Package Index


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Packages in the standard library

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

a4Automated Affymetrix Array Analysis Umbrella Package
a4BaseAutomated Affymetrix Array Analysis Base Package
a4ClassifAutomated Affymetrix Array Analysis Classification Package
a4CoreAutomated Affymetrix Array Analysis Core Package
a4PreprocAutomated Affymetrix Array Analysis Preprocessing Package
a4ReportingAutomated Affymetrix Array Analysis Reporting Package
ABarrayMicroarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
abcTools for Approximate Bayesian Computation (ABC)
abcdeFBAABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.
abdThe Analysis of Biological Data
abindCombine multi-dimensional arrays
abmiData Processing and Analysis for the Alberta Biodiversity Monitoring Institute
abmiOldData Processing and Analysis for the Alberta Biodiversity Monitoring Institute
abnData Modelling with Additive Bayesian Networks
AcceptanceSamplingCreation and evaluation of Acceptance Sampling Plans
ACCLMAACC & LMA Graph Plotting
AceAssay-based Cross-sectional Estimation of incidence rates
acepackace() and avas() for selecting regression transformations
acerThe ACER Method for Extreme Value Estimation
aCGHClasses and functions for Array Comparative Genomic Hybridization data.
aCGH.SplineRobust spline interpolation for dual color array comparative genomic hybridisation data
AcinonyxiPlots eXtreme
ACMEAlgorithms for Calculating Microarray Enrichment (ACME)
ACNEAffymetrix SNP probe-summarization using non-negative matrix factorization
acsDownload and manipulate data from the US Census American Community Survey
ActigraphyActigraphy Data Analysis
actogramActogram plots
actuarActuarial functions
ActuDistnsFunctions for actuarial scientists
adaada: an R package for stochastic boosting
adabagApplies multiclass AdaBoost.M1, AdaBoost-SAMME and Bagging
ADaCGH2Analysis of data from aCGH experiments using parallel computing and ff objects
adagioDiscrete and Global Optimization Routines
AdaptFitAdaptive Semiparametic Regression
AdaptFitOSAdaptive Semiparametric Regression with Simultaneous Confidence Bands
adaptivetauTau-leaping stochastic simulation
adaptMCMCImplementation of a generic adaptive Monte Carlo Markov Chain sampler
adaptTestAdaptive two-stage tests
addendumThings that R needs for day to day use
ade4Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences
ade4TkGUIade4 Tcl/Tk Graphical User Interface
adegenetadegenet: an R package for the exploratory analysis of genetic and genomic data.
adehabitatAnalysis of habitat selection by animals
adehabitatHRHome range Estimation
adehabitatHSAnalysis of habitat selection by animals
adehabitatLTAnalysis of animal movements
adehabitatMATools to Deal with Raster Maps
adephyloadephylo: exploratory analyses for the phylogenetic comparative method.
ADGofTestAnderson-Darling GoF test
adimproAdaptive Smoothing of Digital Images
adkAnderson-Darling K-Sample Test and Combinations of Such Tests
adliftAn adaptive lifting scheme algorithm
ADM3An Interpretation of the ADM method - automated detection algorithm.
adme16cod.dbGE CodeLink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)
AdMitAdaptive Mixture of Student-t distributions
adsSpatial point patterns analysis
adSplitAnnotation-Driven Clustering
AEMTools to construct Asymmetric eigenvector maps (AEM) spatial variables
AERApplied Econometrics with R
afcCalculate afc
afeAnalysis of Factorial Experiments
afexAnalysis of Factorial Experiments
affxparserAffymetrix File Parsing SDK
affyMethods for Affymetrix Oligonucleotide Arrays
affycompGraphics Toolbox for Assessment of Affymetrix Expression Measures
AffyCompatibleAffymetrix GeneChip software compatibility
affycompDataaffycomp data
affyContamstructured corruption of affymetrix cel file data
affycoretoolsFunctions useful for those doing repetitive analyses with Affymetrix GeneChips.
affydataAffymetrix Data for Demonstration Purpose
AffyExpressAffymetrix Quality Assessment and Analysis Tool
affyILMLinear Model of background subtraction and the Langmuir isotherm
affyioTools for parsing Affymetrix data files
affylmGUIGUI for affy analysis using limma package
AffymetrixDataTestFilesAffymetrix data files (CEL, CDF, CHP, EXP, PSI) for testing
affyParaParallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
affypdnnProbe Dependent Nearest Neighbours (PDNN) for the affy package
affyPLMMethods for fitting probe-level models
affyQCReportQC Report Generation for affyBatch objects
AffyRNADegradationAnalyze and correct probe positional bias in microarray data due to RNA degradation
AffyTilingEasy extraction of individual probes in Affymetrix tiling arrays
AFLPAnalysis of AFLP data
afmtoolsEstimation, Diagnostic and Forecasting Functions for ARFIMA models
africaAnother Fast R algorithm for Independent Component Analysis
aftgeeAccelerated Failure Time Model with Generalized Estimating Equations
ag.dbAffymetrix Arabidopsis Genome Array annotation data (chip ag)
agcdfagcdf
AGDAnalysis of Growth Data
AGDEXAgreement of Differential Expression Analysis
agepriorPrior distributions for molecular dating
aggriskEstimate individual level risk using individual case data and spatially aggregated control data
Agi4x44PreProcessPreProcessing of Agilent 4x44 array data
agilpExtracting and preprocessing Agilent express arrays
AgiMicroRnaProcessing and Differential Expression Analysis of Agilent microRNA chips
agprobeProbe sequence data for microarrays of type ag
AgreementStatistical Tools for Measuring Agreement
agricolaeStatistical Procedures for Agricultural Research
agridatAgricultural datasets
agrmtCalculates agreement A
agrometTools for agro-meteorological analysis
AGSDestEstimation in adaptive group sequential trials
ahazRegularization for semiparametric additive hazards regression
AICcmodavgModel selection and multimodel inference based on (Q)AIC(c)
AIGISAreal Interpolation for GIS data
AIMAIM: adaptive index model
akimaInterpolation of irregularly spaced data
ALAData sets and examples for the book "Applied Longitudinal Analysis"
alabamaConstrained nonlinear optimization
alfaApache Log File Analysis
AlgDesignAlgorithmic Experimental Design
ALLA data package
allanAutomated Large Linear Analysis Node
allanvarAllan Variance Analysis
allelematchIdentifying unique multilocus genotypes where genotyping error and missing data may be present
AlleleRetainAllele Retention, Inbreeding, and Demography
allelicA fast, unbiased and exact allelic exact test
ALLMLLA subset of arrays from a large acute lymphoblastic leukemia (ALL) study
AllPossibleSpellingsComputes all of a word's possible spellings.
alphahullGeneralization of the convex hull of a sample of points in the plane
alphashape3dImplementation of the 3D alpha-shape for the reconstruction of 3D sets from a point cloud
alplotPlot array lists
alralternating logistic regression
alr3Data to accompany Applied Linear Regression 3rd edition
ALSmultivariate curve resolution alternating least squares (MCR-ALS)
altcdfenvsalternative CDF environments (aka probeset mappings)
AMAAnderson-Moore Algorithm
amapAnother Multidimensional Analysis Package
AMAP.SeqCompare Gene Expressions from 2-Treatment RNA-Seq Experiments
amburAnalyzing Moving Boundaries Using R
ameiAdaptive Management of Epidemiological Interventions
AmeliaAmelia II: A Program for Missing Data
amenAdditive and multiplicative effects modeling of networks and relational data
amerAdditive mixed models with lme4
AmericanCallOptThis package includes pricing function for selected American call options with underlying assets that generate payouts.
AMOREA MORE flexible neural network package
AmpAffyExampleExample of Amplified Data
anacorSimple and Canonical Correspondence Analysis.
anaglyph3D Anaglyph Plots
analogueAnalogue and weighted averaging methods for palaeoecology
AnalyzeFMRIFunctions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.
anametrixConnects to Anametrix
anapuceTools for microarray data analysis
andrewsAndrews curves
anesrakeANES Raking Implementation
anchorsStatistical analysis of surveys with anchoring vignettes
AnimalAnalyze time-coded animal behavior data
animationA gallery of animations in statistics and utilities to create animations
anmAnalog model for downscaling
ANNFeedforward Artificial Neural Network optimized by Genetic Algorithm
annaffyAnnotation tools for Affymetrix biological metadata
annotateAnnotation for microarrays
AnnotationDbiAnnotation Database Interface
AnnotationFuncsAnnotation translation functions
annotationToolsAnnotate microarrays and perform cross-species gene expression analyses using flat file databases.
AnnotListsAnnotLists: A tool to annotate multiple lists from a specific annotation file.
anointAnalysis of interactions
anopheles.db0Base Level Annotation databases for anopheles
anotaANalysis Of Translational Activity (ANOTA).
antVersion of ant specific to R
aodAnalysis of Overdispersed Data
apclusterAffinity Propagation Clustering
apComplexEstimate protein complex membership using AP-MS protein data
apeAnalyses of Phylogenetics and Evolution
aplAPL array manipulation functions
aplpackAnother Plot PACKage: stem.leaf, bagplot, faces, spin3R, and some slider functions
appellCompute Appell's F1 hypergeometric function
appleApproximate Path for Penalized Likelihood Estimators
approximatorBayesian prediction of complex computer codes
APSIMBatchAnalysis the output of Apsim software
apsrtableapsrtable model-output formatter for social science
aptAsymmetric Price Transmission (apt)
apTreeshapeAnalyses of Phylogenetic Treeshape
aqfigFunctions to help display air quality model output and monitoring data
aqpAlgorithms for Quantitative Pedology
AquaEnvAquaEnv - an integrated development toolbox for aquatic chemical model generation
arabidopsis.db0Base Level Annotation databases for arabidopsis
aratioAssessment ratio analysis
aresEnvironment air pollution epidemiology: a library for time series analysis
arf3DS4Activated Region Fitting, fMRI data analysis (3D).
arfS4Activated Region Fitting, fMRI data analysis.
argosfilterArgos locations filter
argparseCommand line optional and positional argument parser.
archetypesArchetypal Analysis
armData Analysis Using Regression and Multilevel/Hierarchical Models
armliteData Analysis Using Regression
aroma.affymetrixAnalysis of large Affymetrix microarray data sets
aroma.agilentAnalysis of Agilent microarray data [A DRAFT - TRUE]
aroma.apdA probe-level data file format used by aroma.affymetrix [DEPRECATED]
aroma.axonAnalysis of Axon GenePix microarray data [A DRAFT - TRUE]
aroma.cnCopy-number analysis of large microarray data sets
aroma.cn.evalPackage for evaluating copy-number estimates
aroma.coreCore methods and classes used by aroma.* packages part of The Aroma Framework
aroma.illuminaAnalysis of Illumina microarray data [A DRAFT - TRUE]
aroma.lightLight-weight methods for normalization and visualization of microarray data using only basic R data types
aroma.seqSequence analysis in the Aroma Framework
aroma.tcgaMethods for accessing online The Cancer Genome Atlas (TCGA) data
arrayArray factor for 2D periodic arrays
ArrayExpressAccess the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
arrayhelpersConvenience functions for arrays
arrayMvoutmultivariate outlier detection for expression array QA
arrayQualityAssessing array quality on spotted arrays
arrayQualityMetricsQuality metrics on microarray data sets
ArrayToolsgeneChip Analysis Package
arsAdaptive Rejection Sampling
artApplied Regression Tools
ARTIVAWhat the package does (short line)
arulesMining Association Rules and Frequent Itemsets
arulesNBMinerMining NB-Frequent Itemsets and NB-Precise Rules
arulesSequencesMining frequent sequences
arulesVizarulesViz - Visualizing Association Rules and Frequent Itemsets
arulesVizOldarulesViz - Visualizing Association Rules and Frequent Itemsets
ASAtableModel-output formatter for sociological research.
asbioA collection of statistical tools for biologists
asciiExport R objects to several markup languages
ascrdaAugmented SCRDA
asdSimulations for adaptive seamless designs
ASEBPredict Acetylated Lysine Sites
ashDavid Scott's ASH routines
aspaceA collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns
aspectAspects of Multivariables
assertiveReadable check functions to ensure code integrity.
ASSETAn R package for subset-based association analysis of heterogeneous traits and subtypes
assistA Suite of S-Plus Functions Implementing Smoothing Splines
AssotesteRStatistical Tests for Genetic Association Studies
asterAster Models
aster2Aster Models
astroFnsAstronomy: time and position functions, misc. utilities
astsaApplied Statistical Time Series Analysis
asuRAdvanced statistics using R
asympTestAsymptotic statistic
asypowCalculate Power Utilizing Asymptotic Likelihood Ratio Methods
AtelieRA GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests.
ath1121501.dbAffymetrix Arabidopsis ATH1 Genome Array annotation data (chip ath1121501)
ath1121501cdfath1121501cdf
ath1121501probeProbe sequence data for microarrays of type ath1121501
AtmRayAcoustic Traveltime Calculations for 1-D Atmospheric Models
attractMethods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
AUCRFVariable Selection with Random Forest and the Area Under the Curve
audioAudio Interface for R
auditBounds for Accounting Populations
aurelhyHydrometeorological interpolation
austinA package for doing things with words
auteurBayesian sampler of the trait-evolutionary process
automapAutomatic interpolation package
AutoSEARCHGeneral-to-Specific (GETs) Model Selection
awsAdaptive Weights Smoothing
AWS.toolsR package to use Amazon Web Services
awsMethodsClass and Methods definitions for packages aws, adimpro, fmri, dwi
aylmerA generalization of Fisher's exact test
B2ZBayesian Two-Zone Model
BaBooNBayesian Bootstrap Predictive Mean Matching - Multiple and single imputation for discrete data
BACBayesian Analysis of Chip-chip experiment
BACCOBayesian Analysis of Computer Code Output (BACCO)
backgroundThis packages allow users to ``background'' computations.
backtestExploring portfolio-based conjectures about financial instruments
BADGERA package for identifying sample mixups in combined expression and genotyping studies.
BaMFunctions and datasets for books by Jeff Gill.
BAMDBayesian Association Model for Genomic Data with Missing Covariates
bamditBayesian Meta-Analysis of diagnostic test data
bamsBreakpoint annotation model smoothing
banditFunctions for simple A/B split test and multi-armed bandit analysis
barcodeBarcode distribution plots
barkBayesian Additive Regresssion Kernels
barley1cdfbarley1cdf
barley1probeProbe sequence data for microarrays of type barley1
BarnardBarnard's Unconditional Test
BASBayesian Model Averaging using Bayesian Adaptive Sampling
BaSARBayesian Spectrum Analysis in R
baseThe R Base Package
base64Base 64 encoder/decoder
baselineBaseline Correction of Spectra
basicspaceA Package to Recover a Basic Space from Issue Scales
BaSTAA package for estimating age-specific survival from incomplete capture-recapture/recovery data
batadeHTML reports and so on
batchBatching Routines in Parallel and Passing Command-Line Arguments to R
BatchExperimentsStatistical experiments on batch computing clusters.
BatchJobsBatch computing with R.
batchmeansConsistent Batch Means Estimation of Monte Carlo Standard Errors
baybiBayesian Biclustering with Subject and Variable Importance
bayesclustTests/Searches for significant clusters in genetic data.
bayescountPower calculations and Bayesian analysis of count distributions and FECRT data using MCMC
BayesDAFunctions and Datasets for the book "Bayesian Data Analysis"
bayesDemGraphical User Interface for bayesTFR, bayesLife and bayesPop
BayesFactors.gibiCompute Bayes factors using the GIBI interface
bayesGARCHBayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
BayesLCABayesian Latent Class Analysis
bayesLifeBayesian Projection of Life Expectancy
BayesLogitLogistic Regression
bayesmBayesian Inference for Marketing/Micro-econometrics
bayesMCClustMixtures-of-Experts Markov Chain Clustering and Dirichlet Multinomial Clustering
bayesmixBayesian Mixture Models with JAGS
bayespackNumerical Integration for Bayesian Inference
BayesPeakBayesian Analysis of ChIP-seq Data
bayesPopProbabilistic Population Projection
bayesprefHierarchical Bayesian analysis of ecological count data
bayesQRBayesian quantile regression
BayesQTLBICBayesian multi-locus QTL analysis based on the BIC criterion
BayesSingleSubComputation of Bayes factors for interrupted time-series designs
bayesSurvBayesian Survival Regression with Flexible Error and Random Effects Distributions
bayesTFRBayesian Fertility Projection
BayesthreshBayesian thresholds mixed-effects models for categorical data
BayesTreeBayesian Methods for Tree Based Models
BayesValidateBayesValidate Package
BayesXR Utilities Accompanying the Software Package BayesX
BayesXsrcR Package Distribution of the BayesX C++ Sources
BayHapBayesian analysis of haplotype association using Markov Chain Monte Carlo
BayHazR Functions for Bayesian Hazard Rate Estimation
BaylorEdPsychR Package for Baylor University Educational Psychology Quantitative Courses
baySeqEmpirical Bayesian analysis of patterns of differential expression in count data
BAYSTAROn Bayesian analysis of Threshold autoregressive model (BAYSTAR)
BBSolving and Optimizing Large-Scale Nonlinear Systems
bbemkrBayesian bandwidth estimation for multivariate kernel regression with Gaussian error
BBmiscMiscellaneous helper functions for B. Bischl.
bbmleTools for general maximum likelihood estimation
BBMMBrownian bridge movement model
BCABusiness and Customer Analytics
BCBCSFBias-corrected Bayesian Classification with Selected Features
BCEBayesian composition estimator: estimating sample (taxonomic) composition from biomarker data
BCEABayesian Cost Effectiveness Analysis
BclimBayesian Palaeoclimate Reconstruction from Pollen
bclustBayesian clustering using spike-and-slab hierarchical model, suitable for clustering high-dimensional data.
bcpA Package for Performing a Bayesian Analysis of Change Point Problems
BCRANKPredicting binding site consensus from ranked DNA sequences
bcrmBayesian continuous reassessment method (CRM) designs for Phase I dose-finding trials.
bcvCross-Validation for the SVD (Bi-Cross-Validation)
bdaAlgorithms for Binned/Weighted Data Analysis
bdpvInference and design for predictive values in binary diagnostic tests
bdsmatrixRoutines for Block Diagonal Symmetric matrices
beadarrayQuality assessment and low-level analysis for Illumina BeadArray data
beadarrayExampleDataExample data for the beadarray package
beadarrayFilterBead filtering for Illumina bead arrays
beadarrayMSVAnalysis of Illumina BeadArray SNP data including MSV markers
beadarraySNPNormalization and reporting of Illumina SNP bead arrays
BeadArrayUseCasesAnalysing Illumina BeadArray expression data using Bioconductor
BeadDataPackRCompression of Illumina BeadArray data
beanplotVisualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
bearAverage bioequivalence and bioavailability data analysis tool
beeswarmThe bee swarm plot, an alternative to stripchart
beliefContains basic functions to manipulate belief functions and associated mass assignments
benchden28 benchmark densities from Berlinet/Devroye (1994)
benchmarkBenchmark Experiments Toolbox
BenchmarkingBenchmark and frontier analysis using DEA and SFA
bentcableARBent-Cable Regression for Independent Data or Autoregressive Time Series
berBatch Effects Removal
BergmBayesian analysis for exponential random graph models
BerkeleyEarthData Input for Berkeley Earth Surface Temperature
bertinBertin matrix display
BesselBessel -- Bessel Functions Computations and Approximations
bestglmBest Subset GLM
beta7Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7.
betafamDetecting rare variants for quantitative traits using nuclear families
betapartPartitioning beta diversity into turnover and nestedness components
betaperFunctions to incorporate taxonomic uncertainty on multivariate analyses of ecological data
betaregBeta Regression
betategarchEstimation and simulation of the first-order Beta-t-EGARCH model
betfairlyAccess Betfair API from R
bethelBethel's algorithm.
betrIdentify differentially expressed genes in microarray time-course data
bfaBayesian Factor Analysis
bfastBreaks For Additive Season and Trend (BFAST)
bfpBayesian Fractional Polynomials
bgafunBGAfun A method to identify specifity determining residues in protein families
bgmmGaussian Mixture Modeling algorithms. Including the belief-based mixture modeling.
bgraphBayesian Graphical Models
BGSIMDBlock Gibbs Sampler with Incomplete Multinomial Distribution
bgxBayesian Gene eXpression
BHCBayesian Hierarchical Clustering
BHH2Useful Functions for Box, Hunter and Hunter II
BchronBayesian chronologies via compound Poisson-Gamma processes.
BiasedUrnBiased Urn model distributions
bibtexbibtex parser
BicAREBiclustering Analysis and Results Exploration
biclustBiCluster Algorithms
bifactorialInferences for bi- and trifactorial trial designs
biganalyticsA library of utilities for big.matrix objects of package bigmemory.
bigdataBig Data Analytics
BiGGRCreates an interface to BiGG database, provides a framework for simulation and produces flux graphs
biglarsScalable Least-Angle Regression and Lasso
biglmbounded memory linear and generalized linear models
bigmatrixTuning Insensitive Graph Estimation and Regression
bigmemoryManage massive matrices with shared memory and memory-mapped files
bigmlR bindings for the BigML API
bigRRGeneralized Ridge Regression (with special advantage for p >> n cases)
bigtabulatetable-, tapply-, and split-like functionality for matrix and big.matrix objects.
BigTSPTop Scoring Pair based methods for classification
bildbild: a package for BInary Longitudinal Data
bimetallicPower for SNP analyses using silver standard cases
binarySimCLFSimulates Correlated Binary Data
BINCOBootstrap Inference for Network COstruction
bindataGeneration of Artificial Binary Data
binGroupEvaluation and experimental design for binomial group testing
binhfHaar-Fisz functions for binomial data
binMtoAsymptotic simultaneous confidence intervals for many-to-one comparisons of proportions
BinNorSimultaneous generation of multivariate binary and normal variates.
binomBinomial Confidence Intervals For Several Parameterizations
binomlogitEfficient MCMC for Binomial Logit Models
binomToolsPerforming diagnostics on binomial regression models
bio.inferPredict environmental conditions from biological observations
BiobaseBiobase: Base functions for Bioconductor
BioCalcBioclim Variables Calculator
BiocCaseStudiesBiocCaseStudies: Support for the Case Studies Monograph
BiocGenericsGeneric functions for Bioconductor
biocGraphGraph examples and use cases in Bioinformatics
BiocInstallerInstall/Update Bioconductor and CRAN Packages
biocViewsCategorized views of R package repositories
BiodemBiodemography functions
bioDistDifferent distance measures
BiodiversityRGUI for biodiversity and community ecology analysis
BiographExplore life histories
BioMarkFind biomarkers in two-class discrimination problems
BiomarkeRPaired (pBI) and Unpaired Biomarker Identifier (uBI) including a method to infer networks.
biomaRtInterface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)
BIOMODEnsemble platform for species distribution modeling
biomod2Ensemble platform for species distribution modeling
BioMVCClassModel-View-Controller (MVC) Classes That Use Biobase
BioNetRoutines for the functional analysis of biological networks
bionetdataBiological and chemical data networks
bioparaSelf-contained parallel system for R
BioPhysConnectoRBioPhysConnectoR
biOpsImage processing and analysis
biOpsGUIGUI for Basic image operations
bios2mdsFrom BIOlogical Sequences to MultiDimensional Scaling
BioSeqClassClassification for Biological Sequences
BioStatRInitiation a la Statistique avec R
BiostringsString objects representing biological sequences, and matching algorithms
biovizBaseBasic graphic utilities for visualization of genomic data.
bipartiteVisualising bipartite networks and calculating some (ecological) indices.
BiplotGUIInteractive Biplots in R
birchDealing with very large datasets using BIRCH
birtaBayesian Inference of Regulation of Transcriptional Activity
biseAuxiliary functions for phenological data analysis
bisectrTools to find bad commits with git bisect
biseVecAuxiliary functions for phenological data analysis
bisoregBayesian Isotonic Regression with Bernstein Polynomials
bitA class for vectors of 1-bit booleans
bit64A S3 class for vectors of 64bit integers
bitopsFunctions for Bitwise operations
BitSeqTranscript expression inference and differential expression analysis for RNA-seq data
biVarBias-Variance Analysis of the Misclassification Rate
bivarRIpowerSample size calculations for bivariate longitudinal data
biwaveletConduct univariate and bivariate wavelet analyses
biwtFunctions to compute the biweight mean vector and covariance & correlation matrices
bladderbatchBladder gene expression data illustrating batch effects
BlakerCIBlaker's binomial confidence limits
BLCOPBlack-Litterman and copula-opinion pooling frameworks
blenderAnalyze biotic homogenization of landscapes
blightyUnited Kingdom coastlines
blmBinomial linear and linear-expit regression
blmeBayesian Linear Mixed-Effects models
blockclusterCo-Clustering package for Binary, contingency and continuous data-sets.
blockmodelingAn R package for Generalized and classical blockmodeling of valued networks
blockrandRandomization for block random clinical trials
blockToolsBlock, assign, and diagnose potential interference in randomized experiments
blotterTools for transaction-oriented trading systems development.
