregressive Time Series Models 
party  A Laboratory for Recursive Partytioning 
partykit  A Toolkit for Recursive Partytioning 
parviol  Parviol 
PAS  Polygenic Analysis System (PAS) 
Pasha  Preprocessing of Aligned Sequences from HTS Analyses 
pass  Prediction and Stability Selection of Tuning Parameters 
password  Create Random Passwords 
pastecs  Package for Analysis of SpaceTime Ecological Series 
pastis  Phylogenetic Assembly with Soft Taxonomic Inferences 
PASWR  PROBABILITY and STATISTICS WITH R 
PASWR2  Probability and Statistics with R, Second Edition 
patchDVI  Package to Patch .dvi or .synctex Files 
patchPlot  Scatterplots of image patches 
patchSynctex  Communication Between Editor and Viewer for Literate Programs 
PATHChange  A Tool for Identification of Differentially Expressed Pathways
using MultiStatistic Comparison 
pathClass  Classification using biological pathways as prior knowledge 
pathdiagram  Basic functions for drawing path diagrams 
pathmox  Pathmox Approach of Segmentation Trees in Partial Least Squares
Path Modeling 
pathological  Path Manipulation Utilities 
PathSelectMP  Backwards Variable Selection for Paths using M Plus 
patPRO  Visualizing Temporal Microbiome Data 
PatternClass  Classfocused pattern metric comparisons using simulation 
pauwels2014  Bayesian Experimental Design for Systems Biology 
pavo  Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R 
pawacc  Physical activity with accelerometers 
PAWL  Implementation of the PAWL algorithm 
pbapply  Adding Progress Bar to '*apply' Functions 
pbatR  P2BAT 
PBD  Protracted BirthDeath Model of Diversification 
pbdBASE  Programming with Big Data – Base Wrappers for Distributed
Matrices 
pbdDEMO  Programming with Big Data – Demonstrations and Examples Using
'pbdR' Packages 
pbdDMAT  Programming with Big Data – Distributed Matrix Methods 
pbdMPI  Programming with Big Data – Interface to MPI 
pbdNCDF4  Programming with Big Data – Interface to Parallel Unidata
NetCDF4 Format Data Files 
pbdPROF  Programming with Big Data — MPI Profiling Tools 
pbdSLAP  Programming with Big Data – Scalable Linear Algebra Packages 
pbdZMQ  Programming with Big Data – Interface to ZeroMQ 
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' 
pbivnorm  Vectorized Bivariate Normal CDF 
pbkrtest  Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison 
pbmcapply  Tracking the Progress of Mc*pply with Progress Bar 
pbo  Probability of Backtest Overfitting 
pBrackets  Plot Brackets 
pbs  Periodic B Splines 
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 
pca3d  Three Dimensional PCA Plots 
PCA4TS  Segmenting Multiple Time Series by Contemporaneous Linear
Transformation 
pcaBootPlot  Create 2D Principal Component Plots with Bootstrapping 
pcadapt  Fast Principal Component Analysis for Outlier Detection 
pcaL1  Three L1Norm PCA Methods 
pcalg  Methods for Graphical Models and Causal Inference 
PCAmixdata  Multivariate Analysis of Mixed Data 
pcaPP  Robust PCA by Projection Pursuit 
PCDSpline  Semiparametric regression analysis of panel count data using
monotone splines 
pcev  Principal Component of Explained Variance 
pcg  Preconditioned Conjugate Gradient Algorithm for solving Ax=b 
PCGSE  Principal Component Gene Set Enrichment 
pch  Piecewise Constant Hazards Models for Censored and Truncated
Data 
PCICt  Implementation of POSIXct workalike for 365 and 360 day
calendars 
pcIRT  IRT Models for Polytomous and Continuous Item Responses 
PCIT  Partial Correlation Coefficient with Information Theory 
pcnetmeta  PatientCentered Network MetaAnalysis 
pco  Panel Cointegration Tests 
PCovR  Principal Covariates Regression 
PCPS  Principal Coordinates of Phylogenetic Structure 
pcrsim  Simulation of the Forensic DNA Process 
PCS  Calculate the probability of correct selection (PCS) 