BLRBayesian Linear Regression
BMABayesian Model Averaging
bmdBenchmark dose analysis for dose-response data
bmemMediation analysis with missing data using bootstrap
BmixBayesian Sampling for Stick-breaking Mixtures
BMNThe pseudo-likelihood method for pairwise binary markov networks
bmpRead Windows Bitmap (BMP) images
bnlearnBayesian network structure learning, parameter learning and inference
BNPdensityFerguson-Klass type algorithm for posterior normalized random measures
boaBayesian Output Analysis Program (BOA) for MCMC
BolstadBolstad functions
Bolstad2Bolstad functions
bomDataRipperBOM data getter
booleanBoolean Binary Response Models
boolfunCryptographic Boolean Functions
BoolNetGeneration, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
boostSeqOptimized GWAS cohort subset selection for resequencing studies
bootBootstrap Functions (originally by Angelo Canty for S)
bootESBootstrap Effect Sizes
BootPRBootstrap Prediction Intervals and Bias-Corrected Forecasting
bootResBootstrapped Response and Correlation Functions
bootruinA bootstrap test for the probability of ruin in the classical risk process
bootspecdensTesting equality of spectral densities
bootStepAICBootstrap stepAIC
bootstrapFunctions for the Book "An Introduction to the Bootstrap"
BorutaBoruta -- a tool for finding significant attributes in information systems
bossBoosted One-Step Statistics: Fast and accurate approximations for GLM, GEE and Mixed models for use in GWAS
BoSSAa Bunch of Structure and Sequence Analysis
boussinesqAnalytic Solutions for (ground-water) Boussinesq Equation
bovine.dbAffymetrix bovine annotation data (chip bovine)
bovine.db0Base Level Annotation databases for bovine
bovinecdfbovinecdf
bovineprobeProbe sequence data for microarrays of type bovine
bpcaBiplot of Multivariate Data Based on Principal Components Analysis
bpcpBeta Product Confidence Procedure for Right Censored Data
BPHOBayesian Prediction with High-order Interactions
bpkdeBack Projected Kernel Density Estimation
bpmBasic functions for panel data analysis
bptwinCumulative incidence models for twin data
bqtlBayesian QTL mapping toolkit
BradleyTerryBradley-Terry Models -- this package is now deprecated in favour of 'BradleyTerry2'
BradleyTerry2Bradley-Terry Models
BrailleRImproved access for blind useRs
BRAINBaffling Recursive Algorithm for Isotope distributioN calculations
BrainStarsquery gene expression data and plots from BrainStars (B*)
brainwaverBasic wavelet analysis of multivariate time series with a visualisation and parametrisation using graph theory.
breakageSICM pipette tip geometry estimation
breastCancerMAINZGene expression dataset published by Schmidt et al. [2008] (MAINZ).
breastCancerNKIGenexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI).
breastCancerTRANSBIGGene expression dataset published by Desmedt et al. [2007] (TRANSBIG).
breastCancerUNTGene expression dataset published by Sotiriou et al. [2007] (UNT).
breastCancerUPPGene expression dataset published by Miller et al. [2005] (UPP).
breastCancerVDXGene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).
bReezeFunctions for wind resource assessment
brewTemplating Framework for Report Generation
brglmBias reduction in binomial-response GLMs.
bridgeBayesian Robust Inference for Differential Gene Expression
BrobdingnagVery large numbers in R
bronchialIL13time course experiment involving il13
BRugsR interface to the OpenBUGS MCMC software
BSagriStatistical methods for safety assessment in agricultural field trials
BSDABasic Statistics and Data Analysis
BSgenomeInfrastructure for Biostrings-based genome data packages
BSgenome.Alyrata.JGI.v1Arabidopsis lyrata full genome (JGI version V1.0)
BSgenome.Amellifera.BeeBase.assembly4Apis mellifera (Honey Bee) full genome (BeeBase assembly4)
BSgenome.Amellifera.UCSC.apiMel2Apis mellifera (Honey Bee) full genome (UCSC version apiMel2)
BSgenome.Athaliana.TAIR.04232008Arabidopsis thaliana full genome (TAIR version from April 23, 2008)
BSgenome.Athaliana.TAIR.TAIR9Arabidopsis thaliana full genome (TAIR9)
BSgenome.Btaurus.UCSC.bosTau3Bos taurus (Cow) full genome (UCSC version bosTau3)
BSgenome.Btaurus.UCSC.bosTau4Bos taurus (Cow) full genome (UCSC version bosTau4)
BSgenome.Celegans.UCSC.ce2Caenorhabditis elegans (Worm) full genome (UCSC version ce2)
BSgenome.Celegans.UCSC.ce6Caenorhabditis elegans (Worm) full genome (UCSC version ce6)
BSgenome.Cfamiliaris.UCSC.canFam2Canis lupus familiaris full genome (UCSC version canFam2)
BSgenome.Dmelanogaster.UCSC.dm2Drosophila melanogaster (Fly) full genome (UCSC version dm2)
BSgenome.Dmelanogaster.UCSC.dm3Drosophila melanogaster (Fly) full genome (UCSC version dm3)
BSgenome.Drerio.UCSC.danRer5Danio rerio (Zebrafish) full genome (UCSC version danRer5)
BSgenome.Drerio.UCSC.danRer6Danio rerio (Zebrafish) full genome (UCSC version danRer6)
BSgenome.Drerio.UCSC.danRer7Danio rerio (Zebrafish) full genome (UCSC version danRer7)
BSgenome.Ecoli.NCBI.20080805Escherichia coli full genomes
BSgenome.Gaculeatus.UCSC.gasAcu1Gasterosteus aculeatus (Stickleback) full genome (UCSC version gasAcu1)
BSgenome.Ggallus.UCSC.galGal3Gallus gallus (Chicken) full genome (UCSC version galGal3)
BSgenome.Hsapiens.UCSC.hg17Homo sapiens (Human) full genome (UCSC version hg17)
BSgenome.Hsapiens.UCSC.hg18Homo sapiens (Human) full genome (UCSC version hg18)
BSgenome.Hsapiens.UCSC.hg19Homo sapiens (Human) full genome (UCSC version hg19)
BSgenome.Mmulatta.UCSC.rheMac2Macaca mulatta (Rhesus) full genome (UCSC version rheMac2)
BSgenome.Mmusculus.UCSC.mm10Mus musculus (Mouse) full genome (UCSC version mm10)
BSgenome.Mmusculus.UCSC.mm8Mus musculus (Mouse) full genome (UCSC version mm8)
BSgenome.Mmusculus.UCSC.mm9Mus musculus (Mouse) full genome (UCSC version mm9)
BSgenome.Ptroglodytes.UCSC.panTro2Pan troglodytes (Chimp) full genome (UCSC version panTro2)
BSgenome.Rnorvegicus.UCSC.rn4Rattus norvegicus (Rat) full genome (UCSC version rn4)
BSgenome.Scerevisiae.UCSC.sacCer1Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1)
BSgenome.Scerevisiae.UCSC.sacCer2Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2)
BSgenome.Scerevisiae.UCSC.sacCer3Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3)
BSgenome.Tgondii.ToxoDB.7.0Toxoplasma gondii ME49 (ToxoDB-7.0)
BsMDBayes Screening and Model Discrimination
bsmlBasis Selection from Multiple Libraries
bspecBayesian spectral inference
bspmmabspmma: Bayesian Semiparametric Models for Meta-Analysis
bstGradient Boosting
bstatsBasic statistical functions for R
bsubtiliscdfbsubtiliscdf
bsubtilisprobeProbe sequence data for microarrays of type bsubtilis
BTSPASBayesian Time-Strat. Population Analysis
BufferedMatrixA matrix data storage object held in temporary files
BufferedMatrixMethodsMicroarray Data related methods that utlize BufferedMatrix objects
BUGSExamplesCollection of BUGS examples
bujarBuckley-James Regression for Survival Data with High-Dimensional Covariates
BurStFinBurns Statistics Financial
BUSGene network reconstruction
bvennA Simple alternative to proportional Venn diagrams
bvlsThe Stark-Parker algorithm for bounded-variable least squares
bvpSolveSolvers for boundary value problems of ordinary differential equations
BVSBayesian Variant Selection: Bayesian Model Uncertainty Techniques for Genetic Association Studies
bwsurvivalNonparametric conditional survival function for successive survival times
c3netInfering large-scale gene networks with C3NET
caSimple, Multiple and Joint Correspondence Analysis
cacIRTClassification accuracy and consistency under Item Response Theory
CADFtestThis package performs the CADF unit root test proposed in Hansen (1995).
CADStatProvides a GUI to several statistical methods useful for causal assessment.
caGUIA Tcl/Tk GUI for the functions in the ca package
cacherTools for caching and distributing statistical analyses
cacheSweaveTools for caching Sweave computations
CairoR graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output.
cairoDeviceCairo-based cross-platform antialiased graphics device driver.
CalciOMaticAutomatic Calcium Imaging Analysis
CALIBCalibration model for estimating absolute expression levels from microarray data
calibFitStatistical models and tools for assay calibration
calibrateCalibration of Scatterplot and Biplot Axes
calibratorBayesian calibration of complex computer codes
CALINE3R interface to Fortran 77 implementation of CALINE3
calmatePost-calibration of allele-specific copy-number estimates (ASCNs)
CAMERACollection of annotation related methods for mass spectrometry data
cancerdataDevelopment and validation of diagnostic tests from high-dimensional molecular data: Datasets
CancerMutationAnalysisCancer mutation analysis
candiscGeneralized Canonical Discriminant Analysis
candlesticksCandlestick Pattern Recognition
canine.dbAffymetrix canine annotation data (chip canine)
canine.db0Base Level Annotation databases for canine
canine2.dbAffymetrix canine2 annotation data (chip canine2)
canine2cdfcanine2cdf
canine2probeProbe sequence data for microarrays of type canine2
caninecdfcaninecdf
canineprobeProbe sequence data for microarrays of type canine
CANS.worksImport, manipulate and analyze data from the Massachusetts CANS tool
canvasR graphics device targeting the HTML canvas element.
caperComparative Analyses of Phylogenetics and Evolution in R
capusheCapushe, data-driven slope estimation and dimension jump
capwireEstimates population size from non-invasive sampling
carCompanion to Applied Regression
CARBayesSpatial areal unit modelling
CarbonELCarbon Event Loop
cardidatesIdentification of cardinal dates in ecological time series
careHigh-Dimensional Regression and CAR Score Variable Selection
CARE1Statistical package for population size estimation in capture-recapture models.
caretClassification and Regression Training
caretLaTeXLaTeX Classes for the caret Package
caribouEstimation of caribou abundance based on large scale aggregations monitored by radio telemetry
carolineA Collection of Database, Data Structure, Visualization, and Utility Functions for R
CAscalingCA scaling in R
caschronoSÚries temporelles avec R - MÚthodes et cas
casparClustered and sparse regression (CaSpaR)
catAnalysis of categorical-variable datasets with missing values
catdataCategorical Data
CatDynFishery Stock Assessment by Catch Dynamic Models
CategoryCategory Analysis
categoryCompareMeta-analysis of high-throughput experiments using feature annotations
catIrtAn R Package for Simulating IRT-Based Computerized Adaptive Tests
catnetCategorical Bayesian Network Inference
caToolsTools: moving window statistics, GIF, Base64, ROC AUC, etc.
catRProcedures to generate IRT adaptive tests (CAT)
catspecSpecial models for categorical variables
CausalGAMEstimation of Causal Effects with Generalized Additive Models
CAVIARCollection of Functions for Processing, Visualizing and Analyzing Cambial Activity and Wood Formation Monitoring Data
cbaClustering for Business Analytics
cbmiscClaudia's collection of miscellaneous functions
CBPSR Package for Covariate Balancing Propensity Score
CCACanonical correlation analysis
ccaPP(Robust) canonical correlation analysis via projection pursuit
cccdClass Cover Catch Digraphs
cccrmCCC-RM
ccemsCombinatorially Complex Equilibrium Model Selection
ccgarchConditional Correlation GARCH models
CCl4Carbon Tetrachloride (CCl4) treated hepatocytes
cclustConvex Clustering Methods and Clustering Indexes
CCMCorrelation classification method (CCM)
CCMtoolsClustering through "Correlation Clustering Model" (CCM) and cluster analysis tools.
CCPSignificance Tests for Canonical Correlation Analysis (CCA)
ccTutorialData package for ChIP-chip tutorial
cdaCoupled dipole approximation
CDFtStatistical downscaling through CDF-transform
CDMCognitive Diagnosis Modeling
CDNmoneyComponents of Canadian Monetary and Credit Aggregates
CDVineStatistical inference of C- and D-vine copulas
cec2005benchmarkBenchmark for the CEC 2005 Special Session on Real-Parameter Optimization
celegans.dbAffymetrix celegans annotation data (chip celegans)
celeganscdfceleganscdf
celegansprobeProbe sequence data for microarrays of type celegans
cellGrowthFitting cell population growth models
cellHTSAnalysis of cell-based screens
cellHTS2Analysis of cell-based screens - revised version of cellHTS
CellNOptRR version of CellNOpt, boolean features only
CellularAutomatonOne-Dimensional Cellular Automata
cellVolumeDistFunctions to fit cell volume distributions and thereby estimate cell growth rates and division times
cemCEM: Software for Coarsened Exact Matching
cemsConditional expectation manifolds.
censRegCensored Regression (Tobit) Models
CensRegModFitting Normal and Student-t censored regression model.
CENTIPEDECENTIPEDE learns a DNaseI footprint of a transcription factor and predicts its binding sites
CePaCentrality-based pathway enrichment
ceppContext Driven Exploratory Projection Pursuit
ceu1kgCEU (N=60) genotypes from 1000 genomes pilot phase I
ceuhm3ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort
cfaAnalysis of configuration frequencies (CFA)
CFLCompensatory Fuzzy Logic
cgComparison of groups
cgdsrR-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS).
cgdv17Complete Genomics Diversity Panel, chr17 on 46 individuals
CGENAn R package for analysis of case-control studies in genetic epidemiology
CGeneCausal Genetic Analysis
cggdContinuous Generalized Gradient Descent
cghMicroarray CGH analysis using the Smith-Waterman algorithm
CGHbaseCGHbase: Base functions and classes for arrayCGH data analysis.
CGHcallCalling aberrations for array CGH tumor profiles.
cghFLassoDetecting hot spot on CGH array data with fused lasso regression.
cghMCRFind chromosome regions showing common gains/losses
CGHnormaliterNormalization of array CGH data with imbalanced aberrations.
CGHregionsDimension Reduction for Array CGH Data with Minimal Information Loss.
cghsegSegmentation methods for array CGH analysis
CGPComposite Gaussian process models
cimisR package for retrieving data from CIMIS.
cinCausal Inference for Neuroscience
CircNNTSRCircNNTSR: An R package for the statistical analysis of circular data using nonnegative trigonometric sums (NNTS) models
CircStatsCircular Statistics, from "Topics in circular Statistics" (2001)
circularCircular Statistics
CITANCITation ANalysis toolpack
citbcmstAssigning tumor samples to CIT Breast Cancer Molecular Subtypes from gene expression data
citruscdfcitruscdf
citrusprobeProbe sequence data for microarrays of type citrus
CityPlotVisualization of structure and contents of a database
Ckmeans.1d.dpOptimal distance-based clustering for one-dimensional data
classFunctions for Classification
classGraphConstruct Graphs of S4 Class Hierarchies
classiflyExplore classification models in high dimensions
classIntChoose univariate class intervals
clhsConditioned Latin Hypercube Sampling
clim.pactClimate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.
climatesMethods for working with weather & climate
climatolSome Tools for Climatology: series homogenization, plus windrose and Walter&Lieth diagrams
climdex.pcicPCIC implementation of Climdex routines
climeConstrained L1-minimization for Inverse (covariance) Matrix Estimation
climstatsR functions for working with station and gridded climate data.
clinfunClinical Trial Design and Data Analysis Functions
ClinicalRobustPriorsRobust Bayesian Priors in Clinical Trials: An R Package for Practitioners
clinsigClinical significance functions.
clippdaA package for the clinical proteomic profiling data analysis
CLLA Package for CLL Gene Expression Data
ClonalityClonality testing
cloudRmpiCloud-based MPI Parallel Processing for R (cloudRmpi)
cloudRmpiJarsThird-party jars for cloudRmpi
cloudUtilCloud Util Plots
clpAPIR Interface to C API of COIN-OR Clp
CLSOCPA smoothing Newton method SOCP solver
clstClassification by local similarity threshold
clstutilsTools for performing taxonomic assignment.
clueCluster ensembles
cluesClustering Method Based on Local Shrinking
clustDDistClustering Discrete Distributions
clusterCluster Analysis Extended Rousseeuw et al.
clusterConsCalculate the consensus clustering result from re-sampled clustering experiments with the option of using multiple algorithms and parameter
clustergasA hierarchical clustering method based on genetic algorithms
clusterGenerationrandom cluster generation (with specified degree of separation)
clusterPowerPower calculations for cluster-randomized and cluster-randomized crossover trials
clusterProfilerstatistical analysis and visulization of functional profiles for genes and gene clusters
clusterReproReproducibility of gene expression clusters
clusterSimSearching for optimal clustering procedure for a data set
clusterStabCompute cluster stability scores for microarray data
ClustOfVarClustering of variables
clustsigSignificant Cluster Analysis
clustToolGUI for clustering data with spatial information
clvCluster Validation Techniques
clValidValidation of Clustering Results
CMASynthesis of microarray-based classification
cmaesCovariance Matrix Adapting Evolutionary Strategy
cMAPA data package containing annotation data for cMAP
CMCCronbach-Mesbah Curve
cmmCategorical Marginal Models
cMonkeycMonkey intgrated biclustering algorithm
cmprskSubdistribution Analysis of Competing Risks
cmrutilsMisc Functions of the Center for the Mathematical Research
cn.farmscn.farms - Factor Analysis for copy number estimation
cn.mopscn.mops - Mixture of Poissons for CNV detection in NGS data
cnagIOMethods for reading CNAG files
CNAnormA normalization method for Copy Number Aberration in cancer samples
cncaGUICanonical Non-symmetrical Correspondence Analysis in R
cnf2freqsame Chromosome N-loci F2 frequencies
cnf2freqibdtracersame Chromosome N-loci F2 frequencies, with IBD tracing
CNToolsConvert segment data into a region by sample matrix to allow for other high level computational analyses.
CNVassocAssociation analysis of CNV data
cnvGSAGene Set Analysis of (Rare) Copy Number Variants
cnvGSAdataData used in the vignette of the cnvGSA package
CNVtoolsA package to test genetic association with CNV data
coalesceRA pedagogical tool to teach the basics of coalescent theory
coarseDataToolsA collection of functions to help with analysis of coarse infectious disease data
cobsCOBS -- Constrained B-splines (Sparse matrix based)
cobs99Constrained B-splines -- outdated 1999 version
CoCiteStatsDifferent test statistics based on co-citation.
CoClustCopula based cluster analysis
cocorrespCo-correspondence analysis methods
codaOutput analysis and diagnostics for MCMC
codelinkManipulation of Codelink Bioarrays data.
codepMultiscale Codependence Analysis
codetoolsCode Analysis Tools for R
coefplotPlots Coefficients from Fitted Models
coefplot2Coefficient plots
coenoflexGradient-Based Coenospace Vegetation Simulator
coexistSpecies coexistence modeling and analysis
coGPScancer outlier Gene Profile Sets
coildClassification Of Incomplete Longitudinal Datastructures
coinConditional Inference Procedures in a Permutation Test Framework
colbycolRead big text files column by column, sometimes much bigger than available RAM, into R.
colcorTests for column correlation in the presence of row correlation
CollocInferCollocation Inference for Dynamic Systems
colocColocalisation tests of two genetic traits
colonCAexprSet for Alon et al. (1999) colon cancer data
colorRampsBuilds color tables
colorspaceColor Space Manipulation
colortoolsTools for colors in an HSV color model
colourschemesData-driven colour scheme mappers
combinatcombinatorics utilities
CombMSCCombined Model Selection Criteria
commandrCommand pattern in R
CommonJavaJarsUseful libraries for building a Java based GUI under R
CommonTrendExtract and plot common trends from a cointegration system. Calculate P-value for Johansen Statistics.
comorbiditiesCategorizes ICD-9-CM codes based on published comorbidity indices
compareComparing Objects for Differences
compareGroupsdescriptives by groups
compareODMcomparison of medical forms in CDISC ODM format
CompareTestsEstimate diagnostic accuracy (sensitivity, specificity, etc) and agreement statistics when one test is conducted on only a subsample of specimens
comparisonMultivariate likelihood ratio calculation and evaluation
compeirEvent-specific incidence rates for competing risks data
compHclustComplementary Hierarchical Clustering
compilerThe R Compiler Package
complex.surv.dat.simSimulation of complex survival data
CompModSASensitivity Analysis for Complex Computer Models
compoissonConway-Maxwell-Poisson Distribution
COMPoissonRegConway-Maxwell Poisson (COM-Poisson) Regression
compositionsCompositional Data Analysis
compound.CoxRegression estimation based on the compound covariate methed under the Cox proportional hazard model
CompoundingComputing Continuous Distributions
compOverlapCorrComparing overlapping correlation coefficients
CompQuadFormDistribution function of quadratic forms in normal variables
CompRandFldComposite-likelihood based Analysis of Random Fields
compute.esCompute Effect Sizes
concorConcordance
concordConcordance and reliability
concregConcordance regression
condApproximate conditional inference for logistic and loglinear models
condGEEParameter estimation in conditional GEE for recurrent event gap times
condmixtConditional Density Estimation with Neural Network Conditional Mixtures
conf.designConstruction of factorial designs
confRegConfidence Estimators for Individual Regression Predictions
conjointConjoint analysis package
ConjointChecksA package to check the cancellation axioms of conjoint measurement.
CONORCONOR
CONORDataCONORData
ConsensusClusterPlusConsensusClusterPlus
ConsPlanConservation Planning Tools
constantsDefines some physical constants and functions commonly used in optics, plasmonics.
constrainedKrigingConstrained, covariance-matching constrained and universal point or block kriging
contfracContinued fractions
contrastA collection of contrast methods
ConvCalendarConverts dates between calendars
ConvergenceConceptsSeeing convergence concepts in action
convertConvert Microarray Data Objects
convexHazNonparametric MLE/LSE of convex hazard
convoiConvex Optimization in R
COPVariables selection for index models via correlation pursuit
copaFunctions to perform cancer outlier profile analysis.
copasStatistical methods to model and adjust for bias in meta-analysis
copBasicBasic Theoretical Copula, Empirical Copula, and Various Utility Functions
copulaMultivariate Dependence with Copulas
copulaedasEstimation of Distribution Algorithms Based on Copulas
CorbiCorbi - A collection of bioinformatics tools
corcountsGenerate correlated count random variables
CORElearnCORElearn - classification, regression, feature evaluation and ordinal evaluation
CormotifCorrelation Motif Fit
coRNAiAnalysis of co-knock-down RNAi data
corpcorEfficient Estimation of Covariance and (Partial) Correlation
corporaStatistics and data sets for corpus frequency data
CorrBinNonparametrics with clustered binary data
CORREPMultivariate Correlation Estimator and Statistical Inference Procedures.
corrgramPlot a correlogram
corrpermPermutation Tests of Correlation with Repeated Measurements
corrplotVisualization of a correlation matrix
corrsieveCorrSieve
COSINECOndition SpecIfic sub-NEtwork
cosmoSupervised detection of conserved motifs in DNA sequences
cosmoFnsFunctions for cosmological distances, times, luminosities, etc.
cosmoGUIGUI for constructing constraint sets used by the cosmo package
cossoCOSSO, adaptive COSSO, variable selection for nonparametric smoothing spline (quantile) regression models.
costatTime series costationarity determination and tests of stationarity.
cotrendConsistant Cotrend Rank Selection
cottoncdfcottoncdf
cottonprobeProbe sequence data for microarrays of type cotton
COUNTFunctions, data and code for count data.
countregCount Data Regression
countrycodeConvert country names and country codes
CovpathCOVPATH Package
covRobustRobust Covariance Estimation via Nearest Neighbor Cleaning
CoxBoostCox models by likelihood based boosting for a single survival endpoint or competing risks
CoxFlexBoostBoosting Flexible Cox Models (with Time-Varying Effects)
coxmeMixed Effects Cox Models.
coxphfCox regression with Firth's penalized likelihood
coxphwWeighted Cox regression
coxrobustRobust Estimation in Cox Model
COZIGAMConstrained and Unconstrained Zero-Inflated Generalized Additive Models with Model Selection Criterion
CPEConcordance Probability Estimates in Survival Analysis
CpGassocAssociation between Methylation and a phenotype of interest
CPHshapeFind the maximum likelihood estimator of the shape constrained hazard baseline and the effect parameters in the Cox proportional hazards model
cplmCompound Poisson linear models
cpmSequential Parametric and Nonparametric Change Detection
CPMCGLMCorrection of the pvalue after multiple coding
CprobConditional probability function of a competing event
cqnConditional quantile normalization
CRPower Calculation for Weighted Log-Rank Tests in Cure Rate Models
cRackerR-script suite for automated processing of proteomic peptide lists
cramerMultivariate nonparametric Cramer-Test for the two-sample-problem
crankCompleting ranks
crantasticVarious R tools for http://crantastic.org/
crawlFit continuous-time correlated random walk models to animal movement data
crblocksCategorical Randomized Block Data Analysis
CreditMetricsFunctions for calculating the CreditMetrics risk model
cremocremo: Comparative REndering of Model Outputs
CRFCRF - Conditional Random Fields
CRImageCRImage a package to classify cells and calculate tumour cellularity
crimCVGroup-Based Modelling of Longitudinal Data
crlmmGenotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
CRMContinual Reassessment Method (CRM) for Phase I Clinical Trials
crmnCCMN and other noRMalizatioN methods for metabolomics data
crnDownloads and Builds datasets for Climate Reference Network
cropDataModelling crop trial data
croprsimulate crop growth
crossdesDesign and Randomization in Crossover Studies
crosshybDetectorDetection of cross-hybridization events in microarray experiments
crossmatchThe Cross-match Test
crp.CSFPCreditRisk+ portfolio model
crrSCCompeting risks regression for Stratified and Clustered data
crrstepStepwise covariate selection for the Fine & Gray competing risks regression model
crsCategorical Regression Splines
CRTSizeSample Size Estimation Functions for Cluster Randomized Trials
crulesClassification Rules
CrypticIBDcheckIdentifying cryptic relatedness in genetic association studies
csamplingFunctions for Conditional Simulation in Regression-Scale Models
CSARStatistical tools for the analysis of ChIP-seq data
cshapesCShapes Dataset and Utilities
cslogisticConditionally Specified Logistic Regression
csoundAccessing Csound functionality through R
ctarmaEstimation and simulation of CARMA(p,q)
ctcCluster and Tree Conversion.
cthreshComplex Wavelet Denoising software.
ctmConditional Transformation Models
ctsContinuous Time Autoregressive Models
CTTClassical Test Theory Functions
ctvCRAN Task Views
cubatureAdaptive multivariate integration over hypercubes
CubistRule- and Instance-Based Regression Modeling
cudaBayesregDataData sets for the examples used in the package "cudaBayesreg"
cudiaCUDIA Cross-level Imputation
CulturalAnalyticsFunctions for statistical analysis and plotting of image properties
cummeRbundAnalysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
CUMPAnalyze Multivariate Phenotypes by Combining Univariate results
cumplyrExtends ddply to allow calculation of cumulative quantities.
cumSegChange point detection in genomic sequences
curvclustCurve clustering
curveDynamic Systems Estimation - Curvature extensions
curvetestThe 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.
curvHDRcurvHDR filtering of flow cytometry samples
cuspCusp Catastrophe Model Fitting Using Maximum Likelihood
cvm.testDiscrete Cramer von Mises Goodness-of-Fit Tests
CvM2SL1TestL1-version of Cramer-von Mises Two Sample Tests
CvM2SL2TestCramer-von Mises Two Sample Tests
cvplogisticMajorization Minimization by Coordinate Descent Algorithm for Concave Penalized Logistic Regression for High Dimensional Data
CVThreshLevel-Dependent Cross-Validation Thresholding
cvToolsCross-validation tools for regression models
cwhmiscMiscellaneous Functions for maths, plotting, printing, statistics, strings, and tools
cxxfunplusextend cxxfunction by saving the dynamic shared objects
cycleSignificance of periodic expression pattern in time-series data
cyclonesCyclone identification
cyp450cdfcyp450cdf
cyphidCycle and Phase Identification for mastication data
cytoDivCytometric diversity indices
ChainLadderStatistical methods for the calculation of outstanding claims reserves in general insurance
changeLOSChange in LOS
changepointAn R package for changepoint analysis
charlsonConverts listwise icd9 data into comorbidity count and Charlson Index
CHCNCanadian Historical Climate Network
chebDiscrete Linear Chebyshev Approximation
cheddarAnalysis and visualisation of ecological communities
chemCalCalibration functions for analytical chemistry
chemometricsMultivariate Statistical Analysis in Chemometrics
ChemometricsWithRChemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences
ChemometricsWithRDataData for package ChemometricsWithR
ChemoSpecExploratory Chemometrics for Spectroscopy
cherryMultiple testing methods for exploratory research
CHNOSZChemical Thermodynamics and Activity Diagrams
ChoiceModelRChoice Modeling in R
choplumpChoplump tests
chronChronological objects which can handle dates and times
CHsharpChoi and Hall Clustering in 3d
DAAGData Analysis And Graphics data and functions
DAAGbioData Sets and Functions, for demonstrations with expression arrays and gene sequences
DAAGxtrasData Sets and Functions, supplementary to DAAG
daeFunctions useful in the design and ANOVA of experiments
dafsData analysis for forensic scientists
DAGGERConsensus genetic maps
dagRR functions for directed acyclic graphs
DaimDiagnostic accuracy of classification models.
dairyFunctions and models related to dairy production
DAKSData Analysis and Knowledge Spaces
daMAEfficient design and analysis of factorial two-colour microarray data
DAMiscDave Armstrong's Miscellaneous Functions
DandEFADandelion Plot for R-mode Exploratory Factor Analysis
DARTDenoising Algorithm based on Relevance network Topology
dartsStatistical Tools to Analyze Your Darts Game
data.tableExtension of data.frame for fast indexing, fast ordered joins, fast assignment, fast grouping and list columns.
DatABELfile-based access to large matrices stored on HDD in binary format
dataframeFast data frames
dataframes2xlsdataframes2xls writes data frames to xls files
datamapA system for mapping foreign objects to R variables and environments
datamartUnified access to various data sources
datamergeMerging of overlapping and inconsistent data
DatasetHandling survey data in R.
datasetsThe R Datasets Package
dataviewHuman readable data presentation
dateFunctions for handling dates
DATforDCEMRIDeconvolution Analysis Tool for Dynamic Contrast Enhanced MRI
DATRASRead and convert raw data obtained from http://datras.ices.dk/Data_products/Download/Download_Data_public.aspx
DAVIDQueryRetrieval from the DAVID bioinformatics data resource into R
DaviesThe Davies quantile function
dbEmpLikeGOFGoodness-of-fit and two sample comparison tests using sample entropy
DBGSAmethods of distance-based gene set functional enrichment analysis.
DBIR Database Interface
dblcensCompute the NPMLE of distribution from doubly censored data
dbstatsDistance-based statistics (dbstats)
dcemriS4A Package for Medical Image Analysis (S4 implementation)
dcensDoubly censoring estimation
DCGLDifferential Coexpression Analysis of Gene Expression Microarray Data
dcloneData Cloning and MCMC Tools for Maximum Likelihood Methods
DClusterFunctions for the detection of spatial clusters of diseases
dcmleHierarchical Models Made Easy with Data Cloning
dcvConventional Cross-validation statistics for climate-growth model
DDDDiversity-dependent diversification
ddepnDynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.
ddesolveSolver for Delay Differential Equations
DDHFmVariance Stabilization by Data-Driven Haar-Fisz (for Microarrays)
ddstData driven smooth test
dealLearning Bayesian Networks with Mixed Variables
deamerDeconvolution density estimation with adaptive methods for a variable prone to measurement error
debugMVB's debugger for R
DECIDEDEComposition of Indirect and Direct Effects
deconDeconvolution Estimation in Measurement Error Models
DeducerDeducer
DeducerExtrasAdditional dialogs and functions for Deducer
DeducerMMRA Deducer plugin for moderated multiple regressions and simple slopes analysis
DeducerPlugInExampleDeducer Plug-in Example
DeducerPlugInScalingReliability and factor analysis plugin
DeducerSpatialDeducer for spatial data analysis
DeducerSurvivalAdd Survival Dialogue to Deducer
deducorrectDeductive correction of simple rounding, typing and sign errors
DefaultsCreate Global Function Defaults
degenesDetection of differentially expressed genes.
degreenetModels for Skewed Count Distributions Relevant to Networks
deldirDelaunay Triangulation and Dirichlet (Voronoi) Tessellation.
delftfewsdelftfews R extensions
deltEstimation of multivariate densities with adaptive histograms
deltaPlotRIdentification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method
DEMEticsEvaluating the genetic differentiation between populations based on Gst and D values.
demographyForecasting mortality, fertility, migration and population data
denproVisualization of multivariate, functions, sets, and data
denstripDensity strips and other methods for compactly illustrating distributions
DEoptimGlobal optimization by Differential Evolution
DepelaDepela
depend.truncationInference for parametric and semiparametric models based on dependent truncation data
depmixDependent Mixture Models
depmixS4Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
depthDepth functions tools for multivariate analysis
depthToolsDepth Tools Package
descrDescriptive statistics
DescribeDisplayR interface to DescribeDisplay (GGobi plugin)
deseasonalizeOptimal deseasonalization for geophysical time series using AR fitting
DesignPatternsDesign Patterns in R to build reusable object-oriented software
desirabilityDesirabiliy Function Optimization and Ranking
desireDesirability functions
deSolveGeneral solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE), differential algebraic equations (DAE), and delay differential equations (DDE).
detectAnalyzing Wildlife Data with Detection Error
deTestSetTestset for differential equations
detrendeRStart the detrendeR Graphical User Interface (GUI)
DetSelA computer program to detect markers responding to selection
devEMFEMF graphics output device
Devore5Data sets from Devore's "Prob and Stat for Eng (5th ed)"
Devore6Data sets from Devore's "Prob and Stat for Eng (6th ed)"
Devore7Data sets from Devore's "Prob and Stat for Eng (7th ed)"
devtoolsTools to make developing R code easier
dfcrmDose-finding by the continual reassessment method
dfoptimDerivative-free Optimization
dglmDouble generalized linear models
dgmbdgmb Simulating data for PLS structural models
dgofDiscrete Goodness-of-Fit Tests
dhglmDouble Hierarchical Generalized Linear Models
diagramFunctions for visualising simple graphs (networks), plotting flow diagrams
DiagTest3GrpDiagnostic test summary measures for three ordinal groups
diamondsAnalysis and sampling grids from diamond partitions
diceCalculate probabilities of various dice-rolling events
DiceDesignDesigns of Computer Experiments
DiceEvalConstruction and evaluation of metamodels
DiceKrigingKriging methods for computer experiments
DiceOptimKriging-based optimization for computer experiments
DiceViewPlot methods for computer experiments design and surrogate.
dicionariosIBGEDictionaries for reading survey microdata from IBGE
dielectricDefines some physical constants and dielectric functions commonly used in optics, plasmonics.
DierckxSplineR companion to "Curve and Surface Fitting with Splines"
diffStatistics: What's the Difference?
diffEqFunctions from the book Solving Differential Equations in R
diffractometryBaseline identification and peak decomposition for x-ray diffractograms
diffusionMapDiffusion map
difRCollection of methods to detect dichotomous differential item functioning (DIF) in psychometrics
digeRGUI tool for analyzing 2D DIGE data
digestCreate cryptographic hash digests of R objects
digitizedigitize : a plot digitizer in R
dichromatColor schemes for dichromats
DIMEDIME (Differential Identification using Mixture Ensemble)
dinamicDiNAMIC A Method To Analyze Recurrent DNA Copy Number Aberrations in Tumors
diptestHartigan's dip test statistic for unimodality - corrected code
DIRECTBayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior
directlabelsDirect labels for multicolor plots in lattice or ggplot2
DirichletRegDirichlet Regression in R
dirmultEstimation in Dirichlet-Multinomial distribution.
disclapDiscrete Laplace Exponential Family
disclapmixDiscrete Laplace mixture inference using the EM algorithm
DiscreteLaplaceDiscrete Laplace distribution
discreteMTPMultiple testing procedures for discrete test statistics
discretizationData preprocessing, discretization for classification.
diseasemappingCalculate observed and expected disease incidence counts from a case file and population data.
dismoSpecies distribution modeling
disp2D2D Hausdorff and Simplex Dispersion Orderings
dispmodDispersion models
DistanceA simple way to fit detection functions to distance sampling data and calculate abundance/density for biological populations.
distoryDistance Between Phylogenetic Histories
distrObject oriented implementation of distributions
distrDocDocumentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse
distrEllipseS4 classes for elliptically contoured distributions
distrExExtensions of package distr
DistributionUtilsDistribution Utilities
distrModObject oriented implementation of probability models
distrSimSimulation classes based on package distr
distrTeachExtensions of package distr for teaching Stochastics/Statistics in secondary school
distrTEstEstimation and Testing classes based on package distr
divagisProvides tools for quality checks of georeferenced plant species accessions.
diveMoveDive analysis and calibration
diversitreediversitree: comparative phylogenetic analyses of diversification
diveRsityGenetic diversity partition statistics and Informative locus selection.
DiversitySamplerFunctions for re-sampling a community matrix to compute diversity indices at different sampling levels.
divisorsFind the divisors of a number
DivMeltHRM Diversity Assay Analysis Tool
dixonNearest Neighbour Contingency Table Analysis
dkDNADiffusion kernels on a set of genotypes.
dlmBayesian and Likelihood Analysis of Dynamic Linear Models
dlmapDetection Localization Mapping for QTL
dlmodelerGeneralized Dynamic Linear Modeler
dlnmDistributed Lag Non-linear Models
dmaDynamic model averaging
dmtDependency Modeling Toolkit
DMwRFunctions and data for "Data Mining with R"
DNAtoolsTools for analysing forensic genetic DNA data
DnEDnE(Distribution and Equation)
DOBADAnalysis of Discretely Observed linear Birth-And-Death(-and-immigration) Markov Chains
doBydoBy - Groupwise summary statistics, general linear contrasts, population means (least-squares-means), and other utilities
DodgeFunctions for Acceptance Sampling Ideas originated by H.F. Dodge
DoE.baseFull factorials, orthogonal arrays and base utilities for DoE packages
DoE.wrapperWrapper package for design of experiments functionality
doParallelForeach parallel adaptor for the parallel package
doRedisForeach parallel adapter for the rredis package
doRNGGeneric Reproducible Parallel Backend for foreach Loops
DoseFindingPlanning and Analyzing Dose Finding experiments
doSNOWForeach parallel adaptor for the snow package
dostatsCompute statistics helper functions
dpaDynamic Path Approach
dplRDendrochronology Program Library in R
DPM.GGMDirichlet Process Mixtures (DPM) and related models using Gaussian Graphical Models (GGM) for Sparse covariance estimation in heterogeneous samples
dpmixsimDirichlet Process Mixture model simulation for clustering and image segmentation
DPpackageBayesian nonparametric modeling in R
drMethods for dimension reduction for regression
drawExpressionVisualising R syntax through graphics
drcAnalysis of dose-response curves
drfitDose-response data evaluation
DRIDR-Integrator
drmRegression and association models for repeated categorical data
dsDescriptive Statistics
dsampleDiscretization-based Direct Random Sample Generation
dseDynamic Systems Estimation (time series package)
dse1DSE (unbundled transition package).
dse2DSE (unbundled transition package).
DSLDistributed Storage and List
DSpatSpatial modelling for distance sampling data
DTDADoubly truncated data analysis
dtiAnalysis of diffusion weighted imaging (DWI) data
DTKDunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes
dttDiscrete Trigonometric Transforms
dtwDynamic Time Warping algorithms
dummiesCreate dummy/indicator variables flexibly and efficiently
dvfBmDiscrete variations of a fractional Brownian motion
DWDDWD implementation based on A IPM SOCP solver
dynTime Series Regression
dynamicGraphdynamicGraph
dynamicTreeCutMethods for detection of clusters in hierarchical clustering dendrograms.
dynamoDynamic Models
dynaTreeDynamic trees for learning and design
dynCorrDynamic Correlation Package
dynlmDynamic Linear Regression
dynpredCompanion package to "Dynamic Prediction in Clinical Survival Analysis"
dynsurvDynamic models for survival data
e1071Misc Functions of the Department of Statistics (e1071), TU Wien
eafPlots of the Empirical Attainment Function
earthMultivariate Adaptive Regression Spline Models
easiEASI Demand System Estimation
easyanovaAnalysis of variance and other important complementary analyzes
ebaElimination-by-Aspects (EBA) Models
ebalEntropy reweighting to create balanced samples
EbayesThreshEmpirical Bayes Thresholding and Related Methods
ebdbNetEmpirical Bayes Estimation of Dynamic Bayesian Networks
EBMAforecastEnsemble BMA Forecasting
EBSExact Bayesian Segmentation
EcdatData sets for econometrics
ecespaFunctions for spatial point pattern analysis
ecodistDissimilarity-based functions for ecological analysis
EcoHydRologyA community modeling foundation for Eco-Hydrology.
ecolMod"A practical guide to ecological modelling - using R as a simulation platform"
ecoregEcological regression using aggregate and individual data
EcoTrophEcoTroph modelling support
EDanalysisA R Package For Gene Enrichment Disequilibrium Analysis
edccEconomic Design of Control Charts
edesignMaximum entropy sampling
EDISONSoftware for network reconstruction and changepoint detection.
editrulesR package for parsing, applying, and manipulating data cleaning rules
EDREstimation of the effective dimension reduction (EDR) space
edrGraphicalToolsProvide tools for dimension reduction methods
effectsEffect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models
EffectStarsVisualization of Categorical Response Models
egonetTool for ego-centric measures in Social Network Analysis
ehaEvent History Analysis
eigendogEigenDog
eigeninvGenerates (dense) matrices that have a given set of eigenvalues
eigenmodelSemiparametric factor and regression models for symmetric relational data
eiPackeiPack: Ecological Inference and Higher-Dimension Data Management
ELTwo-sample Empirical Likelihood
el.convexempirical likelihood ratio tests for means
elasticnetElastic-Net for Sparse Estimation and Sparse PCA
elecCollection of functions for statistical election audits
elec.stratFunctions for election audits using stratified random samples
ElemStatLearnData 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.
ellipseFunctions for drawing ellipses and ellipse-like confidence regions
ellipticelliptic functions
elmNNImplementation of ELM (Extreme Learning Machine ) algorithm for SLFN ( Single Hidden Layer Feedforward Neural Networks )
elrmExact Logistic Regression via MCMC
EMAEasy Microarray data Analysis
EMCEvolutionary Monte Carlo (EMC) algorithm
EMCCEvolutionary Monte Carlo (EMC) methods for clustering
EMDEmpirical Mode Decomposition and Hilbert Spectral Analysis
emdbookEcological models and data (book support)
emdistEarth Mover's Distance
emgExponentially Modified Gaussian (EMG) Distribution
EMJumpDiffusionEM-Algorithm for Jump Diffusion processes
emmaEvolutionary model-based multiresponse approach
emme2Read and Write to an EMME/2 databank
emoaEvolutionary Multiobjective Optimization Algorithms
emplikEmpirical likelihood ratio for censored/truncated data
emplik2Empirical-likelihood test (two-sample, censored data)
EMTExact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data
emuInterface to the Emu Speech Database System
emudataemudata - datasets for the emu package
emulatorBayesian emulation of computer programs
ENAEnsemble Network Aggregation
endogMNPR Package for Fitting Multinomial Probit Models with Endogenous Selection
endorseR Package for Analyzing Endorsement Experiments
energyE-statistics (energy statistics)
englishTranslate integers into English
EngrExptData sets from "Introductory Statistics for Engineering Experimentation"
ENmiscNeuwirth miscellaenous
EnQuireRA package dedicated to questionnaires
enrichvsEnrichment assessment of virtual screening approaches
ensembleBMAProbabilistic Forecasting using Ensembles and Bayesian Model Averaging
entropyEntropy and Mutual Information Estimation
envelopeEnvelope normality test
epadeEasy Plots
EpiA package for statistical analysis in epidemiology.
epibasixElementary Epidemiological Functions for a Graduate Epidemiology\Biostatistics Course
epicalcEpidemiological calculator
EpiContactTraceEpidemiological tool for contact tracing.
EpiEstimEpiEstim: a package to estimate time varying reproduction numbers from epidemic curves.
epinetA collection of epidemic/network-related tools
epiRAn R package for the analysis of epidemiological data
epitoolsEpidemiology Tools
epsiEdge Preserving Smoothing for Images
EQLExtended-Quasi-Likelihood-Function (EQL)
eqtlTools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis
equateStatistical Methods for Test Score Equating
EquiNormNormalize expression data using equivalently expressed genes
equivalenceProvides tests and graphics for assessing tests of equivalence
ererEmpirical Research in Economics with R
ergmFit, Simulate and Diagnose Exponential-Family Models for Networks
ergm.usertermsUser-specified terms for the statnet suite of packages
eRmExtended Rasch Modeling
esd4allesd4all
esotericResotericR articles from lemnica.com
ESPRESSOPower Analysis and Sample Size Calculation
EstCRMCalibrating Parameters for the Samejima's Continuous IRT Model
estoutEstimates Output
EstSimPDMPEstimation of the jump rate and simulation for piecewise-deterministic Markov processes
etableEasy Table
ETASModeling earthquake data using Epidemic Type Aftershock Sequence model
ETCEquivalence to control
ETLUtilsUtility functions to execute standard ETL operations (using package ff) on large data.
etmEmpirical Transition Matrix
EuclideanMapsDisplays Euclidean Maps
EvalEstDynamic Systems Estimation - extensions
evaluateParsing and evaluation tools that provide more details than the default.
evdFunctions for extreme value distributions
evdbayesBayesian Analysis in Extreme Value Theory
eVenneVenn: A powerful tool to compare lists and draw Venn diagrams.
eventsStore and manipulate event data
EVEREstimation of Variance by Efficient Replication
evirExtreme Values in R
evoraEpigenetic Variable Outliers for Risk prediction Analysis
evtreeEvolutionary Learning of Globally Optimal Trees
ExactUnconditional Exact Tests
exact2x2Exact Conditional Tests and Confidence Intervals for 2x2 tables
exactciExact P-values and Matching Confidence Intervals for simple Discrete Parametric Cases
exactLoglinTestMonte Carlo Exact Tests for Log-linear models
exactmaxselMaximally selected statistics for binary response variables - Exact methods
exactRankTestsExact Distributions for Rank and Permutation Tests
examsAutomatic Generation of Standardized Exams for Large-Lecture Courses
ExomeCNVDetect CNV and LOH from Exome Sequecing Data
ExomeDepthCalls CNV from exome sequence data
ExPD2DExact Computation of Bivariate Projection Depth Based on Fortran Code
ExpDesExperimental Designs package
expectregExpectile and Quantile Regression
experimentexperiment: R package for designing and analyzing randomized experiments
expertModeling without data using expert opinion
expmMatrix exponential
ExPositionExploratory analysis with the singular value decomposition.
expsmoothData sets from "Forecasting with exponential smoothing"
exptestTests for Exponentiality
extfunnelAdditional Funnel Plot Augmentations
extraBinomialExtra-binomial approach for pooled sequencing data
extracatGraphic Extensions for Categorical Data
extrafontTools for using fonts
extrafontdbPackage for holding the database for the extrafont package
extRemesExtreme value toolkit.
extremevaluesUnivariate outlier detection
eyetrackingEyetracking Helper Functions
ezEasy analysis and visualization of factorial experiments.
ezglmselects significant non-additive interaction between two variables using fast GLM implementation.
ezsimprovide an easy to use framework to conduct simulation
FacPadBayesian Sparse Factor Analysis model for the inference of pathways responsive to drug treatment
FactMixtAnalysisFactor Mixture Analysis with covariates
FactoClassCombination of Factorial Methods and Cluster Analysis
FactoMineRMultivariate Exploratory Data Analysis and Data Mining with R
factorQRBayesian quantile regression factor models
factualRthin wrapper for the Factual.com server API
FAdistDistributions that are sometimes used in hydrology
FahrmeirData from the book "Multivariate Statistical Modelling Based on Generalized Linear Models", first edition, by Ludwig Fahrmeir and Gerhard Tutz
FAiRFactor Analysis in R
fairselectFeature Annealed Independence Rules (demo)
faisalconjointFaisal Conjoint Model: A New Approach to Conjoint Analysis
fameInterface for FAME time series database
FamiliasProbabilities for Pedigrees given DNA data
FAmleMaximum Likelihood and Bayesian Estimation of Univariate Probability Distributions
FAMTFactor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data
fancPenalized likelihood factor analysis via nonconvex penalty
fANCOVANonparametric Analysis of Covariance
fanovaGraphBuilding Kriging models from FANOVA graphs
fanplotVisualisations of sequential probability distributions.
faoutlierInfluential case detection methods for factor analysis and SEM
farModelization for Functional AutoRegressive processes
farawayFunctions and datasets for books by Julian Faraway.
fArmaARMA Time Series Modelling
fAsianOptionsEBM and Asian Option Valuation
fAssetsRmetrics - Assets Selection and Modelling
fastImplementation of the Fourier Amplitude Sensitivity Test (FAST)
fastclusterFast hierarchical clustering routines for R and Python
fastcoxLasso and elastic-net penalized Cox's regression in high dimensions models using the cocktail algorithm
fastGHQuadFast Rcpp implementation of Gauss-Hermite quadrature
fastICAFastICA Algorithms to perform ICA and Projection Pursuit
FastImputationLearn from training data then quickly fill in missing data.
fastmatchFast match() function
fastRData sets and utilities for Foundations and Applications of Statistics by R Pruim
FastRWebFast Interactive Framework for Web Scripting Using R
fastVARfastVAR
favirFormatted Actuarial Vignettes in R
FAwRFunctions and Datasets for "Forest Analytics with R".
fBasicsRmetrics - Markets and Basic Statistics
fbatiGene by Environment Interaction and Conditional Gene Tests for Nuclear Families
FBNFISH Based Normalization and Copy Number inference of SNP microarray data
fBondsBonds and Interest Rate Models
fCertificatesfCertificates - Basics of Certificates and Structured Products Valuation
fCopulaeRmetrics - Dependence Structures with Copulas
FDMeasuring functional diversity (FD) from multiple traits, and other tools for functional ecology
fdaFunctional Data Analysis
fda.uscFunctional Data Analysis and Utilities for Statistical Computing (fda.usc)
fdaMixedFunctional data analysis in a mixed model framework
fdimFunctions for calculating fractal dimension.
fdrciPermutation-based FDR Point and Confidence Interval Estimation
fdrtoolEstimation of (Local) False Discovery Rates and Higher Criticism
fdsFunctional data sets
fdthFrequency Distribution Tables, Histograms and Poligons
FeaLectScores features for Feature seLection
featureFeature significance for multivariate kernel density estimation
featuresFeature Extraction for Discretely-Sampled Functional Data
fechnerFechnerian Scaling of Discrete Object Sets
fExoticOptionsExotic Option Valuation
fExtremesRmetrics - Extreme Financial Market Data
ffmemory-efficient storage of large data on disk and fast access functions
ffbaseBasic statistical functions for package ff
FFDFreedom From Disease
ffmanovaFifty-fifty MANOVA
fftwFast FFT and DCT based on FFTW
fgacGeneralized Archimedean Copula
fGarchRmetrics - Autoregressive Conditional Heteroskedastic Modelling
FGNFractional Gaussian Noise, estimation and simulaton
fgofFast Goodness-of-fit Test
fguiFunction GUI
FHtestTests for right and interval-censored survival data based on the Fleming-Harrington class
FIARFunctional Integration Analysis in R
fieldsTools for spatial data
FieldSimRandom fields simulations
filehashSimple key-value database
filehashSQLiteSimple key-value database using SQLite
filterviewRGet started easily with FilterView from R.
fImportRmetrics - Economic and Financial Data Import
financialSolving financial problems in R
FinAsymClassifies implicit trading activity from market quotes and computes the probability of informed trading
FindAllRootsFind all root(s) of the equation and Find root(s) of the equation by dichotomy
finebalanceApproximate fine balance when exact fine balance is not achievable
fingerprintFunctions to operate on binary fingerprint data
FinTSCompanion to Tsay (2005) Analysis of Financial Time Series
FisherEMThe Fisher-EM algorithm
fisheyeRFisheye and Hyperbolic-space-alike Interactive Visualization Tools in R
fishmethodsFisheries Methods and Models in R
fishmovePrediction of Fish Movement Parameters
fit4NMNONMEM platform
FitARSubset AR Model Fitting
FitARMAFitARMA: Fit ARMA or ARIMA using fast MLE algorithm
fitdistrplusHelp to fit of a parametric distribution to non-censored or censored data
fitDRCFitting Density Ratio Classes
FITSioFITS (Flexible Image Transport System) utilities
FKFFast Kalman Filter
flashClustImplementation of optimal hierarchical clustering
flexclustFlexible Cluster Algorithms
flexmixFlexible Mixture Modeling
FlexParamCurveTools to Fit Flexible Parametric Curves
flexsurvFlexible parametric survival models
flipMultivariate Permutation Tests
FLLatFused Lasso Latent Feature Model
flsaPath algorithm for the general Fused Lasso Signal Approximator
flubaseBaseline of mortality free of influenza epidemics
FluryData Sets from Flury, 1997
fluxFlux rate calculation from dynamic closed chamber measurements
fmaData sets from "Forecasting: methods and applications" by Makridakis, Wheelwright & Hyndman (1998)
FMEA Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability, Monte Carlo Analysis.
fmriAnalysis of fMRI experiments
fmsbFunctions for medical statistics book with some demographic data
FMStableFinite Moment Stable Distributions
fMultivarMultivariate Market Analysis
FNNFast Nearest Neighbor Search Algorithms and Applications
fNonlinearNonlinear and Chaotic Time Series Modelling
fobagreedy variable selection
fontcmComputer Modern font for use with extrafont package
foodwebvisualisation and analysis of food web networks
fOptionsBasics of Option Valuation
foramsForaminifera and Community Ecology Analyses
foreachForeach looping construct for R
ForeCAForeCA - Forecastable Component Analysis
forecastForecasting functions for time series and linear models
foreignRead Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...
forensicStatistical Methods in Forensic Genetics
forensimStatistical tools for the interpretation of forensic DNA mixtures
ForImpImputation of missing values through a forward imputation algorithm
FormalSeriesElementary arithemtic in formal series rings
formatRFormat R Code Automatically
FormulaExtended Model Formulas
fortunesR Fortunes
forwardForward search
fossilPalaeoecological and Palaeogeographical Analysis Tools
FourierDescriptorsGenerate images using Fourier descriptors.