pcse  PanelCorrected Standard Error Estimation in R 
pdc  Permutation Distribution Clustering 
pdfCluster  Cluster analysis via nonparametric density estimation 
pdfetch  Fetch Economic and Financial Time Series Data from Public
Sources 
pdftables  Programmatic Conversion of PDF Tables 
pdftools  Extract Text and Data from PDF Documents 
pdist  Partitioned Distance Function 
pdmod  Proximal/distal modeling framework for Pavlovian conditioning
phenomena 
pdolsms  Panel Dynamic OLS Estimation of Cointegrating Vectors 
PDQutils  PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations 
pdR  Threshold Model and Unit Root Tests in Panel Data 
PDSCE  Positive definite sparse covariance estimators 
Peacock.test  Two and Three Dimensional KolmogorovSmirnov TwoSample Tests 
peacots  Periodogram Peaks in Correlated Time Series 
peakPick  Peak Picking Methods Inspired by Biological Data 
Peaks  Peaks 
pear  Package for Periodic Autoregression Analysis 
pearson7  Maximum Likelihood Inference for the Pearson VII Distribution
with Shape Parameter 3/2 
PearsonDS  Pearson Distribution System 
PearsonICA  Independent component analysis using score functions from the
Pearson system 
pec  Prediction Error Curves for Risk Prediction Models in Survival
Analysis 
pedantics  Functions to facilitate power and sensitivity analyses for
genetic studies of natural populations 
PedCNV  An implementation for association analysis with CNV data 
pedgene  GeneLevel Statistics for Pedigree Data 
pedigree  Pedigree functions 
pedigreemm  Pedigreebased mixedeffects models 
pedometrics  Pedometric Tools and Techniques 
pegas  Population and Evolutionary Genetics Analysis System 
PEIP  Geophysical Inverse Theory and Optimization 
PEMM  A Penalized EM algorithm incorporating missingdata mechanism 
pems.utils  Portable Emissions (and Other Mobile) Measurement System
Utilities 
penalized  L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model 
penalizedLDA  Penalized Classification using Fisher's Linear Discriminant 
penalizedSVM  Feature Selection SVM using penalty functions 
pencopula  Flexible Copula Density Estimation with Penalized Hierarchical
BSplines 
PenCoxFrail  Regularization in Cox Frailty Models 
pendensity  Density Estimation with a Penalized Mixture Approach 
penDvine  Flexible PairCopula Estimation in DVines using Bivariate
Penalized Splines 
penMSM  Estimating Regularized Multistate Models Using L1 Penalties 
pensim  Simulation of highdimensional data and parallelized repeated
penalized regression 
peperr  Parallelised Estimation of Prediction Error 
peplib  Peptide Library Analysis Methods 
PepPrep  Insilico peptide mutation, digestion and homologous comparison 
peptider  Evaluation of Diversity in Nucleotide Libraries 
Peptides  Calculate Indices and Theoretical Properties of Protein
Sequences 
pequod  Moderated Regression Package 
perARMA  Periodic Time Series Analysis 
Perc  Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network 
perccal  Implementing Double Bootstrap Linear Regression Confidence
Intervals Using the 'perccal' Method 
PerFit  Person Fit 
PerfMeas  PerfMeas: Performance Measures for ranking and classification
tasks 
PerformanceAnalytics  Econometric tools for performance and risk analysis 
performanceEstimation  An InfraStructure for Performance Estimation of Predictive
Models 
pergola  Toolbox for Polyploid Genetic Data 
perm  Exact or Asymptotic permutation tests 
PermAlgo  Permutational Algorithm to Simulate Survival Data 
PerMallows  Permutations and Mallows Distributions 
permGPU  Using GPUs in Statistical Genomics 
permPATH  Permutation Based Gene Expression Pathway Analysis 
permubiome  A Permutation Based Test for Biomarker Discovery in Microbiome
Data 
permutations  Permutations of a Finite Set 
permute  Functions for Generating Restricted Permutations of Data 
perry  Resamplingbased prediction error estimation for regression
models 
persiandictionary  English to Persian dictionary 
personograph  Pictographic Representation of Treatment Effects 
perspectev  Permutation of Species During Turnover Events 
perturb  Tools for evaluating collinearity 
pesticides  Analysis of single serving and composite pesticide residue
measurements 
PET  Simulation and Reconstruction of PET Images 
pETM  Penalized Exponential Tilt Model 
pewdata  Reproducible Retrieval of Pew Research Center Datasets 
pez  Phylogenetics for the Environmental Sciences 
pfa  Estimates False Discovery Proportion Under Arbitrary Covariance
Dependence 
pgam  PoissonGamma Additive Models 
PGEE  Penalized Generalized Estimating Equations in HighDimension 
PGICA  Parallel Group ICA Algorithm 
pgirmess  Data Analysis in Ecology 
pglm  panel generalized linear model 
pGLS  Generalized Least Square in comparative Phylogenetics 
PGM2  Recursive method for construction of nested resolvable designs
and uniform designs associated 
pGMGM  Estimating Multiple Gaussian Graphical Models (GGM) in Penalized
Gaussian Mixture Models (GMM) 
pgmm  Parsimonious Gaussian Mixture Models 
pgnorm  The pGeneralized Normal Distribution 
pgraph  Build Dependency Graphs using Projection 
PGRdup  Discover Probable Duplicates in Plant Genetic Resources
Collections 
pgs  Precision of Geometric Sampling 
ph2bayes  Bayesian SingleArm Phase II Designs 
ph2bye  Phase II Clinical Trial Design Using Bayesian Methods 
phalen  Phalen Algorithms and Functions 
phangorn  Phylogenetic Analysis in R 
PharmacoGx  Analysis of LargeScale Pharmacogenomic Data 
PharmPow  Pharmacometric Power calculations for mixed study designs 
phaseR  Phase Plane Analysis of One and Two Dimensional Autonomous ODE
Systems 
PhaseType  Inference for Phasetype Distributions 
phcfM  Modelling anthropogenic deforestation 
pheatmap  Pretty Heatmaps 
phenability  Nonparametric Stability Analysis 
phenex  Auxiliary Functions for Phenological Data Analysis 
PHENIX  Phenotypic Integration Index 
phenmod  Auxiliary functions for phenological data processing, modelling
and result handling 
pheno  Auxiliary functions for phenological data analysis 
pheno2geno  HighThroughput Generation of Genetic Markers and Maps from
Molecular Phenotypes for Crosses Between Inbred Strains 
phenology  Tools to Manage a Parametric Function that Describes Phenology 
PHeval  Evaluation of the Proportional Hazards Assumption with a
Standardized Score Process 
phia  PostHoc Interaction Analysis 
phmm  Proportional Hazards Mixedeffects Model (PHMM) 
phonenumber  Convert Letters to Numbers and Back as on a Telephone Keypad 
phonics  Phonetic Spelling Algorithms 
phonR  Tools for Phoneticians and Phonologists 
phonTools  Tools for Phonetic and Acoustic Analyses 
photobiology  'Photobiological' Calculations 
photobiologyInOut  Read Spectral Data from Foreign Files 
photobiologyWavebands  Waveband Definitions for UV, VIS, and IR Radiation 
phreeqc  R Interface to Geochemical Modeling Software 
phtt  Panel Data Analysis with Heterogeneous Time Trends 
PhViD  PhViD: an R package for PharmacoVigilance signal Detection 
Phxnlme  Run Phoenix NLME and Perform PostProcessing 
PhyActBedRest  Marks periods of sleep in Actigraph accelerometer data 
phyclust  Phylogenetic Clustering (Phyloclustering) 
phyext2  An Extension (for Package 'SigTree') of Some of the Classes in
Package 'phylobase' 
phylin  Spatial Interpolation of Genetic Data 
phylobase  Base Package for Phylogenetic Structures and Comparative Data 
phyloclim  Integrating Phylogenetics and Climatic Niche Modeling 
phylocurve  Phylogenetic Comparative Methods for HighDimensional Traits 
PHYLOGR  Functions for Phylogenetically Based Statistical Analyses 
phyloland  Modelling Competitive Exclusion and Limited Dispersal in a
Statisti 