FourScoresFourScores - A game for two players
fpcFlexible procedures for clustering
fpcaRestricted MLE for Functional Principal Components Analysis
fPortfolioRmetrics - Portfolio Selection and Optimization - ebook available at www.rmetrics.org
fpowComputing the noncentrality parameter of the noncentral F distribution
fppData for "Forecasting: principles and practice"
fracdiffFractionally differenced ARIMA aka ARFIMA(p,d,q) models
fracprolifFraction Proliferation via a quiescent growth model
FracSimSimulation of LÚvy motions
fractalFractal Time Series Modeling and Analysis
fractaldimEstimation of fractal dimensions
fractalrockGenerate fractal time series with non-normal returns distribution
FRACTIONNumeric number into fraction
frailtyHLFrailty Models via H-likelihood
frailtypackGeneral Frailty models using a semi_parametrical penalized likelihood estimation or a parametrical estimation
FRBFast and Robust Bootstrap
FRBDataDownload interest rate data from FRB's website
fRegressionRegression Based Decision and Prediction
freqMAPFrequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate
FrF2Fractional Factorial designs with 2-level factors
FrF2.catlg128Catalogues of resolution IV 128 run 2-level fractional factorials up to 24 factors that do have 5-letter words
frmqaThe Generalized Hyperbolic Distribution, Related Distributions and Their Applications in Finance
frontierStochastic Frontier Analysis
frontilesPartial frontier efficiency analysis
frtFull Randomization Test
FSelectorSelecting attributes
FTICRMSPrograms for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data
ftnonparFeatures and Strings for Nonparametric Regression
fTradingTechnical Trading Analysis
ftsR interface to tslib (a time series library in c++)
ftsaFunctional time series analysis
fugeRFUzzy GEnetic, a machine learning algorithm to construct prediction model based on fuzzy logic.
fumeFUME package
funUse R for Fun
FunClusterFunctional Profiling of Microarray Expression Data
FuncMapHive Plots of R Package Function Calls
functionalCurry, Compose, and other higher-order functions
fUnitRootsTrends and Unit Roots
FunNetIntegrative Functional Analysis of Transcriptional Networks
futileFutile base package
futile.anyFutile library to provide some polymorphism
futile.loggerFutile logger subsystem
futile.matrixFutile matrix utilities
futile.optionsFutile options management
futile.paradigmA framework for working in a functional programming paradigm in R
fuzzyFDRExact calculation of fuzzy decision rules for multiple testing
fuzzyOPFuzzy numbers and the main mathematical operations
fuzzyRankTestsFuzzy Rank Tests and Confidence Intervals
fwdmsaForward search for Mokken scale analysis
FWDselectSelecting variables in regression models
fwsimFisher-Wright Population Simulation
fxregimeExchange Rate Regime Analysis
g.dataDelayed-Data Packages
G1DBNA package performing Dynamic Bayesian Network inference.
G2SdGrain-size Statistics and Description of Sediment
GAGenetic Algorithms
GA4StratificationA genetic algorithm approach to determine stratum boundaries and sample sizes of each stratum in stratified sampling
GADGAD: Analysis of variance from general principles
gafitGenetic Algorithm for Curve Fitting
galtsGenetic algorithms and C-steps based LTS (Least Trimmed Squares) estimation
gamGeneralized Additive Models
gamairData for "GAMs: An Introduction with R"
GAMBoostGeneralized linear and additive models by likelihood based boosting
gamboostLSSBoosting Methods for GAMLSS Models
GAMensApplies GAMbag, GAMrsm and GAMens ensemble classifiers for binary classification
gamesStatistical Estimation of Game-Theoretic Models
gamesNwsPlaying games using a NWS Server
gamlssGeneralized Additive Models for Location Scale and Shape.
gamlss.addGAMLSS Additive.
gamlss.censFitting an interval response variable using gamlss.family distributions
gamlss.dataGAMLSS Data.
gamlss.demoDemos for GAMLSS
gamlss.distDistributions to be used for GAMLSS modelling.
gamlss.mxA GAMLSS add on package for fitting mixture distributions
gamlss.nlFitting non linear parametric GAMLSS models
gamlss.trGenerating and fitting truncated (gamlss.family) distributions
gamlss.utilGAMLSS Utilities.
gamm4Generalized additive mixed models using mgcv and lme4
gammSliceGeneralized additive mixed model analysis via slice sampling
GANPAGene Association Network-based Pathway Analysis
GANPAdataThe GANPA Datasets Package
gapGenetic analysis package
gaussDiffDifference measures for multivariate Gaussian probability density functions
gaussquadCollection of functions for Gaussian quadrature
gbGeneralize Lambda Distribution and Generalized Bootstrapping
GB2Generalized Beta Distribution of the Second Kind: properties, likelihood, estimation.
gbmGeneralized Boosted Regression Models
gbRdUtilities for processing Rd objects and files
gbsPackage for Generalized Birnbaum-Saunders Distributions
gcdnetA generalized coordinate descent (GCD) algorithm for computing the solution path of the hybrid Huberized support vector machine (HHSVM) and its generalization.
gcExplorerGraphical Cluster Explorer
gclusClustering Graphics
gcmrGaussian Copula Marginal Regression
gcolorProvides an Inequation Algorithm Function and a solution to import DIMACS files.
gdataVarious R programming tools for data manipulation
gdistancedistances and routes on geographical grids
gdsfmtCoreArray Genomic Data Structure (GDS) R Interface
geeGeneralized Estimation Equation solver
geepackGeneralized Estimating Equation Package
geigerAnalysis of evolutionary diversification
GenABELgenome-wide SNP association analysis
genalgR Based Genetic Algorithm
GENEAreadPackage For Reading Binary files
geneARMASimulate, model, and display data from a time-course microarray experiment with periodic gene expression
GeneCycleIdentification of Periodically Expressed Genes
GeneFPackage for Generalized F-statistics
GenelandDetection of structure from multilocus genetic data.
geneListPieProfiling a gene list into GOslim or KEGG function pie
GeneNetModeling and Inferring Gene Networks
genepiGenetic Epidemiology Design and Inference
GeneralizedHyperbolicThe Generalized Hyperbolic Distribution
GeneRegConstruct time delay gene regulatory network
geneticsPopulation Genetics
GenKernFunctions for generating and manipulating binned kernel density estimates
genlassoPath algorithm for generalized lasso problems
genomaticManages microsatellite projects. Creates 96-well maps, genotyping submission forms, rerun management, and import into statistical software.
genomicperCircular Genomic Permutation using GWAS p-values of association
genoPlotRPlot publication-grade gene and genome maps
GenOrdSimulation of ordinal and discrete variables with given correlation matrix and marginal distributions
genridgeGeneralized ridge trace plots for ridge regression
GenSAR functions for Generalized Simulated Annealing
genSurvGenerating multi-state survival data
GeoLightAnalysis of light based geolocator data
GEOmapTopographic and Geologic Mapping
geomapdataData for topographic and Geologic Mapping
geometryMesh generation and surface tesselation
geonamesInterface to www.geonames.org web service
geophysGeophysics, Continuum Mechanics, Mogi Model
geoPlotGeocodes street or ip addresses and plots them on a map.
geoRAnalysis of geostatistical data
geoRglmgeoRglm - a package for generalised linear spatial models
geosphereSpherical Trigonometry
geosptSpatial geostatistics; some geostatistical and radial basis functions, prediction and cross validation; design of optimal spatial sampling networks based on geostatistical modelling
geotoolsGeo tools
GeoXpInteractive exploratory spatial data analysis
geozooZoo of Geometric Objects
getoptC-like getopt behavior.
GEVcdnGEV conditional density estimation network
GExMapA visual, intuitive, easy to use software giving access to a new type of information buried into your microarray data.
GGallyExtension to ggplot2.
ggcolpairsCombination of GGplot2 plots into a matrix based on data columns.
ggdendroTools for extracting dendrogram and tree diagram plot data for use with ggplot.
GGEBiplotGUIGGEBiplotGUI: Interactive GGE Biplots in R
gglassoGroup Lasso Penalized Learning Using A Unified BMD Algorithm
ggmA package for Graphical Markov Models
ggmapA package for spatial visualization with Google Maps and OpenStreetMap
GGMselectGaussian Graphs Models selection
ggparallelVariations of Parallel Coordinate Plots for Categorical Data
ggplot2An implementation of the Grammar of Graphics
GhcnDailyDownloads and processes GHCN daily
ghypA package on the generalized hyperbolic distribution and its special cases
gibbs.metNaive Gibbs Sampling with Metropolis Steps
GillespieSSAGillespie's Stochastic Simulation Algorithm (SSA)
giRaphThe giRaph package for graph representation in R
GISToolsSome further GIS capabilities for R
glassoGraphical lasso- estimation of Gaussian graphical models
gldEstimation and use of the generalised (Tukey) lambda distribution
gldistAn Asymmetry-Steepness Parameterization of the Generalized Lambda Distribution.
glm2Fitting Generalized Linear Models
glmcFitting Generalized Linear Models Subject to Constraints
glmdmR Code for Simulation of GLMDM
glmmAKGeneralized Linear Mixed Models
glmmBUGSGeneralised Linear Mixed Models and Spatial Models with WinBUGS, BRugs, or OpenBUGS
glmmGSGauss-Seidel Generalized Linear Mixed Model solver
glmmLassoVariable selection for generalized linear mixed models by L1-penalized estimation
glmmMLGeneralized linear models with clustering
glmnetLasso and elastic-net regularized generalized linear models
glmnetcrFit a penalized constrained continuation ratio model for predicting an ordinal response
glmultiModel selection and multimodel inference made easy
globalboosttestTesting the additional predictive value of high-dimensional data
glogisFitting and Testing Generalized Logistic Distributions
glpkAPIR Interface to C API of GLPK
glrtGeneralized Logrank Tests for Interval-censored Failure Time Data
gMCPGraph Based Multiple Comparison Procedures
GMDGeneralized Minimum Distance of distributions
gmmGeneralized Method of Moments and Generalized Empirical Likelihood
GMMBoostLikelihood-based Boosting for Generalized mixed models
gmodelsVarious R programming tools for model fitting
gmpMultiple Precision Arithmetic
gmtInterface between GMT Map-Making Software and R
gnmGeneralized Nonlinear Models
gnmfGeneralized Non-negative Matrix Factorization
gnumericRead data from files readable by gnumeric
goalprogWeighted and lexicographical goal programming and optimization
gofModel-diagnostics based on cumulative residuals
GOFSNGoodness-of-fit tests for the family of skew-normal models
GOGANPAGO-Functional-Network-based Gene-Set-Analysis
gogarchGeneralized Orthogonal GARCH (GO-GARCH) models
googlePublicDataAn R library to build Google's Public Data Explorer DSPL Metadata files
googleVisInterface between R and the Google Visualisation API
gooJSONGoogle JSON Data Interpreter for R
goricGeneralized Order-Restricted Information Criterion
GOSimComputation of functional similarities between GO terms and gene products; GO enrichement analysis
govdatInterface to API methods for government data.
gpairsgpairs: The Generalized Pairs Plot
GPArotationGPA Factor Rotation
gpclibGeneral Polygon Clipping Library for R
gPdtestBootstrap goodness-of-fit test for the generalized Pareto distribution
GPfitGaussian Process Modeling
gplotsVarious R programming tools for plotting data
gppoisGaussian Processes for Poisson-noised Data
GPseqgpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
gptkGaussian Processes Tool-Kit
GPvamMaximum Likelihood Estimation of the Multiple Membership Mixed Models Used in Value-Added Modeling
gradeProvides functions for matching student-answers to teacher answers for a variety of data types.
gRainGraphical Independence Networks
granovaGraphical Analysis of Variance
granovaGGGraphical Analysis of Variance Using ggplot2
graphCompVisual graph comparison
gRapHDEfficient selection of undirected graphical models for high-dimensional datasets
GrapheRA multiplatform GUI for drawing customizable graphs in R
graphicsThe R Graphics Package
graphicsQCQuality Control for Graphics in R
GrassmannOptimGrassmann Manifold Optimization
gRbaseA package for graphical modelling in R
gRcInference in Graphical Gaussian Models with Edge and Vertex Symmetries
grDevicesThe R Graphics Devices and Support for Colours and Fonts
gregmiscGreg's Miscellaneous Functions
gridThe Grid Graphics Package
Grid2PolygonsConvert Spatial Grids to Polygons
gridBaseIntegration of base and grid graphics
gridDebugDebugging Grid Graphics
gridExtrafunctions in Grid graphics
gridGraphvizDrawing Graphs with Grid
GridRExecutes functions on remote hosts, clusters or grids.
gridSVGExport grid graphics as SVG
GriegSmithUses Grieg-Smith method on 2 dimentional spatial data
gRimGraphical Interaction Models
grImportImporting Vector Graphics
grofitThe package was developed to fit fit many growth curves obtained under different conditions.
groupedRegression Analysis of Grouped and Coarse Data
GroupSeqPerforming computations related to group sequential designs.
growcurvesBayesian semi and nonparametric growth curve models that additionally include multiple membership random effects.
growthrateBayesian reconstruction of growth velocity
grplassoFitting user specified models with Group Lasso penalty
grpregRegularization paths for regression models with grouped covariates
GRRGIGauge R and R Confidence Intervals
grtGeneral Recognition Theory
GSAGene set analysis
gsarimaTwo functions for Generalized SARIMA time series simulation
gsbDesignGroup Sequential Bayes Design
gsDesignGroup Sequential Design
gslwrapper for the Gnu Scientific Library
GSMGamma Shape Mixture
gsmaRtGene Set Microarray Testing
gsmoothrSmoothing tools
gssGeneral Smoothing Splines
gstatspatial and spatio-temporal geostatistical modelling, prediction and simulation
gstudioGeneticStudio packages for R.
gsubfnUtilities for strings and function arguments.
gtcorrCalculate efficiencies of group testing algorithms with correlated responses
gtoolsVarious R programming tools
GuerryMaps, data and methods related to Guerry (1833) "Moral Statistics of France"
gumbelGumbel copula
GUniFracGeneralized UniFrac distances
GUTSGUTS: Fast Calculation of the Likelihood of a Stochastic Survival Model
gvcm.catRegularized Categorial Effects/Categorial Effect Modifiers in GLMs
gvlmaGlobal Validation of Linear Models Assumptions
GWAFGenome-wide association/interaction analyses with family data
GWASExactHWExact Hardy-Weinburg testing for Genome Wide Association Studies
gwerAMControlling the genome-wide type I error rate in association mapping experiments
gWidgetsgWidgets API for building toolkit-independent, interactive GUIs
gWidgetsRGtk2Toolkit implementation of gWidgets for RGtk2
gWidgetstcltkToolkit implementation of gWidgets for tcltk package
gWidgetsWWWToolkit implementation of the gWidgets API for use with web pages
GWRMGWRM
gwrrGeographically weighted regression with penalties and diagnostic tools
h5rInterface to HDF5 Files
haarfiszSoftware to perform Haar Fisz transforms
HACEstimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC)
HadoopStreamingUtilities for using R scripts in Hadoop streaming
hapassocInference of trait associations with SNP haplotypes and other attributes using the EM Algorithm
HapEstXXRHapEstXXR
HAPimHapIM
HaplinAnalyzing case-parent triad and/or case-control data with SNP haplotypes
haplo.ccsEstimate Haplotype Relative Risks in Case-Control Data
haplo.statsStatistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
HaploSimHaploSim
hapsimHaplotype Data Simulation
HardyWeinbergGraphical tests for Hardy-Weinberg equilibrium
harvestrA Parallel Simulation Framework
hashFull feature implementation of hash/associated arrays/dictionaries
hbimHill/Bliss Independence Model for Combination Vaccines
hbmemHierarchical Bayesian Analysis of Recognition Memory
hdaHeteroscedastic Discriminant Analysis
HDclassifHigh Dimensionnal Supervised Classification and Clustering
hddplotUse known groups in high-dimensional data to derive scores for plots
hdecoHierarchical DECOmposition of Entropy for Categorical Map Comparisons
hdlmFitting High Dimensional Linear Models
HDMDStatistical Analysis Tools for High Dimension Molecular Data (HDMD)
hdrcdeHighest density regions and conditional density estimation
heatmap.plusHeatmap with more sensible behavior.
heavyPackage for outliers accomodation using heavy-tailed distributions
helloJavaWorldHello Java World
helprHelp for R.
heplotsVisualizing Hypothesis Tests in Multivariate Linear Models
hergmHierarchical Exponential-Family Random Graph Models
hettHeteroscedastic t-regression
hexbinHexagonal Binning Routines
hexViewViewing Binary Files
HFWutilscsv import, csv export, garbage collection,string matching and passing by reference
hgamHigh-dimensional Additive Modelling
hglmHierarchical Generalized Linear Models
HGLMMMHierarchical Generalized Linear Models
HGNChelperHandy functions for working with HGNC gene symbols and Affymetrix probeset identifiers.
HHStatistical Analysis and Data Display: Heiberger and Holland
HISimulation from distributions supported by nested hyperplanes
HIBAGHIBAG -- HLA Genotype Imputation with Attribute Bagging
HiddenMarkovHidden Markov Models
HiDimDAHigh Dimensional Discriminant Analysis
hier.partHierarchical Partitioning
hierarchicalDSFunctions for performing hierarchical analysis of distance sampling data
hierfstatEstimation and tests of hierarchical F-statistics
hierNetA Lasso for Hierarchical Interactions
HIestHybrid index estimation
highlightSyntax highlighter
hintsProvide hints on what to do next
hiPODhierarchical Pooled Optimal Design
hisemiHierarchical Semiparametric Regression of Test Statistics
HistDataData sets from the history of statistics and data visualization
histogramConstruction of regular and irregular histograms with different options for automatic choice of bins
hitandrun"Hit and Run" method for sampling uniformly form convex shapes.
hiveHadoop InteractiVE
HiveR2D and 3D Hive Plots for R
HLMdiagDiagnostic tools for two-level normal hierarchical linear models
hlrHidden Logistic Regression
HmiscHarrell Miscellaneous
HMMHMM - Hidden Markov Models
hmm.discnpHidden Markov models with discrete non-parametric observation distributions.
HMMmixThe HMMmix (HMM with mixture of gaussians as emission distribution) package
HMPHypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
HMPTreesStatistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data: Modeling, Visualization, and Two-Group Comparison
HMRFlux estimation with static chamber data
hofMore higher order functions for R.
holdemTexas Holdem simulator
HolidaysHoliday and halfday data, for use with the TimeWarp package
homalsGifi Methods for Optimal Scaling
homeRFunctions useful for building physics
homtestHomogeneity tests for Regional Frequency Analysis
hotComputation on micro-arrays
HotellingHotelling's T-squared test and variants
hotspotsHot spots
howmanyA lower bound for the number of correct rejections
HPbayesHeligman Pollard mortality model parameter estimation using Bayesian Melding with Incremental Mixture Importance Sampling
HSAURA Handbook of Statistical Analyses Using R
HSAUR2A Handbook of Statistical Analyses Using R (2nd Edition)
HSROCJoint meta-analysis of diagnostic test sensitivity and specificity with or without a gold standard reference test
HTMLUtilsFacilitates automated HTML report creation
htsHierarchical and grouped time series
HTSClusterClustering high throughput sequencing (HTS) data
httpRequestBasic HTTP Request
httrTools for working with URLs and HTTP
hugeHigh-dimensional Undirected Graph Estimation
HumMeth27QCReportHumMeth27QCReport: quality control and preprocessing of Illumina's Infinium methylation assays.
HW.pvalTesting Hardy-Weinberg Equilibrium for Multiallelic Genes
hwdeModels and tests for departure from Hardy-Weinberg equilibrium and independence between loci.
HWEBayesBayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing.
HWEintrinsicObjective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem
hwriterHTML Writer - Outputs R objects in HTML format
hybridHclustHybrid hierarchical clustering
HybridMCImplementation of the Hybrid Monte Carlo and Multipoint Hybrid Monte Carlo sampling techniques
hydroGOFGoodness-of-fit functions for comparison of simulated and observed hydrological time series
HydroMeEstimation of Soil Hydraulic Parameters from Experimental Data
hydroPSOModel-Independent Particle Swarm Optimisation for Environmental Models
hydroTSMTime series management, analysis and interpolation for hydrological modelling
HyperbolicDistThe hyperbolic distribution
hyperdirichletA generalization of the Dirichlet distribution
hypergeoThe hypergeometric function
hyperSpecInterface for hyperspectral data, i.e. spectra + meta info (spatial, time, concentration, ...)
HyPhyMacroevolutionary phylogentic analysis of species trees and gene trees
hypothesestestConfidence Intervals and Tests of Statistical Hypotheses
hypredSimulation of genomic data in applied genetics
hzarHybrid Zone Analysis using R
ibdregRegression Methods for IBD Linkage With Covariates
IBDsimSimulation of chromosomal regions shared by family members.
ibrIterative Bias Reduction
IBrokersR API to Interactive Brokers Trader Workstation
iBUGSAn Interface to R2WinBUGS by gWidgets
ic.inferInequality constrained inference in linear normal situations
IC2Inequality and Concentration Indices and Curves
ic50Standardized high-throughput evaluation of cell-based compound screens
icaOcularCorrectionIndependent Components Analysis (ICA) based eye-movement correction.
ICCFunctions facilitating the estimation of the Intraclass Correlation Coefficient
ICEIterated Conditional Expectation
ICEinferIncremental Cost-Effectiveness (ICE) Statistical Inference from Two Unbiased Samples
iClusterIntegrative clustering of multiple genomic data types
icompICOMP criterion
ICSTools for Exploring Multivariate Data via ICS/ICA
ICSNPTools for Multivariate Nonparametrics
idbgR debugger
iDEMOintegrated degradation models
identityJacquard Condensed Coefficients of Identity
IDPmiscUtilities of Institute of Data Analyses and Process Design (www.idp.zhaw.ch)
idrIrreproducible discovery rate
iFadAn integrative factor analysis model for drug-pathway association inference
IFPIdentifying functional polymorphisms in genetic association studies
ifsIterated Function Systems
ifultoolsInsightful Research Tools
iGassoGenetic association tests and utilities
iGenomicViewerTool for sending interactive bioinformatic heatmaps with tool-tip content.
IgorRRead binary files saved by Igor Pro (including Neuromatic data)
igraphNetwork analysis and visualization
igraph0Network analysis and visualization, old, deprecated package.
igraphdataA collection of network data sets for the igraph package
igraphtosoniaConvert iGraph graps to SoNIA .son files
iid.testiid-test
ImageMetricsFacilitates image analysis for social scientists.
ImapInteractive Mapping
imguRShare plots using the imgur.com image hosting service
IMISIncreamental Mixture Importance Sampling
ImpactIVIdentifying Causal Effect for Multi-Component Intervention Using Instrumental Variable Method
imprProbEstMinimum distance estimation in an imprecise probability model
imputationimputation
imputeMDRThe Multifactor Dimensionality Reduction (MDR) Analysis for Imcomplete Data
imputeYnImputing the last largest censored datum under weighted least squares
IndependenceTestsNonparametric tests of independence between random vectors.
indicspeciesFunctions to assess the strength and significance of relationship of species site group associations
ineqMeasuring Inequality, Concentration, and Poverty
InfDimInfine-dimensional model (IDM) to analyse phenotypic variation in growth trajectories.
inferenceFunctions to extract inferential values of a fitted model object
influence.METools for detecting influential data in mixed effects models
infoDecompuTEInformation Decomposition of Two-phase Experiments
informRR Tools for Creating Sequence Statistics
infotheoInformation-Theoretic Measures
infutilInformation Utility
inlineInline C, C++, Fortran function calls from R
inlinedocsConvert inline comments to documentation
insideRODEinsideRODE includes buildin functions with deSolve solver and C/FORTRAN interfaces to nlme, together with compiled codes.
insolSolar Radiation
int6464 bit integer types
intamapprocedures for automated interpolation
intamapInteractiveprocedures for automated interpolation - methods only to be used interactively, not included in intamap package
intcoxIterated Convex Minorant Algorithm for interval censored event data
integrativeMEintegrative mixture of experts
integrOmicsend of integrOmics package
InteractTests for marginal interactions in a 2 class response model
intergraphCoercion routines for network data objects in R
InterpolInterpolation of amino acid sequences
Interpol.THourly interpolation of multiple temperature daily series
intervalWeighted Logrank Tests and NPMLE for interval censored data
intervalsTools for working with points and intervals
intpointlinear programming solver by the interior point method and graphically (two dimensions)
intRegInterval Regression
intRegGOFIntegrated Regression Goodness of Fit
introgressmethods for analyzing introgression between divergent lineages
ipdmetaTools for subgroup analyses with multiple trial data using aggregate statistics
iplotsiPlots - interactive graphics for R
IPMpackBuilds and analyses Integral Projection Models (IPMs).
ipptoolboxIPP Toolbox
ipredImproved Predictors
IPSURIntroduction to Probability and Statistics Using R
ipwEstimate inverse probability weights.
IQCCImproved Quality Control Charts
iraceIterated Racing Procedures
iRefRiRefIndex Manager
iRegressionRegression methods for interval-valued variables
irlbaFast partial SVD by implicitly-restarted Lanczos bidiagonalization
irrVarious Coefficients of Interrater Reliability and Agreement
irtoysSimple interface to the estimation and plotting of IRT models
irtProbUtilities and Probability Distributions Related to Multidimensional Person Item Response Models (IRT)
irtreesEstimation of Tree-Based Item Response Models
isa2The Iterative Signature Algorithm
ISBFIterative Selection of Blocks of Features - ISBF
ISDA.Rinterval symbolic data analysis for R
isdalsProvides datasets for Introduction to Statistical Data Analysis for the Life Sciences
ISIPTAISIPTA network analysis
ismevAn Introduction to Statistical Modeling of Extreme Values
IsoFunctions to perform isotonic regression.
isocirIsotonic Inference for Circular data
ISOcodesSelected ISO codes
IsoGeneTesting for monotonic relationship between gene expression and doses in a microarray experiment.
isopamIsopam (Clustering)
isopatCalculation of isotopic pattern for a given molecular formula
isotoneActive set and generalized PAVA for isotone optimization
IsotopeRStable isotope analysis
ISOweekWeek of the year and weekday according to ISO 8601
iSubpathwayMinerThe package can implement the graph-based reconstruction and analyses of the KEGG pathways.
isvaIndependent Surrogate Variable Analysis
ISwRIntroductory Statistics with R
iteRatesParametric rate comparison
iteratorsIterator construct for R
iterLapApproximate probability densities by iterated Laplace Approximations
itertoolsIterator Tools
itsIrregular Time Series
itsmrTime series analysis package for students
ivbmaBayesian Instrumental Variable Estimation and Model Determination via Conditional Bayes Factors
ivivcA data analysis tool for in vitro-in vivo correlation (IVIVC)
iWebPlotsInteractive web-based plots
iwtpNumerical evaluation willingness to pay based on interval data
JADEJADE and other BSS methods as well as some BSS performance criteria
JavaGDJava Graphics Device
JGLPerforms the Joint Graphical Lasso for sparse inverse covariance estimation on multiple classes
JGRJGR - Java Gui for R
jitJust-in-time compiler for the R language
JJcorrCalculates polychorical correlations for several copula families.
JMJoint Modeling of Longitudinal and Survival Data
jmecFit joint model for event and censoring with cluster-level frailties
JmiscJulian Miscellaneous Function
JMLSDJoint Modeling of Longitudinal and Survival Data - Power Calculation
JohnsonJohnson Transformation
JohnsonDistributionJohnson Distribution
joineRJoint modelling of repeated measurements and time-to-event data
jointDiagJoint Approximate Diagonalization of a set of square matrices
JointModelingJoint Modelling of Mean and Dispersion
JOPJoint Optimization Plot
JoSAEFunctions for unit-level small area estimators and their variances
jpegRead and write JPEG images
JPSurvMethods for population-based cancer survival analysis
JudgeItJudgeIt
JuliaFractal Image Data Generator
kappalabNon-additive measure and integral manipulation functions
kappaSizeSample Size Estimation Functions for Studies of Interobserver Agreement
kapsK Adaptive Partitioning for Survival data
kBestShortestPathskbest: Finds K best paths in a given graph.
KendallKendall rank correlation and Mann-Kendall trend test
kequateThe kernel method of test equating
kerdiestNonparametric kernel estimation of the distribution function. Bandwidth selection and estimation of related functions.
kerfdrsemi-parametric kernel-based approach to local fdr estimations
kernlabKernel-based Machine Learning Lab
KernSmoothFunctions for kernel smoothing for Wand & Jones (1995)
KernSmoothIRTNonparametric Item Reponse Theory
KFASKalman Filter and Smoother for Exponential Family State Space Models.
kin.cohortAnalysis of kin-cohort studies
kinfitRoutines for fitting kinetic models to chemical degradation data
kinship2Pedigree functions
kknnWeighted k-Nearest Neighbors
klaRClassification and visualization
klausuRMultiple Choice Test Evaluation
klinLinear equations with Kronecker structure
km.ciConfidence intervals for the Kaplan-Meier estimator
kmiKaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting
kmlK-means for Longitudinal data
kml3dK-means for joint Longitudinal data
KMsurvData sets from Klein and Moeschberger (1997), Survival Analysis
knitcitationsCitations for knitr markdown files
knitrA general-purpose package for dynamic report generation in R
knnknn-gcv
knnGardenMulti-distance based k-Nearest Neighbors
knormMicroarray Data From Multiple Biologically Interrelated Experiments
kohonenSupervised and unsupervised self-organising maps
KoNLPKorean NLP Package
koRpusAn R Package for Text Analysis
KpartSpline Fitting
krigingOrdinary Kriging
KrigInvKriging-based Inversion for Deterministic and Noisy Computer Experiments
KRLSKernel-based Regularized Least Squares (KRLS)
ksKernel smoothing
KsPlotCheck the power of seveal statistical models.
kstKnowledge Space Theory
ktspairk-Top Scoring Pairs for Microarray Classification
kulifeDatasets and functions from the Faculty of Life Sciences, University of Copenhagen
kzaKolmogorov-Zurbenko Adaptive Filters
kzftKolmogorov-Zurbenko Fourier Transform and Applications
kzsKolmogorov-Zurbenko Spatial Smoothing and Applications
labdsvOrdination and Multivariate Analysis for Ecology
labeledLoopLabeled Loop
labelingAxis Labeling
labeltodendroConvert labels or tables to a dendrogram
labstatRLibreria del Laboratorio di Statistica con R
laekenEstimation of indicators on social exclusion and poverty
laercioDuncan test, Tukey test and Scott-Knott test.
LaFFast access to large ASCII files
LahmanSean Lahman's Baseball Database
Lambda4Estimation techniques for the reliability estimate: Maximized Lambda4
LambertWAnalyze and Gaussianize skewed, heavy-tailed data
lancet.iraqmortalitySurveys of Iraq Mortality Published in The Lancet
landsatRadiometric and topographic correction of satellite imagery
languageRData sets and functions with "Analyzing Linguistic Data: A practical introduction to statistics".
LaplacesDemonComplete Environment for Bayesian Inference
LargeRegressionLarge Regressions
larsLeast Angle Regression, Lasso and Forward Stagewise
laserLikelihood Analysis of Speciation/Extinction Rates from Phylogenies
lasso2L1 constrained estimation aka `lasso'
lassoshootingL1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting
latdiagDraws diagrams useful for checking latent scales
latentnetLatent position and cluster models for statistical networks
latticeLattice Graphics
latticeDensityDensity estimation and nonparametric regression on irregular regions
latticedlLattice direct labels
latticeExtraExtra Graphical Utilities Based on Lattice
LatticeKrigMultiresolution Kriging based on Markov random fields
latticistA graphical user interface for exploratory visualisation
lavaLinear Latent Variable Models
lava.tobitLVM with censored and binary outcomes
lavaanLatent Variable Analysis
lawstatAn R package for biostatistics, public policy, and law
lazyLazy Learning for Local Regression
lazyWeaveLaTeX Wrappers for R Users
LCAextendLatent Class Analysis (LCA) with familial dependence in extended pedigrees
lcdaLatent Class Discriminant Analysis
LCFdataData sets for package ``LMERConvenienceFunctions''
lcmmEstimation of latent class mixed models, joint latent class mixed models and mixed models for curvilinear outcomes
lcmrlcmr package
lda.cvCross-validation for linear discriminate analysis
ldboundsLan-DeMets Method for Group Sequential Boundaries
LDcorSVLDcorSV
ldDesignDesign of experiments for detection of linkage disequilibrium
LDdiagLink Function and Distribution Diagnostic Test for Social Science Researchers
LDheatmapGraphical display of pairwise linkage disequilibria between SNPs
ldlassoLD LASSO Regression for SNP Association Study
LDtestsExact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium
LeafAngleFits, plots, and summarizes leaf angle distributions.
LEAPFrOGLikelihood Estimation of Admixture in Parents From Offspring Genotypes
leapplatent effect adjustment after primary projection
leapsregression subset selection
LearnBayesFunctions for Learning Bayesian Inference
LearnEDAFunctions for Learning Exploratory Data Analysis
leivBivariate linear errors-in-variables estimation
LeLogicielRFunctions and datasets to accompany the book "Le logiciel R: Maitriser le langage, Effectuer des analyses statistiques" (french)
lemmaLaplace approximated EM Microarray Analysis
lessRLess Code, More Results
lestatA package for LEarning STATistics
lfeLinear Group Fixed Effects
lgaTools for linear grouping analysis (LGA)
lgcpLog-Gaussian Cox Process
LGSsimulating Linkage Group Selection (LGS)
lgtdlA set of methods for longitudinal data objects.
lhsLatin Hypercube Samples
libamtrackComputational routines for proton and ion radiotherapy
LiblineaRLinear Predictive Models Based On The Liblinear C/C++ Library.
lifecontingenciesPackage to perform actuarial mathematics for life contingencies insurances
LifeTablesA package to implement HMD model life table system
LIHNPSDPoisson Subordinated Distribution
likelihoodMethods for maximum likelihood estimation
LIMLinear Inverse Model examples and solution methods.
limitplotJitter/CI Plot with Ordered Points Below the Limit of Detection
limSolveSolving Linear Inverse Models
LinearizedSVRLinearized Support Vector Regression
linkcommTools for Generating, Visualizing, and Analysing Link Communities in Networks
linLIRlinear Likelihood-based Imprecise Regression
linprogLinear Programming / Optimization
lintTools to check R code style
lisoFitting lasso penalised additive isotone models
lispList-processing a la SRFI-1
listStatistical Methods for the Item Count Technique and List Experiment
LIStestLongest Increasing Subsequence Independence Test
ljrLogistic Joinpoint Regression
lleLocally linear embedding
lmbcLinear Model Bias Correction for RNA-Seq Data
lme4Linear mixed-effects models using S4 classes
lmecLinear Mixed-Effects Models with Censored Responses
LMERConvenienceFunctionsA suite of functions to back-fit fixed effects and forward-fit random effects, as well as other miscellaneous functions.
lmeSplineslmeSplines
lmfFunctions for estimation and inference of selection in age-structured populations
lmmLinear mixed models
lmmfitGoodness-of-fit-measures for linear mixed models with one-level-grouping
lmmlassoLinear mixed-effects models with Lasso
lmodel2Model II Regression
lmomL-moments
lmomcoL-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
LmomentsL-moments and quantile mixtures
lmomRFARegional frequency analysis using L-moments
lmPermPermutation tests for linear models
lmSupportSupport for Linear Models
lmtestTesting Linear Regression Models
LN3GVLN3GV
localdepthLocal Depth
locfdrComputes local false discovery rates
locfitLocal Regression, Likelihood and Density Estimation.
locpolKernel local polynomial regression
log4rA simple logging system for R, based on log4j.
LogConcDEADLog-concave Density Estimation in Arbitrary Dimensions
logconcensMaximum likelihood estimation of a log-concave density based on censored data
logcondensEstimate a Log-Concave Probability Density from iid Observations
logcondiscrEstimate a Log-Concave Probability Mass function from Discrete i.i.d. Observations
logginga tentative logging package
LogicForestLogic Forest
LogicRegLogic Regression
logistfFirth's bias reduced logistic regression
LogitNetInfer network based on binary arrays using regularized logistic regression
loglognormDouble log normal distribution functions
logregpermInference in Logistic Regression
logsplineLogspline density estimation routines
lokernKernel Regression Smoothing with Local or Global Plug-in Bandwidth
longclustModel-Based Clustering and Classification for Longitudinal Data
longitudinalAnalysis of Multiple Time Course Data
longitudinalDataLongitudinal Data
longmemoStatistics for Long-Memory Processes (Jan Beran) -- Data and Functions
longpowerSample size calculations for longitudinal data
longRPartRecursive partitioning of longitudinal data using mixed-effects models
loopA package for performing loop decomposition of weighted directed graphs in life cycle analysis, providing general network plotting methods, and analyzing food chain properties in ecology.
LoopAnalystA collection of tools to conduct Levins' Loop Analysis
lordifLogistic Regression Differential Item Functioning using IRT
lorecLOw Rand and sparsE Covariance matrix estimation
lossDevRobust Loss Development Using MCMC
LOSTMissing morphometric data simulation and estimation
LowRankQPLow Rank Quadratic Programming
lpcLassoed principal components for testing significance of features
LPCMLocal principal curve methods
lpridgeLocal Polynomial (Ridge) Regression
lpSolveInterface to Lp_solve v. 5.5 to solve linear/integer programs
lpSolveAPIR Interface for lp_solve version 5.5.2.0
lqaPenalized Likelihood Inference for GLMs
lqmmLinear Quantile Mixed Models
LS2WLocally stationary two-dimensional wavelet process estimation scheme
lsaLatent Semantic Analysis
LSDLots of Superior Depictions
lsmeansLeast-squares means
lsplsLS-PLS Models
lsrCompanion to "Learning Statistics with R"
lssthe accelerated failure time model to right censored data based on least-squares principle
ltmLatent Trait Models under IRT
LTPDvarLTPD plans for sampling inspection by variables
LTRPerform LTR analysis on microarray data
ltsaLinear time series analysis
lubridateMake dealing with dates a little easier
lucaLikelihood inference from case-control data Under Covariate Assumptions (LUCA)
LuminescencePackage for Luminescence Dating data analysis
LVQToolsLearning Vector Quantization Tools
lxbFast LXB file reader
MAcMeta-Analysis with Correlations
MAclinicalClass prediction based on microarray data and clinical parameters
MAdMeta-Analysis with Mean Differences
madaMeta-Analysis of Diagnostic Accuracy (mada)
MADAMThis package provides some basic methods for meta-analysis
MaeswrapWrapper functions for MAESTRA/MAESPA.
magiccreate and investigate magic squares
magicaxisPretty scientific plotting with minor-tick and log minor-tick support
magnetsSimulate micro-magnets dynamics
mailSending Email Notifications from R
MAINT.DataModel and Analize Interval Data
makeProjectCreates an empty package framework for the LCFD format
makeRPackage for managing projects with multiple versions derived from a single source repository.
malaria.emEM Estimation of Malaria Haplotype Probabilities from Multiply Infected Human Blood Samples
MALDIquantQuantitative Analysis of Mass Spectrometry Data
MAMSDesigning Multi-Arm Multi-Stage Studies
MAMSECalculation of Minimum Averaged Mean Squared Error (MAMSE) weights.
MangroveRisk prediction on trees
mapdataExtra Map Databases
mapLDLinkage Disequilibrium Mapping
MAPLESSmoothed age profile estimation
mapplotsData visualisation on maps
mapprojMap Projections
mapReducemapReduce - flexible mapReduce algorithm for parallel computation
mapsDraw Geographical Maps
maptoolsTools for reading and handling spatial objects
maptreeMapping, pruning, and graphing tree models
mArMultivariate AutoRegressive analysis
mar1sMultiplicative AR(1) with Seasonal Processes
marelacTools for Aquatic Sciences
margApproximate marginal inference for regression-scale models
marginalmodelplotsMarginal Mean Model Plots
marginTreemarginTree: margin trees for high-dimensional classification
markdownMarkdown rendering for R
MarkedPointProcessAnalysis of Marks of Marked Point Processes
maRketSimMarket simulator for R
marqLevAlgAn algorithm for least-squares curve fitting
MARSSMultivariate Autoregressive State-Space Modeling
MASSSupport Functions and Datasets for Venables and Ripley's MASS
MasterBayesML and MCMC Methods for Pedigree Reconstruction and Analysis
MATMultidimensional Adaptive Testing (MAT)
mathgraphDirected and undirected graphs
MatchingMultivariate and Propensity Score Matching with Balance Optimization
MatchItMatchIt
matlabMATLAB emulation package
MatrixSparse and Dense Matrix Classes and Methods
matrixcalcCollection of functions for matrix differential calculus
MatrixEQTLMatrix eQTL: Ultra fast eQTL analysis via large matrix operations
MatrixModelsModelling with Sparse And Dense Matrices
matrixStatsMethods that apply to rows and columns of a matrix
MATTOOLSModern Calibration Functions for the Modern Analog Technique (MAT)
MAVTgsaOrdinary least square test and Multivariate Analysis Of Variance test with n contrasts
MaXactExact max-type Cochran-Armitage trend test(CATT)
maxentLow-memory Multinomial Logistic Regression with Support for Text Classification
maxLikMaximum Likelihood Estimation
maxlikeModel species distributions by estimating the probability of occurrence using presence-only data.
maxLinearConditional Samplings for Max-Linear Models
maxstatMaximally Selected Rank Statistics
MBAMultilevel B-spline Approximation
MBCluster.SeqModel-Based Clustering for RNA-seq Data
MBESSMBESS
mblmMedian-Based Linear Models
mbmdrModel Based Multifactor Dimensionality Reduction
mboostModel-Based Boosting
mc2dTools for Two-Dimensional Monte-Carlo Simulations
MCAPSMCAPS data and results
mcbiopiMatrix Computation Based Identification Of Prime Implicants
mcclustProcess an MCMC Sample of Clusterings
MCETools for evaluating Monte Carlo Error
mcgaMachine coded genetic algorithms for real-valued optimization problems
mcgibbsitWarnes and Raftery's MCGibbsit MCMC diagnostic
MCLIMESimultaneous Estimation of the Regression Coefficients and Precision Matrix
mclogitMixed Conditional Logit
mclustNormal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation
mcmcMarkov Chain Monte Carlo
MCMCglmmMCMC Generalised Linear Mixed Models
MCMCpackMarkov chain Monte Carlo (MCMC) Package
mcmcplotsCreate Plots from MCMC Output
mcmcseMonte Carlo Standard Errors for MCMC
MCMChybridGPHybrid Markov chain Monte Carlo using Gaussian Processes
mcoMulti criteria optimization algorithms and related functions
McompData from the M-competitions
MCPANMultiple comparisons using normal approximation
McParreRun a Regenerative Markov chain in Parallel on a Cluster
MCPModDesign and Analysis of Dose-Finding Studies (see also DoseFinding package)
mcprofileMultiple Contrast Profiles
mcrMethod Comparison Regression
mcsmFunctions for Monte Carlo Methods with R
McSpatialNonparametric spatial data analysis
MCUSUMMultivariate Cumulative Sum (MCUSUM) Control Chart
mdaMixture and flexible discriminant analysis
mdedMeasuring the difference between two empirical distributions
MDMMultinomial Diversity Model
MDRDetect gene-gene interactions using multifactor dimensionality reduction
mebootMaximum Entropy Bootstrap for Time Series
medAdherenceMedication Adherence: Commonly Used Definitions
mederrRankBayesian Methods for Identifying the Most Harmful Medication Errors
mediationR Package for Causal Mediation Analysis
MeDiChIMeDiChI ChIP-chip deconvolution library
mefaMultivariate Data Handling in Ecology and Biogeography
mefa4Multivariate Data Handling with S4 Classes and Sparse Matrices
meiflyInteractive model exploration using GGobi
memMoving Epidemics Method R Package.
memiscTools for Management of Survey Data, Graphics, Programming, Statistics, and Simulation
memoiseMemoise functions
MEMSSData sets from Mixed-effects Models in S
MergeGUIA GUI for Merging Datasets in R
merrorAccuracy and Precision of Measurements
MESSMiscellaneous esoteric statistical scripts
metaMeta-Analysis with R
MetABELmeta-analysis of genome-wide SNP association results
MetabolAnalyzeProbabilistic latent variable models for metabolomic data.
MetabonomicGUI for Metabonomic Analysis
metacorMeta-analysis of correlation coefficients
MetadataCollates Metadata for Climate Surface Stations
MetaDEMetaDE: Microarray meta-analysis for differentially expressed gene detection
metaforMeta-Analysis Package for R
metaLikLikelihood inference in meta-analysis and meta-regression models.
metaMAMeta-analysis for MicroArrays
MetaPathPerform the Meta-Analysis for Pathway Enrichment analysis (MAPE).
MetaPCAMetaPCA: Meta-analysis in the Dimension Reduction of Genomic data
MetaQCMetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis
metatestFit and test metaregression models
Meth27QCMeth27QC: sample quality analysis, and sample control analysis
MethCompFunctions for analysis of method comparison studies.
methodsFormal Methods and Classes
MetricsEvaluation metrics for machine learning
metRologySupport for metrological applications
metrumrgPharmacometric tools for data preparation, modeling, simulation, and reporting
metsAnalysis of Multivariate Event Times
MEWMAMultivariate Exponentially Weighted Moving Average (MEWMA) Control Chart
MExPositionMulti-table ExPosition
MFDAModel Based Functional Data Analysis
MFDFModeling Functional Data in Finance
mFilterMiscellaneous time series filters
mfpMultivariable Fractional Polynomials
MFSASCreation and Evaluation of Multilevel Fixed and Sequential Sampling Plans
mgcvMixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
mgpdmgpd: Functions for multivariate generalized Pareto distribution (MGPD of Type II)
mgraphGraphing map attributes and non-map variables in R
MHadaptiveGeneral Markov Chain Monte Carlo for Bayesian Inference using adaptive Metropolis-Hastings sampling
mhsmmParameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences.
mhtMultiple Hypotheses Testing For Variable Selection
mhurdleEstimation of models with limited dependent variables
MChtestMonte Carlo hypothesis tests with Sequential Stopping
miMissing Data Imputation and Model Checking
miceMultivariate Imputation by Chained Equations
micEconMicroeconomic Analysis and Modelling
micEconAidsDemand Analysis with the Almost Ideal Demand System (AIDS)
micEconCESAnalysis with the Constant Elasticity of Scale (CES) function
micEconSNQPSymmetric Normalized Quadratic Profit Function
microbenchmarkSub microsecond accurate timing functions.
MIfunsPharmacometric tools for data preparation, modeling, simulation, and reporting
MigClimImplementing dispersal into species distribution models
miguiGraphical User Interface of the mi Package
MImixMixture summary method for multiple imputation
mimRA package for graphical modelling in R
MindOnStatsData sets included in Utts and Heckard's Mind on Statistics
MineyImplementation of the Well-Known Game to Clear Bombs from a Given Field (Matrix)
minimaxMinimax distribution family
minpack.lmR interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK, plus support for bounds
minPtestGene region-level testing procedure for SNP data, using the min P test resampling approach
minqaDerivative-free optimization algorithms by quadratic approximation
minxentEntropy Optimization Distributions
miPMultiple Imputation Plots
MIPHENOMutant Identification through Probabilistic High throughput Enabled NOrmalization
mirtMultidimensional Item Response Theory
miRtestcombined miRNA- and mRNA-testing
MISABayesian Model Search and Multilevel Inference for SNP Association Studies
misc3dMiscellaneous 3D Plots
miscFuncsMiscellaneous Useful Functions
MiscPsychoMiscellaneous Psychometric Analyses
miscToolsMiscellanneous Tools and Utilities
missForestNonparametric Missing Value Imputation using Random Forest
MissingDataGUIA GUI for Missing Data Exploration
missMDAHandling missing values with/in multivariate data analysis (principal component methods)
mitoolsTools for multiple imputation of missing data
mixEstimation/multiple Imputation for Mixed Categorical and Continuous Data
mixAKMixture of methods including mixtures
mixdistFinite Mixture Distribution Models
mixedQFEstimator with Qudratics Forms in Mixeds Models
mixerRandom graph clustering
mixexpDesign and analysis of mixture experiments
mixfdrComputes false discovery rates and effect sizes using normal mixtures
mixlowmixlow method for assessing drug synergism
MixModAnalysis of Mixed Models
mixOmicsOmics Data Integration Project
mixPHMMixtures of proportional hazard models.
mixRaschMixture Rasch Models with JMLE
mixregFunctions to fit mixtures of regressions.
mixsepForensic Genetics DNA Mixture Separation
MixSimSimulating Data to Study Performance of Clustering Algorithms
mixsmsnFitting finite mixture of scale mixture of skew-normal distributions .
mixstockfunctions for mixed stock analysis
mixtoolsTools for analyzing finite mixture models
mkinRoutines for fitting kinetic models with one or more state variables to chemical degradation data
MKLEMaximum kernel likelihood estimation.
MKmiscMiscellaneous Functions from M. Kohl
mkssdEfficient multi-level k-circulant supersaturated designs
mlbenchMachine Learning Benchmark Problems
MLCMMaximum Likelihood Conjoint Measurement
MLDAMethylation Linear Discriminant Analysis (MLDA)
MLDSMaximum Likelihood Difference Scaling
MLEcensComputation of the MLE for bivariate (interval) censored data
mlegpMaximum Likelihood Estimates of Gaussian Processes
MLEPMaximum likelihood estimate of penetrance parameters
mleurMaximum likelihood unit root test
mlgtMulti-Locus Geno-Typing
mlica2Independent Component Analysis using Maximum Likelihood
mlmmmML estimation under multivariate linear mixed models with missing values
mlmRevExamples from Multilevel Modelling Software Review
mlogitmultinomial logit model
mlogitBMABayesian Model Averaging for Multinomial Logit Models
MLPAstatsMLPA analysis to detect gains and loses in genes
MMThe multiplicative multinomial distribution
mmandMathematical Morphology in Any Number of Dimensions
mmapMap Pages of Memory
mmcmModified Maximum Contrast Method
mmdsMixture Model Distance Sampling (mmds)
mmelnMMELN : Estimation of multinormal mixture distribution.
mmetaMultivariate Meta-Analysis Using Sarmanov Beta Prior Distributions
MMIXModel selection uncertainty and model mixing
mmm2Multivariate marginal models with shared regression parameters
mmodModern measures of population differentiation
MMSTDATASETS FROM MMST
MNMMultivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks
mnormtThe multivariate normal and t distributions
MNPR Package for Fitting the Multinomial Probit Model
mnspcMultivariate Nonparametric Statistical Process Control
mobForestModel based Random Forest analysis
MobilizeMobilize plots and functions
mocGENERAL NONLINEAR MIXTURES OF CURVES
MOCCAMulti-objective optimization for collecting cluster alternatives
ModalclustHierarchical Modal Clustering
modeestMode Estimation
modehuntMultiscale Analysis for Density Functions
modelcfModeling physical computer codes with functional outputs using clustering and dimensionality reduction
modelfreeModel-free estimation of a psychometric function
ModelGoodValidation of prediction models
ModelMapCreates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps.
modeltoolsTools and Classes for Statistical Models
modTempEffModelling temperature effects using time series data
moduleColorBasic module functions
mokkenMokken Scale Analysis in R
mombfMoment and Inverse Moment Bayes factors
momentsMoments, cumulants, skewness, kurtosis and related tests
MomocsShape Analysis of Outlines
mondateKeep track of dates in terms of months
monmlpMonotone multi-layer perceptron neural network
monomvnEstimation for multivariate normal and Student-t data with monotone missingness
monregNonparametric monotone regression
moonsunBasic astronomical calculations with R
MorseGenSimple raw data generator based on user-specified summary statistics.
MortalitySmoothSmoothing and forecasting Poisson counts with P-splines
mosaicProject MOSAIC (mosaic-web.org) statistics and mathematics teaching utilities
motmotModels of Trait Macroevolution on Trees
moultModels for Analysing Moult Data
movMFMixtures of von Mises-Fisher Distributions
mpaCoWords Method
mpcMPC - Multiple Precision Complex Library
MPCIMultivariate Process Capability Indices (MPCI)
MPDiRData sets and scripts for Modeling Psychophysical Data in R
MplusAutomationAutomating Mplus Model Estimation and Interpretation
mpmMultivariate Projection Methods
mpMapMulti-parent RIL genetic analysis
mpmcorrelogramMultivariate Partial Mantel Correlogram
mpolySymbolic computation and more with multivariate polynomials
mprobitMultivariate probit model for binary/ordinal response
mptMultinomial Processing Tree (MPT) Models
MPTinRAnalyze Multinomial Processing Tree Models
MPVData Sets from Montgomery, Peck and Vining's Book
mraAnalysis of Mark-Recapture data
mratiosInferences for ratios of coefficients in the general linear model
MRCEMRCE
mrdrcModel-robust concentration-response analysis
mrdsMark-Recapture Distance Sampling (mrds)
mritcMRI tissue classification.
mRmAn R package for conditional maximum likelihood estimation in mixed Rasch models.
msapStatistical analysis for Methylation-Sensitive Amplification Polimorphism data
MsatAlleleVisualizes the scoring and binning of microsatellite fragment sizes
msBreastProtein Mass Spectra Dataset from a Breast Cancer Study
MSBVARMarkov-Switching, Bayesian, Vector Autoregression Models
msDilutionProtein Mass Spectra Dataset from a Dilution Experiment
mseapcaMetabolite set enrichment analysis for factor loading in principal component analysis
MSeasyPreprocessing of Gas Chromatography-Mass Spectrometry (GC-MS) data
MSeasyTkGUIMSeasy Tcl/Tk Graphical User Interface
mseqModeling non-uniformity in short-read rates in RNA-Seq data
MSGData and functions for the book Modern Statistical Graphics
msgpsDegrees of freedom of elastic net, adaptive lasso and generalized elastic net
msirModel-based Sliced Inverse Regression
msmMulti-state Markov and hidden Markov models in continuous time
mspathMulti-state Path-Dependent Models in Discrete Time
msProcessProtein Mass Spectra Processing
msProstateProtein Mass Spectra Dataset from a Prostate Cancer Study
MSQCMultivariate Statistical Quality Control
msrMorse-Smale approximation, regression and visualization
msSurvNonparametric Estimation for Multistate Models
mstateData preparation, estimation and prediction in multi-state models
MSToolkitThe MSToolkit library for clinical trial design
mtcreatorCreating MAGE-TAB files using mtcreator
mtsdiMultivariate time series data imputation
MTSKNNMultivariate two-sample tests based on K-nearest-neighbors
MUCflightsMunich Franz-Josef-Strauss Airport Pattern Analysis
mugnetMixture of Gaussian Bayesian Network Model
muhazHazard Function Estimation in Survival Analysis
multcompSimultaneous Inference in General Parametric Models
multcompViewVisualizations of Paired Comparisons
MultEqMultiple Equivalence Tests and Simultaneous Confidence Intervals
multibiplotGUIMultibiplot Analysis in R
MulticlasstestingPerformance of N-ary classification testing
multicoolPermutations of multisets in cool-lex order.
MultiChIPmixHMMMultiChIPmixHMM
MultiLCIRTMultidimensional latent class Item Response Theory models
multilevelMultilevel Functions
multinomRobRobust Estimation of Overdispersed Multinomial Regression Models
MultiOrdGeneration of multivariate ordinal variates.
MultiPhenMultiPhen, a package for the genetic association testing of multiple phenotypes
multiPIMVariable Importance Analysis with Population Intervention Models
multipolmultivariate polynomials
multisensiMultivariate Sensitivity Analysis
multitableSimultaneous manipulation of multiple arrays of data, with data.list objects
multitaperMultitaper Spectral Analysis
multivatorA multivariate emulator
multmodTesting of multiple outcomes
multxpertCommon Multiple Testing Procedures and Gatekeeping Procedures
mumaMetabolomic Univariate and Multivariate Analysis
MuMInMulti-model inference
munfoldMetric Unfolding
munsellMunsell colour system
muRLMailmerge using R, LaTeX, and the Web
mutatrMutable objects for R.
mutossUnified multiple testing procedures
mutossGUIA graphical user interface for the MuToss Project
MVAAn Introduction to Applied Multivariate Analysis with R
mvabundstatistical methods for analysing multivariate abundance data
MVBMutivariate Bernoulli log-linear model
mvbutilsWorkspace organization, code and documentation editing, package prep and editing, etc.
mvcMulti-View Clustering
mvmetaMultivariate meta-analysis and meta-regression
mvnaNelson-Aalen estimator of the cumulative hazard in multistate models
mvngGrAdSoftware for moving grid adjustment in plant breeding field trials
mvnmleML estimation for multivariate normal data with missing values.
mvnormtestNormality test for multivariate variables
mvoutlierMultivariate outlier detection based on robust methods
mvpartMultivariate partitioning
MVPARTwrapMVPARTwrap: Additional functionnalities for package mvpart.
MVpowerGive power for a given effect size using multivariate classification methods
mvProbitMultivariate Probit Models
MVRMean-Variance Regularization
mvsfShapiro-Francia Multivariate Normality Test
mvShapiroTestGeneralized Shapiro-Wilk test for multivariate normality
mvtBinaryEPGenerates Correlated Binary Data
mvtmetaMultivariate meta-analysis
mvtnormMultivariate Normal and t Distributions
mvtsplotMultivariate Time Series Plot
mxkssdEfficient mixed-level k-circulant supersaturated designs
myepisodesMyEpisodes RSS/API functions
nacopulaNested Archimedean Copulas
NADANondetects And Data Analysis for environmental data
nadivFunctions to construct non-additive genetic relatedness matrices
nanoptools for nanoparticle simulation and PDF calculation
NanoStringNormNormalize NanoString miRNA and mRNA data
NbClustAn examination of indices for determining the number of clusters : NbClust Package
NBDdirichletNBD-Dirichlet model of consumer buying behavior for marketing research
nbpMatchingfunctions for non-bipartite optimal matching
NBPSeqNegative Binomial Models for RNA-Sequencing Data
NCBI2RNCBI2R-An R package to navigate and annotate genes and SNPs
ncdfInterface to Unidata netCDF data files
ncfspatial nonparametric covariance functions
ncgComputes the noncentral gamma function
ncvregRegularization paths for SCAD- and MCP-penalized regression models
ndlNaive Discriminative Learning
ndvitsNDVI Time series extraction and analysis
nearisoNear-Isotonic Regression
NeatMapNon-clustered heatmap alternatives
negenesEstimating the number of essential genes in a genome
neldermeadR port of the Scilab neldermead module
NeMoExceptionnal Network Motifs in biological networks
NestedCohortSurvival Analysis for Cohorts with Missing Covariate Information
NetClusterClustering for networks
NetCompNetwork Generation and Comparison
NetDataNetwork Data for McFarland's SNA R labs
NetIndicesEstimating network indices, including trophic structure of foodwebs in R
NetPreProcNetPreProc: Network Pre-Processing and normalization.
networkClasses for Relational Data
NetworkAnalysisStatistical inference on populations of weighted or unweighted networks.
networkDynamicDynamic Extensions for Network Objects
networksisSimulate bipartite graphs with fixed marginals through sequential importance sampling
neuralnetTraining of neural networks
neuroblastomaNeuroblastoma
neuRosimFunctions to generate fMRI data including activated data, noise data and resting state data.
nFactorsParallel Analysis and Non Graphical Solutions to the Cattell Scree Test
nfdaNonparametric Functional Data Analysis
nFDRNonparametric Estimate of FDR Based on Bernstein Polynomials
ngaNGA Earthquake Ground Motion Prediction Equations
ngspatialClasses for Spatial Data
NHPoissonModelling and validation of non homogeneous Poisson processes
NightDayNight and Day Boundary Plot Funtion
NipponJapanese utility functions and data
NISTnlsNonlinear least squares examples from NIST
nlADGRegression in the Normal Linear ADG Model
nleqslvSolve systems of non linear equations
nlmeLinear and Nonlinear Mixed Effects Models
nlmeODENon-linear mixed-effects modelling in nlme using differential equations
nlmrtFunctions for nonlinear least squares solutions
nloptrR interface to NLopt
nlregHigher Order Inference for Nonlinear Heteroscedastic Models
NLRootsearching for the root of equation
nlrwrNonlinear regression with R
nls2Non-linear regression with brute force
nlsmsnFitting nonlinear models with scale mixture of skew-normal distributions.
nlstoolsTools for nonlinear regression diagnostics
NlsyLinksUtilities and kinship information for Behavior Genetics and Developmental research using the NLSY.
nltA nondecimated lifting transform for signal denoising
nltmNon-linear Transformation Models
nlts(non)linear time series analysis
NMFAlgorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFNNon-negative Matrix Factorization
NMMAPSliteNMMAPS Data Lite
NMOFNumerical Methods and Optimization in Finance
NMRSNMR Spectroscopy
nnclustNearest-neighbour tools for clustering
nnetFeed-forward Neural Networks and Multinomial Log-Linear Models
nnlsThe Lawson-Hanson algorithm for non-negative least squares (NNLS)
nodeHarvestNode Harvest for regression and classification
noiaImplementation of the Natural and Orthogonal InterAction (NOIA) model
nonbinROCROC-type analysis for non-binary gold standards
nor1mixNormal (1-d) Mixture Models (S3 Classes and Methods)
normAnalysis of multivariate normal datasets with missing values
NormalGammaNormal-gamma convolution model
normalpPackage for exponential power distributions (EPD)
NORMT3Evaluates complex erf, erfc, Faddeeva, and density of sum of Gaussian and Student's t
normwhn.testNormality and White Noise Testing
nortestTests for Normality
notifyRSend push notifications to your smartphone via pushover.net (ACCOUNT REQUIRED!)
npNonparametric kernel smoothing methods for mixed data types
nparcompnparcomp-package
nparLDNonparametric Analysis of Longitudinal Data in Factorial Experiments
npdeNormalised prediction distribution errors for nonlinear mixed-effect models
NPHMCSample Size Calculation for the Proportional Hazards Cure Model
nplplotPlotting non-parametric linkage results
npmlregNonparametric maximum likelihood estimation for random effect models
NPMPMtertiary probabilistic model in predictive microbiology for use in food manufacture
npmvNonparametric Comparison of Multivariate Samples
nppbibNonparametric Partially-Balanced Incomplete Block Design Analysis
NPsimexNonparametric Smoothing for contaminated data using Simulation-Extrapolation
npstGeneralization of Hewitt's Seasonality Test
NRAIAData sets from "Nonlinear Regression Analysis and Its Applications"
NSAPost-normalization of total copy numbers
nsRFANon-supervised Regional Frequency Analysis
nullaborTools for graphical inference
numConversionTest of accuracy of formatting numbers.
numDerivAccurate Numerical Derivatives
nutshellData for "R in a Nutshell"
nvisCombination of visualization functions for nuclear data using ggplot2 and ggcolpairs.
nwsR functions for NetWorkSpaces and Sleigh
OAIHarvesterHarvest Metadata Using OAI-PMH v2.0
OarrayArrays with arbitrary offsets
objectPropertiesA factory of self-describing properties.
objectSignalsobjectSignals
obliclusCluster-based factor rotation
oblique.treeOblique Trees for Classification Data
obliqueRFOblique Random Forests from Recursive Linear Model Splits
obsSensSensitivity analysis for Observational studies.
ocOC Roll Call Analysis Software.
occEstimates PET neuroreceptor occupancies
oceAnalysis of Oceanographic data
ocompositionGibbs sampler for ordered compositional data
ODBOpen Document Databases (.odb) management
odesolveSolvers for Ordinary Differential Equations
odfWeaveSweave processing of Open Document Format (ODF) files
odfWeave.surveySupport for odfWeave on the survey package
odprismOptimal design and performance of random intercept and slope models.
OhmageR Client for Mobilize/Andwellness server
OIdataData sets and supplements (OpenIntro)
OIsurvSurvival analysis supplement to OpenIntro guide
OjaNPMultivariate Methods Based on the Oja Median and Related Concepts
okmesonetRetrieve Oklahoma Mesonet climatological data
OligoSpecificitySystemOligo Specificity System
OLScurveOLS growth curve trajectories
omdfilter the molecular descriptors for QSAR
oncomodelMaximum likelihood tree models for oncogenesis
OncotreeEstimating oncogenetic trees
OneHandClappingPrediction of condition-specific transcription factor interactions
onemapSoftware for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses
onionoctonions and quaternions
OOmiscOzgur-Ozlem Miscellaneous
OPEOuter-product emulator
opefimorOption Pricing and Estimation of Financial Models in R
openairTools for the analysis of air pollution data
opencpu.demoOpenCPU Demo apps.
opencpu.encodeopencpu object encoder/decoder
openintroOpenIntro data sets and supplemental functions
openNLPopenNLP Interface
openNLPmodels.enopenNLP Models for English
openNLPmodels.esopenNLP Models for Spanish
OpenRepGridTools to analyse repertory grid data
OpenStreetMapAccess to open street map raster images
operatorsAdditional binary operators for the R language
OPIOpen Perimetry Interface
opmTools for analysing OmniLog(R) Phenotype Microarray data
oposSOMPackage for analysis and visualization of metagenes
opsOptimal Power Space Transformation
optBiomarkerEstimation of optimal number of biomarkers for two-group microarray based classifications at a given error tolerance level for various classification rules
OptimalCutpointsComputing optimal cutpoints in diagnostic tests
optimbaseR port of the Scilab optimbase module
optimsimplexR port of the Scilab optimsimplex module
optimxA Replacement and Extension of the optim() Function
optmatchFunctions for optimal matching
optparseCommand line option parser.
orclusORCLUS subspace clustering
ORCMEOrder Restricted Clustering for Microarray Experiments
orddomOrdinal Dominance Statistics
ORDER2PARENTEstimate parent distributions with data of several order statistics
OrdFacRegLeast squares, logistic, and Cox-regression with ordered predictors
ordinalRegression Models for Ordinal Data
OrdMonRegCompute least squares estimates of one bounded or two ordered isotonic regression curves
ordPensSelection and/or Smoothing of Ordinal Predictors
OrgMassSpecROrganic Mass Spectrometry
ORIClustOrder-restricted Information Criterion-based Clustering Algorithm
orientlibSupport for orientation data
orlocaThe package deals with Operations Research LOCational Analysis models
orloca.esSpanish version of orloca package
ORMDRORMDR
oro.dicomRigorous - DICOM Input / Output
oro.niftiRigorous - NIfTI+ANALYZE+AFNI Input / Output
oro.petRigorous - Positron Emission Tomography
orQAOrder Restricted Assessment Of Microarray Titration Experiments
orskConverting Odds Ratio to Relative Risk in Cohort Studies with Partial Data Information
orthMultivariate Logistic Regressions Using Orthogonalized Residuals.
orthogonalsplinebasisOrthogonal Bspline Basis Functions
orthopolynomCollection of functions for orthogonal and orthonormal polynomials
osDesignDesign and analysis of observational studies
osmarOpenStreetMap and R
ouchOrnstein-Uhlenbeck models for phylogenetic comparative hypotheses
outliersTests for outliers
OUwieAnalysis of evolutionary rates in an OU framework
ozPlot the Australian coastline and states
p2distanceWelfare's Synthetic Indicator
p3state.msmAnalyzing survival data
paPerformance Attribution for Equity Portfolios
packConvert values to/from raw vectors
packClassicToy example of Pack Classic
packdepMapping dependencies among R packages
packS4Toy example of S4 package
pacoseiPACOSE, PACOSE and other methods for covariance selection
pairedCIConfidence intervals for the ratio of locations and for the ratio of scales of two paired samples
PairedDataPaired Data Analysis
pairheatmapA tool for comparing heatmaps
PairTradingclassical pair trading based on cointegration in finance
PairVizVisualization using Eulerian tours and Hamiltonian decompositions
pairwiseCIConfidence intervals for two sample comparisons
palaeoSigSignificance tests for palaeoenvironmental reconstructions
paleoMASPaleoecological Analysis
paleotreePaleontological and Phylogenetic Analyses of Evolution
paleoTSAnalyze paleontological time-series
palomaPoisson Approximation for LOcal Motif Assessment
paltranWA, WA-PLS, MW for paleolimnology
pamctdpPrincipal Axes Methods for Contingency Tables with Partition Structures on Rows and Columns
pammPower analysis for random effects in mixed models
pamrPam: prediction analysis for microarrays
panMultiple imputation for multivariate panel or clustered data
panderAn R pandoc writer
panelPanel
parallelSupport for Parallel computation in R
ParamHelpersHelpers for parameters in black-optimization, tuning and maching learning.
paramlinkParametric linkage analysis in R
paranHorn's Test of Principal Components/Factors
parcorRegularized estimation of partial correlation matrices
parfmParametric Frailty Models
parfossilParallelized functions for palaeoecological and palaeogeographical analysis
parmigeneParallel Mutual Information estimation for Gene Network reconstruction.
parserDetailed R source code parser
partDSAPartitioning using deletion, substitution, and addition moves
partitionMetricCompute a distance metric between two partitions of a set
partitionsAdditive partitions of integers
partsmPeriodic Autoregressive Time Series Models
partyA Laboratory for Recursive Partytioning
partykitA Toolkit for Recursive Partytioning
parviolParviol
PASPolygenic Analysis System (PAS)
pastecsPackage for Analysis of Space-Time Ecological Series
PASWRPROBABILITY and STATISTICS WITH R
pathClassClassification using biological pathways as prior knowledge
pathmoxSegmentation Trees in Partial Least Squares Path Modeling
PAWLImplementation of the PAWL algorithm
pbapplyAdding Progress Bar to '*apply' Functions
pbatRP2BAT
PBImiscA set of datasets used in my classes or in the book ,,Modele liniowe i mieszane w R, wraz z przykladami w analizie danych''
pbivnormVectorized Bivariate Normal CDF
pbkrtestParametric bootstrap and Kenward Roger based methods for mixed model comparison
PBSadmbPBS ADMB
PBSddesolveSolver for Delay Differential Equations
PBSmappingMapping Fisheries Data and Spatial Analysis Tools
PBSmodellingGUI Tools Made Easy: Interact with Models, Explore Data, Give Dynamic Presentations
pcaL1Three L1-Norm PCA Methods
pcalgEstimation of CPDAG/PAG and causal inference using the IDA algorithm
pcaPAParallel Analysis for ordinal and numeric data using polychoric and Pearson correlations with S3 classes.
pcaPPRobust PCA by Projection Pursuit
pcenumPermutations and Combinations Enumeration
PCICtImplementation of POSIXct work-alike for 365 and 360 day calendars.
PCITPCIT algorithm - Partial Correlation Coefficient with Information Theory
pcrcoalA package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997).
PCSCalculate the probability of correct selection (PCS)
pcsePanel-Corrected Standard Error Estimation in R
pcurvePrincipal curve analysis
pdcPermutation Distribution Clustering
pdfClusterCluster analysis via nonparametric density estimation
pdistPartitioned Distance Function
Peak2TroughEstimation of the peak-to-trough ratio of a seasonal variation component
PeaksPeaks
pearPackage for Periodic Autoregression Analysis
PearsonDSPearson Distribution System
PearsonICAIndependent component analysis using score functions from the Pearson system
pecPrediction Error Curves for Survival Models
pedanticsFunctions to facilitate power and sensitivity analyses for genetic studies of natrual popualtions
pedigreePedigree functions
pedigreemmPedigree-based mixed-effects models
pegasPopulation and Evolutionary Genetics Analysis System
PEIPFunctions for Aster Book on Inverse Theory
penalizedL1 (lasso and fused lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model
penalizedLDAPenalized classification using Fisher's linear discriminant
penalizedSVMFeature Selection SVM using penalty functions
pencopulaFlexible Copula Density Estimation with Penalized Hierarchical B-Splines
pendensityDensity Estimation with a Penalized Mixture Approach
penDvineFlexible Pair-Copula Estimation in D-vines with Penalized Splines
pensimSimulation of high-dimensional data and parallelized repeated penalized regression
peperrParallelised Estimation of Prediction Error
pequodModerated regression package
PerfMeasPerfMeas: Performance Measures for ranking and classification tasks
PerformanceAnalyticsEconometric tools for performance and risk analysis.
permExact or Asymptotic permutation tests
PermAlgoPermutational algorithm to simulate survival data
permaxpermax
permtestPermutation test to compare variability within and distance between two groups
permuteFunctions for generating restricted permutations of data
PERregressRegression Functions and Datasets
perturbTools for evaluating collinearity
pesticidesAnalysis of single serving and composite pesticide residue measurements
PETSimulation and Reconstruction of PET Images
PFFunctions related to prevented fraction.
pfdaPaired Functional Data Analysis
pgamPoisson-Gamma Additive Models.
pgirmessData analysis in ecology
pglmpanel generalized linear model
pGLSGeneralized Least Square in comparative Phylogenetics
pgmmParsimonious Gaussian mixture models
pgnormThe p-generalized normal distribution
pgsPrecision of Geometric Sampling
phangornPhylogenetic analysis in R
PhaseTypeInference for Phase-type Distributions
phcfMModelling anthropogenic deforestation
pheatmapPretty Heatmaps
phenologyTools to manage a parametric function that describes phenology
phiaPost-Hoc Interaction Analysis
phitestNonparametric goodness-of-fit methods based on phi-divergences
phmmProportional Hazards Mixed-effects Model (PHMM)
phomPersistent Homology in R
phonRR tools for phoneticians and phonologists
phonToolsA collection of functions useful for phonetics work.
phullp-hull: a generalization of convex hull, X-Y hull and bounding rectangle
PhViDPhViD: an R package for PharmacoVigilance signal Detection.
phybaseBasic functions for phylogenetic analysis
phyclustPhylogenetic Clustering (Phyloclustering)
phyextAn extension of some of the classes in phylobase. Tree objects now support subnodes on branches
phylobaseBase package for phylogenetic structures and comparative data
phyloclimIntegrating phylogenetics and climatic niche modelling
PHYLOGRFunctions for phylogenetically based statistical analyses
phylosimR packge for simulating biological sequence evolution
phylotoolsPhylogenetic tools for Eco-phylogenetics
PhysicalActivityProcess Physical Activity Accelerometer Data
phytoolsPhylogenetic Tools for comparative biology (and other things)
pi0Estimating the proportion of true null hypotheses for FDR
picanteR tools for integrating phylogenies and ecology
PIPSPredicted Interval Plots
pixmapBitmap Images (``Pixel Maps'')
PKBasic Non-Compartmental Pharmacokinetics
PKfitA Data Analysis Tool for Pharmacokinetics
pkgmakerPackage development utilities
PKgraphModel diagnostics for population pharmacokinetic models
PKmodelFinderSoftware for Pharmacokinetic model
PKPDmodelsPharmacokinetic/pharmacodynamic models
PKreportA reporting pipeline for checking population pharmacokinetic model assumption
pksProbabilistic Knowledge Structures
PKtoolsunified computational interfaces for pop PK
PL.popNPopulation Size Estimation
planTools for project planning
planarMultilayer optics
PlayerRatingsDynamic Updating Methods For Player Ratings Estimation
playitbyrRepresenting and exploring data through sound
playwithA GUI for interactive plots using GTK+
plgpParticle Learning of Gaussian Processes
plinkIRT Separate Calibration Linking Methods
PLISMultiplicity control using Pooled LIS statistic
plmLinear Models for Panel Data
plmDEAdditive partially linear models for differential gene expression analysis
plnPolytomous logit-normit (graded logistic) model estimation
plotGoogleMapsPlot SP data as HTML map mashup over Google Maps
plotKMLVisualization of spatial and spatio-temporal objects in Google Earth
plotmoPlot a model's response while varying the values of the predictors.
plotpcPlot principal component histograms around a scatter plot.
plotrixVarious plotting functions
plotSEMMGraphing nonlinear latent variable interactions in SEMM
plRaschLog Linear by Linear Asscociation models
plsPartial Least Squares and Principal Component regression
plsdofDegrees of Freedom and Statistical Inference for Partial Least Squares Regression
plsgenomicsPLS analyses for genomics
plspmPartial Least Squares Data Analysis Methods
plugdensityPlug-in Kernel Density Estimation
plumbrMutable and dynamic data models
plusPenalized Linear Unbiased Selection
plyrTools for splitting, applying and combining data
PMAPenalized Multivariate Analysis
pmcPhylogenetic Monte Carlo
pmgPoor Man's GUI
pmlrPenalized Multinomial Logistic Regression
pmmlGenerate PMML for various models
pmrProbability Models for Ranking Data
pngRead and write PNG images
poibinThe Poisson Binomial Distribution
PoiClaCluClassification and clustering of sequencing data based on a Poisson model
poilogPoisson lognormal and bivariate Poisson lognormal distribution
poisson.glm.mixFit high dimensional mixtures of Poisson GLM's
PoissonSeqSignificance analysis of sequencing data based on a Poisson log linear model
poistweediePoisson-Tweedie exponential family models
poLCAPolytomous variable Latent Class Analysis
polsplinePolynomial spline routines
polyapostSimulating from the Polya posterior
polycorPolychoric and Polyserial Correlations
polydectpolydect
polynomA collection of functions to implement a class for univariate polynomial manipulations
PolynomFPolynomials in R
polysatTools for Polyploid Microsatellite Analysis
polySegratioSimulate and test marker dosage for dominant markers in autopolyploids
polySegratioMMBayesian mixture models for marker dosage in autopolyploids
polytomousPolytomous logistic regression for fixed and mixed effects
polywogBootstrapped Basis Regression with Oracle Model Selection
PomicPattern Oriented Modelling Information Criterion
PoMoSPolynomial (ordinary differential equation) Model Search
pompStatistical inference for partially observed Markov processes
poohPartial Orders and Relations
popbioConstruction and analysis of matrix population models
popdemoProvides Tools For Demographic Modelling Using Projection Matrices
popgenStatistical and Population Genetics
PopGenKitUseful functions for (batch) file conversion and data resampling in microsatellite datasets
PopGenomePopulation genetic analysis
popPKSummary of Population Pharmacokinetic Analysis
portesPortmanteau Tests for Time Series Models
portfolioAnalysing equity portfolios
portfolioSimFramework for simulating equity portfolio strategies
postCPA package to estimate posterior probabilities in change-point models using constrained HMM
POTGeneralized Pareto Distribution and Peaks Over Threshold
pottsMarkov Chain Monte Carlo for Potts Models
PottsUtilsUtility Functions of the Potts Models
powellPowell's UObyQA algorithm
powerGWASinteractionPower Calculations for Interactions for GWAS
powerMediationPower/Sample size calculation for mediation analysis
powerpkgPower analyses for the affected sib pair and the TDT design
powerSurvEpiPower and sample size calculation for survival analysis of epidemiological studies
PowerTOSTPower and Sample size based on two one-sided t-tests (TOST) for (bio)equivalence studies
PPPerson Parameter estimation
ppcorPartial and Semi-partial (Part) correlation
ppiPrePredict protein-protein interactions based on functional and topological similarities.
pplsPenalized Partial Least Squares
ppMeasuresPoint pattern distances and prototypes.
ppsFunctions for PPS sampling
ppstatPoint Process Statistics
PPtreeProjection pursuit classification tree
prabclusFunctions for clustering of presence-absence, abundance and multilocus genetic data
pracmaPractical Numerical Math Functions
pragmaProvides a pragma / directive / keyword syntax for R.
PrecipStatPrecipitation Statistics
predbayescorClassification rule based on Bayesian naive Bayes models with feature selection bias corrected
PredictABELAssessment of risk prediction models
PredictiveRegressionPrediction Intervals for Three Basic Statistical Models
predmixcorClassification rule based on Bayesian mixture models with feature selection bias corrected
prefmodUtilities to fit paired comparison models for preferences
PresenceAbsencePresence-Absence Model Evaluation.
prettyGraphsprettyGraphs: publication-quality graphics.
prettyRPretty descriptive stats.
prevREstimating regional trends of a prevalence from a DHS
primPatient Rule Induction Method (PRIM)
primerFunctions and data for A Primer of Ecology with R
princurveFits a Principal Curve in Arbitrary Dimension
PrivateLRDifferentially private regularized logistic regression
prLogisticEstimation of Prevalence Ratios using Logistic Models
probElementary Probability on Finite Sample Spaces
probemapperConnects to QBRC's ProbeMapper platform
ProbForecastGOPProbabilistic weather forecast using the GOP method
pROCdisplay and analyze ROC curves
processdataProcess Data
ProDenICAProduct Density Estimation for ICA using tilted Gaussian density estimates
prodlimProduct Limit Estimation for event history and survival analysis
productplots
profdpmProfile Dirichlet Process Mixtures
ProfessRGrades Setting and Exam Maker
ProfileLikelihoodProfile Likelihood for a Parameter in Commonly Used Statistical Models
profileModelTools for profiling inference functions for various model classes
profrAn alternative display for profiling information
proftoolsProfile Output Processing Tools for R
ProgGUIinRsupport package for "Programming Graphical User Interfaces in R"
proj4A simple interface to the PROJ.4 cartographic projections library
ProjectTemplateAutomates the creation of new statistical analysis projects.
PropCIsVarious confidence interval methods for proportions
proptestTests of the Proportional Hazards Assumption
protoPrototype object-based programming
protoclustHierarchical clustering with prototypes
proxyDistance and Similarity Measures
PSAgraphicsPropensity Score Analysis Graphics
PSCBSAnalysis of Parent-Specific DNA Copy Numbers
psclPolitical Science Computational Laboratory, Stanford University
PSCNParent Specific DNA Copy Number Estimation
pseudoPseudo - observations
psgpProjected Spatial Gaussian Process (psgp) methods
PSMNon-Linear Mixed-Effects modelling using Stochastic Differential Equations.
psoParticle Swarm Optimization
pspearmanSpearman's rank correlation test
psplinePenalized Smoothing Splines
psyVarious procedures used in psychometry
psychProcedures for Psychological, Psychometric, and Personality Research
psychometricApplied Psychometric Theory
psychomixPsychometric Mixture Models
psychotoolsInfrastructure for Psychometric Modeling
psychotreeRecursive Partitioning Based on Psychometric Models
psyphyFunctions for analyzing psychophysical data in R
PTAkPrincipal Tensor Analysis on k modes
ptinpolyPoint-In-Polyhedron Test (2D and 3D)
PtProcessTime Dependent Point Process Modelling
ptwParametric Time Warping
PVAClonePopulation Viability Analysis with Data Cloning
pvclassP-values for Classification
pvclustHierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
PVRComputes PVR and PSR
pwrBasic functions for power analysis
PwrGSDPower in a Group Sequential Design
pwtPenn World Table
pxRPC-Axis with R
pycnoPycnophylactic Interpolation
pyramidFunctions to draw population pyramid
qatQuality Assurance Toolkit
QCAQualitative Comparative Analysis
QCA3Yet another package for Qualitative Comparative Analysis
QCAGUIQCA Graphical User Interface
qccQuality Control Charts
qgraphNetwork representations of relationships in data
qLearnEstimation and inference for Q-learning
qlspackQuasi Least Square Package
QLSplineQLSpline
qmapQuantile-mapping for post-processing climate model output
qmrparserParser combinator in R
qpq-order partial correlation graph search algorithm
qpcRModelling and analysis of real-time PCR data
qPCR.CTqPCR data analysis and plot package
qqplotterQuantile-quantile analysis of 24-hr precipitation using a frame work based on the exponential distribution
qrfactorSimultaneous simulation of Q and R mode factor analyses
QRMProvides R-language code to examine Quantitative Risk Management concepts
qrnnQuantile regression neural network
QSARdataQuantitative Structure Activity Relationship (QSAR) Data Sets
QTQT Knowledge Management System
qtlTools for analyzing QTL experiments
qtlbimQTL Bayesian Interval Mapping
qtlbookDatasets for the R/qtl book
qtlDesignDesign of QTL experiments
qtlhotInference for QTL Hotspots
qtlmtTools for mapping multiple complex traits
qtlnetCausal Inference of QTL Networks
QTLNetworkRInteractive software package for QTL visualization
QTLRelTools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree
QuACNQuACN: Quantitative Analysis of Complex Networks
quadprogFunctions to solve Quadratic Programming Problems.
qualityToolsStatistical Methods for Quality Science
qualVQualitative Validation Methods
quantchemQuantitative chemical analysis: calibration and evaluation of results
quantmodQuantitative Financial Modelling Framework
QuantPsycQuantitative Psychology Tools
quantregQuantile Regression
quantregForestQuantile Regression Forests
quantspecQuantile-based Spectral Analysis of Time Series
QuasiSeqQuasiSeq
quaternionsArithmetics and linear algebra with Quaternions
queueingBasic Markovian queueing models
QUICEstimate sparse inverse correlation matrix using regularization
qvcalcQuasi variances for factor effects in statistical models
R.cacheFast and light-weight caching (memoization) of objects
R.devicesEnhanced methods for handling graphical devices
R.filesetsEasy handling of and access to files organized in structured directories
R.hugeMethods for accessing huge amounts of data [DEPRECATED]
R.matlabRead and write of MAT files together with R-to-Matlab connectivity
R.methodsS3Utility function for defining S3 methods
R.ooR object-oriented programming with or without references
R.rspDynamic generation of scientific reports
R.utilsVarious programming utilities
R0Estimation of R0 and real-time reproduction number from epidemics
R1magicCompressive Sampling: Sparse signal recovery utilities
R2admbADMB to R interface functions
R2BayesXEstimate Structured Additive Regression Models with BayesX
R2CubaMultidimensional Numerical Integration
r2dRue2d Rain Use Efficience model
R2G2Converting R CRAN outputs into Google Earth.
R2HTMLHTML exportation for R objects
R2jagsA Package for Running jags from R
r2lhR to LaTeX and HTML
R2OpenBUGSRunning OpenBUGS from R
R2PPTSimple R Interface to Microsoft PowerPoint using rcom or RDCOMClient.
R2STATSA GTK GUI for fitting and comparing GLM and GLMM in R
R2SWFConvert R Graphics to Flash Animations
R2wdWrite MS-Word documents from R
R2WinBUGSRunning WinBUGS and OpenBUGS from R / S-PLUS
R330An R package for Stats 330
r4ssR code for Stock Synthesis
raceRacing methods for the selection of the best
RADFit RAD models to biological data
RadioSondeTools for plotting skew-T diagrams and wind profiles
RAFMAdmixture F-model
rainbowRainbow plots, bagplots and boxplots for functional data
rakeNormalize sample weights using marginal total population weights.
rampsBayesian Geostatistical Modeling with RAMPS
randaesRandom number generator based on AES cipher
RandForestGUIRandForestGUI
randomTrue random numbers using random.org
random.polychor.paA Parallel Analysis With Polychoric Correlation Matrices
RandomFieldsSimulation and Analysis of Random Fields
randomForestBreiman and Cutler's random forests for classification and regression
randomizeBEFunction to create a random list for crossover studies
randomLCARandom Effects Latent Class Analysis
randomNamesRandom name generating function and data set
randomSurvivalForestRandom Survival Forests
randtoolboxtoolbox for pseudo and quasi random number generation and RNG tests.
RandVarImplementation of random variables
rangeMapperA platform for the study of macroecology of life history traits
RankAggregWeighted rank aggregation
rankhazardRank-hazard plots
RANNFast Nearest Neighbour Search
rapportA report templating system
RArcInfoFunctions to import data from Arc/Info V7.x binary coverages
rasclassSupervised Raster Image Classification
RaschSamplerRasch Sampler
RassocRobust tests for case-control genetic association studies
rasterGeographic analysis and modeling with raster data
rasterVisVisualization methods for the raster package
rateratio.testExact rate ratio test
RatingsModel-based Ratings Figures
rationalfunManipulation of Rational Functions
RAtmosphereStandard Atmosperic profiles
rattleGraphical user interface for data mining in R
rAverageParameter estimation for the averaging model of Information Integration Theory
rbamtoolsReading, manipulation and writing BAM (Binary alignment) files.
rbenchmarkBenchmarking routine for R
rBeta2009The Beta Random Number and Dirichlet Random Vector Generating Functions
rboundsPerform Rosenbaum bounds sensitivity tests for matched and unmatched data.
rbugsFusing R and OpenBugs
RCReproducible Computing
RCALICalculation of the Integrated Flow of Particles between Polygons
RcaptureLoglinear Models for Capture-Recapture Experiments
RCassandraR/Cassandra interface
rcddrcdd (Computational Geometry)
rcdkrcdk - Interface to the CDK Libraries
rcdklibsrcdklib - CDK libraries packaged for R
RcellMicroscopy Based Cytometry Data Analysis Package
RcgminConjugate gradient minimization of nonlinear functions with box constraints
RclusterppLinkable C++ clustering
RcmdrR Commander
RcmdrPlugin.BCARcmdr Plug-In for Business and Customer Analytics
RcmdrPlugin.coinRcmdr Coin Plug-In
RcmdrPlugin.depthToolsR commander Depth Tools Plug-In
RcmdrPlugin.doByRcmdr doBy Plug-In
RcmdrPlugin.DoER Commander Plugin for (industrial) Design of Experiments
RcmdrPlugin.doexRcmdr plugin for Stat 4309 course
RcmdrPlugin.EACSPIRPlugin de R-Commander para el manual EACSPIR
RcmdrPlugin.EBMRcmdr Evidence Based Medicine Plug-In package
RcmdrPlugin.epackRcmdr plugin for time series
RcmdrPlugin.ExportGraphically export output to LaTeX or HTML
RcmdrPlugin.FactoMineRGraphical User Interface for FactoMineR
RcmdrPlugin.HHRcmdr support for the HH package
RcmdrPlugin.IPSURAn IPSUR Plugin for the R Commander
RcmdrPlugin.KMggplot2Rcmdr Plug-In for Kaplan-Meier Plot and Other Plots by Using the ggplot2 Package
RcmdrPlugin.MAcMeta-Analysis with Correlations (MAc) Rcmdr Plug-in
RcmdrPlugin.MAdMeta-Analysis with Mean Differences (MAd) Rcmdr Plug-in
RcmdrPlugin.mosaicAdds menu items to produce mosaic plots and assoc plots to Rcmdr
RcmdrPlugin.MPAStatsR Commander Plug-in for MPA Statistics
RcmdrPlugin.orlocaorloca Rcmdr Plug-in
RcmdrPlugin.pointGRcmdr Graphical POINT of view for questionnaire data Plug-In
RcmdrPlugin.PTSome discrete exponential dispersion models: Poisson-Tweedie
RcmdrPlugin.qccRcmdr qcc Plug-In
RcmdrPlugin.qualRcmdr plugin for quality control course
RcmdrPlugin.SCDARcmdr plugin for designing and analyzing single-case experiments
RcmdrPlugin.SensoMineRGraphical User Interface for SensoMineR
RcmdrPlugin.SLCSLC Rcmdr Plug-in
RcmdrPlugin.sosEfficiently search R Help pages
RcmdrPlugin.StatisticalURVStatistical URV Rcmdr Plug-In
RcmdrPlugin.steepnessSteepness Rcmdr Plug-in
RcmdrPlugin.survivalR Commander Plug-in for the survival Package
RcmdrPlugin.SurvivalTRcmdr Survival Plug-In
RcmdrPlugin.TeachingDemosRcmdr Teaching Demos Plug-In
RcmdrPlugin.TextMiningRcommander plugin for "tm" package
RcmdrPlugin.UCAUCA Rcmdr Plug-in
RColorBrewerColorBrewer palettes
rcomR COM Client Interface and internal COM Server
rconifersR interface to the CONIFERS forest growth model
RcppSeamless R and C++ Integration
RcppArmadilloRcpp integration for Armadillo templated linear algebra library
RcppBDTRcpp bindings for the Boost Date_Time library
rcppbugsR binding for cppbugs
RcppClassicDeprecated 'classic' Rcpp API
RcppCNPyRcpp bindings for NumPy files
RcppDEGlobal optimization by differential evolution in C++
RcppEigenRcpp integration for the Eigen templated linear algebra library.
RcppExamplesExamples using Rcpp to interface R and C++
RcppGSLRcpp integration for GNU GSL vectors and matrices
RcppSMCRcpp bindings for Sequential Monte Carlo
RcsdpR interface to the CSDP semidefinite programming library
rCURCUR decomposition package
Rd2roxygenConvert Rd to roxygen documentation and utilities to improve documentation
rdaShrunken Centroids Regularized Discriminant Analysis
rdatamarketData access API for DataMarket.com
rdetoolsRelevant Dimension Estimation (RDE) in Feature Spaces
RdistanceDistance sampling analyses
rDNAR Bindings for the Discourse Network Analyzer
RdroolsA rules engine for R based on Drools
RdroolsjarsRdrools jars
rdryadDryad API interface.
RDSR Functions for Respondent-Driven Sampling
RdsmThreads Environment for R
rdyncallImproved Foreign Function Interface (FFI) and Dynamic Bindings to C Libraries (e.g. OpenGL)
ReacTranReactive transport modelling in 1D, 2D and 3D
Read.isiAutomated access to old World Fertility Survey data saved in fixed-width format based on ISI-formatted codebooks.
readbitmapRead bitmap images (BMP,JPEG,PNG) without external dependencies
readBrukerFlexDataReads mass spectrometry data in Bruker *flex format
ReadImagesImage Reading Module for R
readMLDataReading machine learning benchmark data sets from different sources in their original format.
readMzXmlDataReads mass spectrometry data in mzXML format
realizedRealized
reamsResampling-Based Adaptive Model Selection
RearrangementMonotonize point and interval functional estimates by rearrangement
rebmixThe Rebmix Package
ReCiPaRedundancy Control in Pathways databases
recommenderlabLab for Developing and Testing Recommender Algorithms
recommenderlabBXBook-Crossing Dataset (BX) for recommenderlab
recommenderlabJesterJester Dataset for recommenderlab
RecordLinkageRecord Linkage in R
RecordsRecord Values and Record Times
REEMtreeRegression Trees with Random Effects for Longitudinal (Panel) Data
refReferences for R
refundRegression with Functional Data
REGENTREGENT: Risk Estimation for Genetic and Environmental Traits
registryRegistry infrastructure
reglogitSimulation-based Regularized Logistic Regression
regressGaussian linear models with linear covariance structure
regsubseqDetect and Test Regular Sequences and Subsequences
regtestRegression testing
rehhSearching for footprints of selection using Haplotype Homozygosity based tests
relaItem Analysis Package with Standard Errors
relaimpoRelative importance of regressors in linear models
relationsData Structures and Algorithms for Relations
RelativeRiskRelative Risk
relaxrelax -- R Editor for Literate Analysis and lateX
relaxoRelaxed Lasso
reldistRelative Distribution Methods
releventRelational Event Models
ReliabilityFunctions for estimating parameters in software reliability models
reliaRPackage for some probability distributions.
relimpRelative Contribution of Effects in a Regression Model
relSimRelative Simulator
relsurvRelative survival
remixRemix your data
rEMMExtensible Markov Model (EMM) for Data Stream Clustering in R
remMapRegularized Multivariate Regression for Identifying Master Predictors
RenextRenewal method for extreme values extrapolation
RenextGUIGUI for Renext
RepeatedHighDimDetection of global group effect in microarrays data
replicationDemosAgnotology
repolrRepeated measures proportional odds logistic regression
reportrA general message and error reporting system
reporttoolsGenerate LaTeX tables of descriptive statistics
representDetermine the representativity of two multidimensional data sets
REQSR/EQS Interface
ResearchMethodsUsing GUIs to help teach statistics to non-statistics students
reshapeFlexibly reshape data.
reshape2Flexibly reshape data: a reboot of the reshape package.
reshapeGUIA GUI for the reshape2 and plyr packages.
ResistorArrayelectrical properties of resistor networks
ResourceSelectionResource Selection (Probability) Functions for Use-Availability Data
reviewManage Review Logs
reweightAdjustment of Survey Respondent Weights
RExcelInstallerIntegration of R and Excel, (use R in Excel, read/write XLS files)
RFARegional Frequency Analysis
rFernsRandom ferns classifier
RFinanceYJRFinanceYJ
rfishbaseR Interface to FishBASE
RfitRank Estimation for Linear Models
RFLPtoolsTools to analyse RFLP data
RfmriVCVarying stimulus coefficient fMRI models in R
RFOCGraphics for Spherical Distributions and Earthquake Focal Mechanisms
RForcecomRForcecom provides the connection to Force.com (Salesforce.com) from R.
rfPermuteEstimate permutation p-values for importance metrics.
RfunFuny application of R
rgamRobust Generalized Additive Model
rgbifInterface to the Global Biodiversity Information Facility API methods
RGCCARegularized Generalized Canonical Correlation Analysis
rgcvpackR Interface for GCVPACK Fortran Package
rgdalBindings for the Geospatial Data Abstraction Library
rgenoudR version of GENetic Optimization Using Derivatives
rgeosInterface to Geometry Engine - Open Source (GEOS)
rgexfAn R library to build GEXF network files
rggobiInterface between R and GGobi
RghcnV3Global Historical Climate Network Version 3
RGIFTCreate quizzes in GIFT Format
rgl3D visualization device system (OpenGL)
RglpkR/GNU Linear Programming Kit Interface
RgoogleMapsOverlays on Google map tiles in R
rgpR genetic programming framework
rgrThe GSC Applied Geochemistry EDA Package
RGraphicsData and Functions from the book R Graphics, Second Edition
rgrsFunctions to make R usage in social sciences easier (in french)
RGtk2R bindings for Gtk 2.8.0 and above
RGtk2ExtrasData frame editor and dialog making wrapper for RGtk2
RH2DBI/RJDBC interface to h2 Database
RhhCalculating multilocus heterozygosity and heterozygosity-heterozygosity correlation
RHiveR and Hive
rhospSide effect risks in hospital : simulation and estimation
rHpccInterface between HPCC and R
RHRVHeart rate variability analysis of ECG data
RHTRegularized Hotelling's T-square Test for Pathway (Gene Set) Analysis
rChoiceDialogsrChoiceDialogs collection
riri: R package for performing randomization-based inference for experiments
ridgeRidge Regression with automatic selection of the penalty parameter
RiDMCR interface to the idmclib library
RIFSRandom Iterated Function System (RIFS)
RigroupRigroup: Provides small integer group functions
richComputes and compares species richnesses
rindexIndexing for R
ringscaleRingscale
RInsideC++ classes to embed R in C++ applications
riojaAnalysis of Quaternary Science Data
risaacA fast cryptographic random number generator using ISAAC by Robert Jenkins.
riskRegressionRisk regression for survival analysis
RISmedDownload content from NCBI databases
RItoolsRandomization inference tools
rivRobust instrumental variables estimator
RJaCGHReversible Jump MCMC for the analysis of CGH arrays.
rjagsBayesian graphical models using MCMC
rJavaLow-level R to Java interface
RJDBCProvides access to databases through the JDBC interface
rjeMiscellaneous useful functions
RjmsR messaging using ActiveMQ and jms
RjmsjarsRjms jars
rJPSGCSR-interface to gene drop Java Programs for Statistical Genetics and Computational Statistics (JPSGCS)
rjsonJSON for R
RJSONIOSerialize R objects to JSON, JavaScript Object Notation
rJythonR interface to Python via Jython
RKEAR/KEA interface
rknnRandom KNN Classification and Regression
RknotsRknots
RlabFunctions and Datasets Required for ST370 class
RlabkeyData exchange between R and LabKey Server
RLastFMR interface to last.fm API
rlecuyerR interface to RNG with multiple streams
RLRsimExact (Restricted) Likelihood Ratio tests for mixed and additive models.
RM2Revenue Management and Pricing Package
rmaccalculate RMAC or FMAC agreement coefficients
RMallowFit Multi-Modal Mallows' Models to ranking data.
RmalschainsContinuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains) in R
RMarkR Code for MARK Analysis
RMAWGENRMAWGEN (R Multi-site Auto-regressive Weather GENerator): a package to generate daily time series from monthly mean values
RMCFunctions for fitting Markov models
RMediationAn R Package for Mediation Analysis Confidence Intervals
RMendeleyInterface to Mendeley API methods
rmetaMeta-analysis
rminerSimpler use of data mining methods (e.g. NN and SVM) in classification and regression.
RmiscRmisc: Ryan Miscellaneous
RmixmodAn interface of MIXMOD
rmmseg4jR interface to the Java Chinese word segmentation system of mmseg4j
RMongoMongoDB Client for R
rmongodbR-MongoDB driver
RmpfrR MPFR - Multiple Precision Floating-Point Reliable
rmsRegression Modeling Strategies
RMTstatDistributions, Statistics and Tests derived from Random Matrix Theory
RnavGraphUsing graphs as a navigational infrastructure.
RnavGraphImageDataSome image data used in the RnavGraph package demos
RNCBIThe java ncbi interface to R
RNCBIAxis2LibsAxis2 libraries for use in the R environment.
RNCBIEUtilsLibsEUtils libraries for use in the R environment.
RNCEPObtain, organize, and visualize NCEP weather data
rneosrneos: XML-RPC Interface to NEOS
RNetCDFR Interface to NetCDF Datasets
RNetLogoProvides an interface to the agent-based modelling plattform NetLogo
rngSetSeedInitialization of the R base random number generator Mersenne-Twister with a vector of an arbitrary length.
rngWELLtoolbox for WELL random number generators.
rngwell19937WELL19937a random number generator implemented with 53 bit output
RniftilibRniftilib - R Interface to NIFTICLIB (V2.0.0: 2010-07-20)
RNiftyRegMedical image registration using the NiftyReg library
ROAuthR interface for OAuth
RobAStBaseRobust Asymptotic Statistics
robCompositionsRobust Estimation for Compositional Data.
robethR functions for robust statistics
robfilterRobust Time Series Filters
RobLoxOptimally robust influence curves and estimators for location and scale
RobLoxBioCInfinitesimally robust estimators for preprocessing omics data
RobRexOptimally robust influence curves for regression and scale
robustInsightful Robust Library
RobustAFTTruncated Maximum Likelihood fit and Robust Accelerated Failure Time regression for Gaussian and logWeibull case.
robustbaseBasic Robust Statistics
robustfaAn Object Oriented Framework for Robust Factor Analysis
robustHDRobust methods for high-dimensional data
RobustRankAggregMethods for robust rank aggregation
robustregRobust Regression Functions
robustXeXperimental eXtraneous eXtraordinary ... Functionality for Robust Statistics
roccROC based classification
rockchalkRegression Estimation and Presentation
rococoRObust rank COrrelation COefficient and test
rocplusROC, Precision-Recall, Convex Hull and other plots.
ROCRVisualizing the performance of scoring classifiers.
ROCwoGSNon-parametric estimation of ROC curves without Gold Standard Test
RODBCODBC Database Access
RODMR interface to Oracle Data Mining
ROIR Optimization Infrastructure
ROI.plugin.glpkROI-plugin GLPK
ROI.plugin.quadprogROI-plugin quadprog
ROI.plugin.symphonyROI-plugin symphony
rolasizedSolarized colours in R
RookRook - a web server interface for R
rootSolveNonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations
ROptEstOptimally robust estimation
ROptEstOldOptimally robust estimation - old version
ROptRegTSOptimally robust estimation for regression-type models
rorRobust Ordinal Regression MCDA library
roxygenLiterate Programming in R
roxygen2In-source documentation for R
RpadWorkbook-style, web-based interface to R
rpanelSimple Interactive Controls for R Using the tcltk Package.
rpartRecursive Partitioning
rpart.plotPlot rpart models. An enhanced version of plot.rpart.
rpartOrdinalOrdinal classification tree functions
rpartScoreClassification trees for ordinal responses
RPCLRRPCLR (Random-Penalized Conditional Logistic Regression)
rpfResponse Probability Functions
RpgSQLDBI/RJDBC interface to PostgreSQL Database
rphastR interface to PHAST software for comparative genomics
rplosInterface to PLoS Journals API methods
rplotengineR as a plotting engine
RPMGGraphical User Interface (GUI) for interactive R analysis sessions
RPMMRecursively Partitioned Mixture Model
rPortaR/PORTA interface
rportfoliosRandom portfolio generation
RPostgreSQLR interface to the PostgreSQL database system
rpsychiStatistics for psychiatric research
rpubchemrpubchem - Interface to the PubChem Collection
RPyGeoArcGIS Geoprocessing in R via Python
RQDAR-based Qualitative Data Analysis
rqmcmb2Markov Chain Marginal Bootstrap for Quantile Regression
RquakeSeismic Hypocenter Determination
RQuantLibR interface to the QuantLib library
RramasMatrix population models
rrBLUPRidge regression and other kernels for genomic selection
rrBlupMethod6Re-parametrization of RR-BLUP to allow for a fixed residual variance
rrcovScalable Robust Estimators with High Breakdown Point
rrcovHDRobust multivariate Methods for High Dimensional Data
rrcovNAScalable Robust Estimators with High Breakdown Point for Incomplete Data
rrdfrrdf - support for the Resource Description Framework
rrdflibsrrdflibs - package with Jena and Apache HTTP libraries for use with rrdf
rredisRedis client for R
rrevalRemote R Evaluator (rreval)
RRFRegularized Random Forest
rriskBayesPredefined Bayes models fitted with Markov chain Monte Carlo (MCMC) (related to the 'rrisk' project)
rriskDistributionsCollection of functions for fitting distributions (related to the 'rrisk' project)
rrldaRobust Regularized Linear Discriminant Analysis
rrulesGeneric rule engine for R
rsaeRobust Small Area Estimation
RSAGASAGA Geoprocessing and Terrain Analysis in R
rscproxystatconn: provides portable C-style interface to R (StatConnector)
rsdepthRay Shooting Depth (i.e. RS Depth) functions for bivariate analysis
RSearchYJRSearchYJ
RSeedborenstein analysis
rseedcalcEstimation of Proportion of GM Stacked Seeds in Seed Lots
RSEISSeismic Time Series Analysis Tools
rsemRobust Structural Equation Modeling with Missing Data and Auxiliary Variables
RserveBinary R server
rSFASlow Feature Analysis in R
rsgccGini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data
RsgeInterface to the SGE Queuing System
RSienaSiena - Simulation Investigation for Empirical Network Analysis
RSiteSearchRSiteSearch
RSKCRobust sparse K-means
rsmResponse-surface analysis
RSNNSNeural Networks in R using the Stuttgart Neural Network Simulator (SNNS)
RSofiaPort of sofia-ml (http://code.google.com/p/sofia-ml/) to R
RsolnpGeneral Non-linear Optimization
rsprngR interface to SPRNG (Scalable Parallel Random Number Generators)
RSQLiteSQLite interface for R
RSQLite.extfunsMath and String Extension Functions for RSQLite
RssaA collection of methods for singular spectrum analysis
rstiefelRandom orthonormal matrix generation on the Stiefel manifold
rstreamStreams of random numbers
RsundialsSuite of Nonlinear Differential Algebraic Equations Solvers in R
RSurveyAnalysis of Spatially Distributed Data
RsymphonySymphony in R
rSymPyR interface to SymPy computer algebra system
rtapeManage and manipulate large collections of R objects stored as tape-like files
RTAQRTAQ: Tools for the analysis of trades and quotes in R
RTDAmeritradeRTDAmeritrade
RTextToolsAutomatic Text Classification via Supervised Learning
rtfRich Text Format (RTF) Output
rtfbsR Transcription Factor Binding Site identification tool
RthroughExcelWorkbooksInstallerExcel Workbooks supporting Statistics courses using 'R through Excel'
rtiffA tiff reader for R.
RTiseanR interface to Tisean algorithms
rTOFsPROTime-of-flight mass spectra signal processing
RTOMOVisualization for seismic tomography
Rttf2pt1Package for ttf2pt1 program
rugarchUnivariate GARCH models
RUnitR Unit test framework
RuniversalRuniversal - Package for converting R objects to Java variables and XML.
runjagsInterface utilities for JAGS (using BUGS syntax) and Apple Xgrid distributed computing clusters
RunuranR interface to the UNU.RAN random variate generators
RunuranGUIA GUI for the UNU.RAN random variate generators
rvSimulation-based random variable object class in R
RVAideMemoireDiverse basic statistical and graphical functions
RvelslantDownhole Seismic Analysis in R
rvgtestTools for Analyzing Non-Uniform Pseudo-Random Variate Generators
RVideoPokerPlay Video Poker with R
rvmbinaryRVM-Classification and Regression
RvmminVariable metric nonlinear function minimization with bounds constraints
RVtestsRare Variant Tests Using Multiple Regression Methods
RwaveTime-Frequency analysis of 1-D signals
RWeatherR wrapper around the Yahoo! Weather, Google Weather and NOAA APIs
RWebMARWebMA
RWekaR/Weka interface
RWekajarsR/Weka interface jars
RWinEdtR-WinEdt
RwinstepsRunning Winsteps in R
rwmR Workspace Management
rworldmapFor mapping global data : rworldmap
rwtRice Wavelet Toolbox wrapper
RxCEcolInfR x C Ecological Inference With Optional Incorporation of Survey Information
RXKCDGet XKCD comic from R
RXMCDARXMCDA
RXshrinkMaximum Likelihood Shrinkage via Generalized Ridge or Least Angle Regression
RyacasR interface to the yacas computer algebra system
rysgranGrain size analysis, textural classifications and distribution of unconsolidated sediments
RzGUI Tool for Data Management like SPSS or Stata
s20xStats 20x
s4vdBiclustering via sparse singular value decomposition incorporating stability selection
sabreRMultivariate Generalized Linear Mixed Models
sacSemiparametric Analysis of Changepoint
saemixStochastic Approximation Expectation Maximization (SAEM) algorithm
SAFDStatistical Analysis of Fuzzy Data
safeBinaryRegressionSafe Binary Regression
sampflingSampford sampling (w/o replacement and unequal probabilities)
SamplerCompareA framework for comparing the performance of MCMC samplers
sampleSelectionSample Selection Models
samplesizea collection of sample size functions
SampleSizeMeansSample size calculations for normal means
SampleSizeProportionsCalculating sample size requirements when estimating the difference between two binomial proportions
samplingSurvey Sampling
samplingbookSurvey Sampling Procedures
SamplingStrataOptimal stratification of sampling frames for multipurpose sampling surveys
sampSurfSampling Surface Simulation for Areal Sampling Methods
samrSAM: Significance Analysis of Microarrays
sandwichRobust Covariance Matrix Estimators
sapaSpectral Analysis for Physical Applications
SAPPStatistical Analysis of Point Processes
sas7bdatSAS Database Reader (experimental)
SASciiImport ASCII files directly into R using only a SAS input script
SASmixedData sets from "SAS System for Mixed Models"
SASPECTSignificant AnalysiS of PEptide CounTs.
SASxportRead and Write SAS XPORT Files
savesFast load variables
sawsSmall-Sample Adjustments for Wald tests Using Sandwich Estimators
sBFSmooth Backfitting
sbgcopSemiparametric Bayesian Gaussian copula estimation and imputation
SBSASimplified Bayesian Sensitivity Analysis
scaSimple Component Analysis
scagnosticsCompute scagnostics - scatterplot diagnostics
scalebootApproximately Unbiased P-values via Multiscale Bootstrap
scalesScale functions for graphics.
scamShape constrained additive models
scapeStatistical Catch-at-Age Plotting Environment
scapeMCMCMCMC Diagnostic Plots
scaRabeeOptimization Toolkit for Pharmacokinetic-Pharmacodynamic Models
scatterplot3d3D Scatter Plot
scioSparse Column-wise Inverse Operator
sciplotScientific Graphing Functions for Factorial Designs
SciViewsSciViews GUI API - Main package
SCMASingle-Case Meta-Analysis
ScottKnottThe ScottKnott Clustering Algoritm
scoutImplements the Scout method for Covariance-Regularized Regression
SCperfSupply Chain Perform
scrapeRTools for Scraping Data from HTML and XML Documents
scrimeAnalysis of High-Dimensional Categorical Data such as SNP Data
scriptestsTranscript-based unit tests that are easy to create and maintain
SCRTSingle-Case Randomization Tests
scubaScuba diving calculations and decompression models
sculpt3dA simple toolbar GUI for brushing RGL plots
SCVASingle-Case Visual Analysis
sdaShrinkage Discriminant Analysis and CAT Score Variable Selection
SDaASampling: Design and Analysis
sdcMicroStatistical Disclosure Control methods for the generation of public- and scientific-use files.
sdcMicroGUIGraphical user interface for package sdcMicro
sdcTableMethods for SDC (statistical disclosure control) in tabular data
SDDAStepwise Diagonal Discriminant Analysis
sddpackSemidiscrete Decomposition
sdeSimulation and Inference for Stochastic Differential Equations
sdefSynthesizing List of Differentially Expressed Features
SDiscIntegrated methodology for the identification of homogeneous subtypes in data
SDMToolsSpecies Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
sdpriskMeasures of Risk for the Compound Poisson Risk Process with Diffusion
sdtoolkitScenario Discovery Tools to Support Robust Decision Making
SE.IGEStandard errors of estimated genetic parametes
seacarbseawater carbonate chemistry with R
SearchTreesSpatial Search Trees
seasonSeasonal analysis of health data
SECPStatistical Estimation of Cluster Parameters (SECP)
secrSpatially explicit capture-recapture
SEER2Rreading and writing SEER*STAT data files
SEERaBombSEER Setup and Use with A-Bomb Data
seewaveTime wave analysis and graphical representation
segA set of tools for residential segregation research
segmentedSegmented relationships in regression models with breakpoints/changepoints estimation
Segmentor3IsBackA Fast Segmentation Algorithm
SELSemiparametric elicitation
selectiongainA tool for efficient calculation and optimization of the expected gain from multi-stage
selectMetaEstimation of weight functions in meta analysis
SeleMixSelective Editing via Mixture models
semStructural Equation Models
semdiagStructural equation modeling diagnostics
semGOFGoodness-of-fit indexes for structural equation models
SemiParSemiparametic Regression
SemiParBIVProbitSemiparametric Bivariate Probit Modelling
SemiParSampleSelSemiparametric Sample Selection Modelling with Continuous Response
SEMModCompModel Comparisons for SEM
semPLSStructural Equation Modeling Using Partial Least Squares
semToolsUseful tools for structural equation modeling.
sendmailRsend email using R
sendplotTool for sending interactive plots with tool-tip content.
sensitivitySensitivity Analysis
sensitivityPStratPrincipal Stratification Sensitivity Analysis Functions
SensoMineRSensory data analysis with R
sensRThurstonian models for sensory discrimination
SenSrivastavaDatasets from Sen & Srivastava
sentimentTools for Sentiment Analysis
separationplotSeparation Plots
seqCBSCN Profiling using Sequencing and CBS
seqinrBiological Sequences Retrieval and Analysis
seqmonSequential Monitoring of Clinical Trials
seqRFLPSimulation and visualization of restriction enzyme cutting pattern from DNA sequences.
seriationInfrastructure for seriation
sessionFunctions for interacting with, saving and restoring R sessions.
sessionToolsTools for saving, restoring and teleporting R sessions.
setRNGSet (Normal) Random Number Generator and Seed
setsSets, Generalized Sets, Customizable Sets and Intervals
sfaStochastic Frontier Analysis
sfsmiscUtilities from Seminar fuer Statistik ETH Zurich
sftFunctions for Systems Factorial Technology Analysis of Data
SGCSSpatial Graph based Clustering Summaries for spatial point patterns
sgeostatAn Object-oriented Framework for Geostatistical Modeling in S+
SGLFit a GLM (or cox model) with a combination of lasso and group lasso regularization
SGPAn R Package for the Calculation and Visualization of Student Growth Percentiles & Percentile Growth Trajectories.
SGPdataExemplar data sets for SGP analyses.
shapeFunctions for plotting graphical shapes, colors
shapefilesRead and Write ESRI Shapefiles
shapesStatistical shape analysis
sharxModels and Data Sets for the Study of Species-Area Relationships
SHIPSHrinkage covariance Incorporating Prior knowledge
shotGroupsAnalyze shot group data
schoolmathFunctions and datasets for math used in school
schwartz97A package on the Schwartz two-factor commodity model
siarStable Isotope Analysis in R
sideChannelAttackSide Channel Attack
sifdsSwedish inflation forecast data set
sigPrint function signatures.
sigclustStatistical Significance of Clustering
SightabilityModelWildlife Sightability Modeling
signalSignal processing
signalextractionReal-Time Signal Extraction (Direct Filter Approach)
sigoraSIGNATURE OVERREPRESENTATION ANALYSIS
SigWinRSigWin-detector implementation in R
SIICalculate ANSI S3.5-1997 Speech Intelligibility Index
Sim.DiffProcSimulation of Diffusion Processes
Sim.DiffProcGUIGraphical User Interface for Simulation of Diffusion Processes
simbaA Collection of functions for similarity analysis of vegetation data
simbootSimultaneous inference for diversity indices.
simcoA package to import Structure files and deduce similarity coefficients from them
SimCompSimultaneous Comparisons for Multiple Endpoints
simctestSafe implementation of Monte Carlo tests.
simecolSimulation of ecological (and other) dynamic systems
simexSIMEX- and MCSIMEX-Algorithm for measurement error models
simexaftsimexaft
simFrameSimulation framework
SimHapA comprehensive modeling framework for epidemiological outcomes and a simulation-based approach to haplotypic analysis of population-based data
SimileInteract with Simile models
simoneStatistical Inference for MOdular NEtworks (SIMoNe)
simplebootSimple Bootstrap Routines
SimpleTableBayesian Inference and Sensitivity Analysis for Causal Effects from 2 x 2 and 2 x 2 x K Tables in the Presence of Unmeasured Confounding
simPopulationSimulation of synthetic populations for surveys based on sample data
simsemSIMulated Structural Equation Modeling.
simSummarySimulation summary
SimultAnRCorrespondence and Simultaneous Analysis
SINA SINful Approach to Selection of Gaussian Graphical Markov Models
sinartraA simple web app framework for R, based on sinatra.
SISSure Independence Screening
sisusSISUS: Stable Isotope Sourcing using Sampling
sitoolsFormat a number to a string with SI prefix
SixSigmaSix Sigma Tools for Quality and Process Improvement
SiZerSiZer: Significant Zero Crossings
SKATSNP-set (Sequence) Kernel Association Test
skellamSkellam distribution
SkewHyperbolicThe Skew Hyperbolic Student t-Distribution
skewtThe Skewed Student-t Distribution
skewtoolsInformation Tools for analyze Skew-Elliptical distributions and related models
skmeansSpherical k-Means Clustering
slamSparse Lightweight Arrays and Matrices
SLCSlope and level change
Sleuth2Data sets from Ramsey and Schafer's "Statistical Sleuth (2nd ed)"
SlimPLSSlimPLS multivariate feature selection
smSmoothing methods for nonparametric regression and density estimation
smacofSMACOF for Multidimensional Scaling.
smatr(Standardised) Major Axis Estimation and Testing Routines
SMCSequential Monte Carlo (SMC) Algorithm
smcoA simple Monte Carlo optimizer using adaptive coordinate sampling
SMCPSmoothed minimax concave penalization (SMCP) method for genome-wide association studies.
smcureFit Semiparametric Mixture Cure Models
smcUtilsUtility functions for sequential Monte Carlo
smeSmoothing-splines Mixed-effects Models
smfsbSMfSB 2e: Stochastic Modelling for Systems Biology, second edition
SMIRCompanion to Statistical Modelling in R
smirnovProvides two taxonomic coefficients from E. S. Smirnov "Taxonomic analysis" (1969) book
smoothmestSmoothed M-estimators for 1-dimensional location
smoothSurvSurvival Regression with Smoothed Error Distribution
smoothtailSmooth Estimation of GPD Shape Parameter
SMPracticalsPracticals for use with Davison (2003) Statistical Models
SMVarStructural Model for variances
snThe skew-normal and skew-t distributions
snaTools for Social Network Analysis
snortSocial Network-Analysis On Relational Tables
snowSimple Network of Workstations
SnowballSnowball Stemmers
snowfallEasier cluster computing (based on snow).
snowFTFault Tolerant Simple Network of Workstations
snp.plottersnp.plotter
SNPassocSNPs-based whole genome association studies
SNPMaPSNP Microarrays and Pooling in R
SNPMaP.cdmAnnotation for SNP Microarrays and Pooling in R
SNPmaxselMaximally selected statistics for SNP data
SNPRelateParallel Computing Toolset for Genome-Wide Association Studies (GWAS)
SNSequateStandard and Nonstandard Statistical Models and Methods for Test Equating
SOARMemory management in R by delayed assignments
SoDAFunctions and Exampels for "Software for Data Analysis"
softclassvalSoft classification performance measures
soil.specSoil spectral data exploration and regression functions
soilDBSoil Database Interface
SoilRModels of Soil Organic Matter Decomposition
soiltextureFunctions for soil texture plot, classification and transformation
solaRSolar Photovoltaic Systems
somSelf-Organizing Map
somaGeneral-purpose optimisation with the Self-Organising Migrating Algorithm
someKfwerControlling the Generalized Familywise Error Rate
someMTPSome Multiple Testing Procedures
somplotVisualisation of hexagonal Kohonen maps
soobenchSingle Objective Optimization Benchmark Functions
SortableHTMLTablesTurns a data frame into an HTML file containing a sortable table.
sossos
sos4RAn R client for the OGC Sensor Observation Service
soundA Sound Interface for R
spclasses and methods for spatial data
spaImplements The Sequential Predictions Algorithm
SPA3GSPA3G: R package for the method of Li and Cui (2012)
spaaSPecies Association Analysis
spaceSparse PArtial Correlation Estimation
SPACECAPA Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models
spaceExtExtension of SPACE
spacetimeclasses and methods for spatio-temporal data
spacodiRSpatial and Phylogenetic Analysis of Community Diversity
spacomSpatially weighted context data for multilevel modelling
spamSPArse Matrix
sparclPerform sparse hierarchical clustering and sparse k-means clustering
sparkTableSparklines and graphical tables for tex and html
SPARQLSPARQL client
sparrThe sparr package: SPAtial Relative Risk
SparseGridSparse grid integration in R
sparseLDASparse Discriminant Analysis
sparseLTSEigenRcppEigen back end for sparse least trimmed squares regression
SparseMSparse Linear Algebra
sparsenetFit sparse linear regression models via nonconvex optimization
spartanSpartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
spatcountsSpatial count regression
spatgraphsGraphs for spatial point patterns
spatialFunctions for Kriging and Point Pattern Analysis
spatialCovarianceComputation of spatial covariance matrices for data on rectangles
SpatialEpiPerforms various spatial epidemiological analyses
SpatialExtremesModelling Spatial Extremes
spatialkernelNonparameteric estimation of spatial segregation in a multivariate point process
SpatialNPMultivariate nonparametric methods based on spatial signs and ranks
SpatialPackPackage for analysis of spatial data
spatialprobitSpatial Probit Models
spatialsegregationSegregation measures for multitype spatial point patterns
SpatialToolsSpatialTools
SpatialVxSpatial Forecast Verification
SpatioTemporalSpatio-Temporal Model Estimation
spatstatSpatial Point Pattern analysis, model-fitting, simulation, tests
spBayesUnivariate and Multivariate Spatial Modeling
spcStatistical Process Control
spcadjustFunctions for calibrating control charts
spclustSelective phenotyping for experimental crosses
spcosaSpatial Coverage Sampling and Random Sampling from Compact Geographical Strata
spcovSparse Estimation of a Covariance Matrix
spdSemi Parametric Distribution
spdepSpatial dependence: weighting schemes, statistics and models
speStochastic Proximity Embedding
SPECIESStatistical package for species richness estimation
SpeciesMixFit Mixtures of Archetype species
SpectralGEMDiscovering Genetic Ancestry Using Spectral Graph Theory
spectralGPApproximate Gaussian processes using the Fourier basis
speedglmFitting Linear and Generalized Linear Models to large data sets.
speedRA GUI based importing and filtering tool
speedRlibsPackage containing the required libraries (jars) for speedR
speedRlibTFspeedR's table filter library
spefSemiparametric estimating functions.
speff2trialSemiparametric efficient estimation for a two-sample treatment effect
SPEICalculation of the Standardised Precipitation-Evapotranspiration Index
sperichAuxiliary functions to estimate centers of biodiversity
sperrorestSpatial Error Estimation and Variable Importance
spgrass6Interface between GRASS 6+ geographical information system and R
spgwrGeographically weighted regression
sphereplotSpherical plotting
SpherWaveSpherical Wavelets and SW-based Spatially Adaptive Methods
sphetSpatial Models with heteroskedastic innovations
spiCompute SPI index
SPIAssayA genetic-based assay for the identification of cell lines
spiderSpecies Identity and Evolution in R
spikeslabPrediction and variable selection using spike and slab regression
spikeSlabGAMBayesian variable selection and model choice for generalized additive mixed models
SPInOptimal Shortest Probability Intervals
splancsSpatial and Space-Time Point Pattern Analysis
splinesRegression Spline Functions and Classes
splinesurvNonparametric bayesian survival analysis
splmEconometric Models for Spatial Panel Data
splsSparse Partial Least Squares (SPLS) Regression and Classification
splus2RSupplemental S-PLUS functionality in R
spMCContinuous Lag Spatial Markov Chains
spormSemiparametric proportional odds rate model
SportsAnalyticsInfrastructure for Sports Analytics
SPOTSequential Parameter Optimization
SPSLSite Percolation on Square Lattice (SPSL)
spsmoothAn Extension Package for 'mgcv'.
spssDDIRead SPSS System files and produce valid DDI Version 3.0 documents
spsurveySpatial Survey Design and Analysis
sptSierpinski Pedal Triangle
spTimerSpatio-Temporal Bayesian Modelling Using R
spuRsFunctions and Datasets for "Introduction to Scientific Programming and Simulation Using R".
sqldfPerform SQL Selects on R Data Frames
SQLiteMapWrapper to spatialite functions
SQNsubset quantile normalization
SQUAREMSquared extrapolation methods for accelerating fixed-point iterations
squashColor-based plots for multivariate visualization
sraSelection Response Analysis
SRMASRMA Analysis of Array-based Sequencing Data
sROCNonparametric Smooth ROC Curves for Continuous Data
SRPMShared Reproducibility Package Management
ssanvSample Size Adjusted for Nonadherence or Variability of input parameters
ssize.fdrSample Size Calculations for Microarray Experiments
sspirState Space Models in R
ssplineSmoothing Splines on the Sphere
sssTools for importing files in the triple-s .(Standard Survey Structure) format
SSsimpleState space models
stShrinkage t Statistic and CAT Score
stabdata analysis of drug stability for shelf life estimation
stabledistStable Distribution Functions
stamSpatio-Temporal Analysis and Modelling
standGLStandardized Group Lasso
STARSpike Train Analysis with R
startupmsgUtilities for start-up messages
stashRA Set of Tools for Administering SHared Repositories
StatDAStatistical Analysis for Environmental Data
StatDataMLimplementation of the StatDataML proposal
StateTraceBayesian Ordinal Analysis for State Trace Designs
StatFingerprintsStatFingerprints
StatMatchStatistical Matching
statmodStatistical Modeling
statnetSoftware tools for the Statistical Analysis of Network Data
statsThe R Stats Package
stats4Statistical Functions using S4 Classes
steepnessTesting Steepness of Dominance Hierarchies
SteinerNetSteiner approach for Biological Pathway Graph Analysis
stellaRstellar evolution tracks and isochrones
StemSpatio-temporal models in R
steppSubpopulation Treatment Effect Pattern Plot (STEPP)
stepPlrL2 penalized logistic regression with a stepwise variable selection
stepwiseStepwise detection of recombination breakpoints
stinepackStineman, a consistently well behaved method of interpolation
StMoSimSimulate QQ-Norm-Plot
stockPortfolioBuild stock models and analyze stock portfolios.
StochaTRSolving stochastic linear programs with a single risk constraint
stochmodStochastic Modeling
stoichcalcR Functions for Solving Stoichiometric Equations
stppSpace-Time Point Pattern simulation, visualisation and analysis
stratasphereStratified Spherical Approximate Conditional Modeling
stratificationUnivariate Stratification of Survey Populations
stratigraphToolkit for the plotting and analysis of stratigraphic and palaeontological data
stream.netBuilding and analyzing binary stream networks
StreamMetabolismStream Metabolism-A package for calculating single station metabolism from diurnal Oxygen curves
stremoFunctions to help the process of learning structural equation modelling
StressStrengthComputation and estimation of reliability of stress-strength models
stringrMake it easier to work with strings.
strucchangeTesting, Monitoring, and Dating Structural Changes
StructRStructural geology tools
subplexSubplex optimization algorithm
subselectSelecting variable subsets
sudokuSudoku Puzzle Generator and Solver
sudokuplusSudoku Puzzle (9*9 12*12 16*16) Generator and Solver
sugaRPlots to help optimising diabetes therapy
SunterSamplingSunter's sampling design
supclustSupervised Clustering of Predictor Variables such as Genes
superdiagR Code for Testing Markov Chain Nonconvergence
SuperLearnerSuper Learner Prediction
superMDSImplements the supervised multidimensional scaling (superMDS) proposal of Witten and Tibshirani (2011)
superpcSupervised principal components
SuppDistsSupplementary distributions
support.CEsBasic functions for supporting an implementation of choice experiments
surv2sampleTwo-Sample Tests for Survival Analysis
survAUCEstimators of prediction accuracy for time-to-event data.
survBayesFits a proportional hazards model to time to event data by a Bayesian approach
survC1C-statistics for risk prediction models with censored survival data
surveillanceTemporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
surveyanalysis of complex survey samples
SurvginiThe Gini concentration test for survival data
survIDINRIIDI and NRI for comparing competing risk prediction models with censored survival data
survivalSurvival analysis, including penalised likelihood.
survivalBIVEstimation of the bivariate distribution function
survivalROCTime-dependent ROC curve estimation from censored survival data
survJamdaSurvival prediction by joint analysis of microarray gene expression data
survJamda.datasurvJamda.data
survPresmoothPresmoothed Estimation in Survival Analysis
survrecSurvival analysis for recurrent event data
survSNPPower and Sample Size Calculations for SNP Association Studies with Censored Time to Event Outcomes
svcm2d and 3d Space-Varying Coefficient Models
svdInterfaces to various state-of-art SVD and eigensolvers
svDialogsSciViews GUI API - Dialog boxes
SVGMappingMap experimental data on custom-made SVG file
svGUISciViews GUI API - Functions to manage GUIs
svHttpSciViews GUI API - R HTTP server
svIDESciViews GUI API - IDE and code editor functions
svKomodoSciViews GUI API - Functions to interface with Komodo Edit/IDE
svMiscSciViews GUI API - Miscellaneous functions
SVMMajSVMMaj algorithm
svmpathsvmpath: the SVM Path algorithm
svSocketSciViews GUI API - R Socket Server
svSweaveSciViews GUI API - Sweave functions
svToolsSciViews GUI API - Tools (wrapper for packages tools and codetools)
svUnitSciViews GUI API - Unit testing
svWidgetsSciViews GUI API - Widgets & Windows
swampAnalysis and visualization of high-dimensional data in respect to sample annotations.
SWATmodelA multi-OS implementation of the TAMU SWAT model.
SweaveListingUtilsUtilities for Sweave together with TeX listings package
SwissAirAir Quality Data of Switzerland for one year in 30 min Resolution
SWordInstallerSWord: Use R in Microsoft Word (Installer)
sybilSyBiL - Efficient constrained based modelling in R
sybilDynFBADynamic FBA : dynamic flux balance analysis
sybilSBMLSBML integration in SyBiL
symbolsSymbol plots
symmomentsSymbolic Central Moments of the Multivariate Normal Distribution
synbreedFramework for the analysis of genomic prediction data using R
synbreedDataData for the synbreed package
SYNCSASYNCSA - Analysis of functional and phylogenetic patterns in metacommunities.
SynergizeRInterface to The Synergizer service for translating between sets of biological identifiers.
SyNetInference and Analysis of Sympatry Networks
SynthSynthetic Control Group Method for Comparative Case Studies
systemfitEstimating Systems of Simultaneous Equations
tableplotRepresents tables as semi-graphic displays
tablesFormula-driven table generation
tabplotTableplot, a visualization of large datasets
tabplotGTKA graphical user interface for the tabplot package
tabuSearchR based tabu search algorithm
TAHMMAnnotMixture model approach to compare two samples of Tiling Array data
TANOVATime Course Analysis of Variance for Microarray
taRifxCollection of utility and convenience functions.
taRifx.geoCollection of various spatial functions
tauText Analysis Utilities
TauP.REarthquake Traveltime Calculations for 1-D Earth Models
tawnyProvides various portfolio optimization strategies including random matrix theory and shrinkage estimators
tawny.typesCommon types for tawny
TaxonstandTaxonomic standardization of plant species names
TBSSurvivalTBS Model R package
TCCTCC: tag count comparison package
tcltkTcl/Tk Interface
tcltk2Tcl/Tk Additions
tclustRobust Trimmed Clustering
tdmA Tool for Therapeutic Drug Monitoring (TDM)
TDMRTuned Data Mining in R
tdthapTDT tests for extended haplotypes
TeachingDemosDemonstrations for teaching and learning
TeachingSamplingSampling designs and parameter estimation in finite population
teigenteigen: Model-based clustering and classification with the multivariate t-distribution
tempdisaggMethods for Temporal Disaggregation and Interpolation of Time Series
tensorTensor product of arrays
tensorAAdvanced tensors arithmetic with named indices
TEQRTarget Equavelence Range Design
TERAplusBTest for A+B Traditional Escalation Rule
termstrcZero-coupon Yield Curve Estimation
ternvisVisualisation, verification and calibration of ternary probabilistic forecasts
TestSurvRecStatistical tests to compare two survival curves with recurrent events
testthatTestthat code. Tools to make testing fun :)
texmexThreshold exceedences and multivariate extremes
TExPositionTwo-table ExPosition
texregConversion of R regression output to LaTeX tables.
textcatN-Gram Based Text Categorization
textirInverse Regression for Text Analysis
TextRegressionPredict continuous valued outputs associated with text documents.
tferForensic Glass Transfer Probabilities
tfplotTime Frame User Utilities
tframeTime Frame coding kernel
tframePlusTime Frame coding kernel extensions
tgpBayesian treed Gaussian process models
tgramFunctions to compute and plot tracheidograms
TGUICoreTeaching GUI - Core functionality
TGUITeachingTeaching GUI - prototype
thgeneticsGenetic Rare Variants Tests
ThreeGroupsML Estimator for Baseline-Placebo-Treatment (Three-group) designs
ThreeWayThree-way component analysis
ThresholdROCOptimum threshold estimation based on cost function in a two and three state setting
tiffRead and write TIFF images
tigerTIme series of Grouped ERrors
tileHMMHidden Markov Models for ChIP-on-Chip Analysis
TilePlotCharacterization of functional genes in complex microbial communities using tiling DNA microarrays
tiltingVariable selection via Tilted Correlation Screening algorithm
timeDateRmetrics - Chronological and Calendarical Objects
timeorderedTime-ordered and time-aggregated network analyses
timeregtimereg package for Flexible regression models for survival data.
timeSeriesRmetrics - Financial Time Series Objects
timetoolsprovides objects and tools to manipulate irregular unhomogeneous time data and subtime data.
TimeWarpDate calculations and manipulation
TIMPa problem solving environment for fitting separable nonlinear models in physics and chemistry applications
timsacTIMe Series Analysis and Control package
TinflexTinflex - Universal non-uniform random number generator
TinnRResources of Tinn-R GUI/Editor for R Environment
tisTime Indexes and Time Indexed Series
titanTitration analysis for mass spectrometry data
tkrglTK widget tools for rgl package
tkrplotTK Rplot
tlemixTrimmed Maximum Likelihood Estimation
tlmecLinear Student-t Mixed-Effects Models with Censored Data
tlniseTwo-level normal independent sampling estimation
tmText Mining Package
tm.plugin.dcText Mining Distributed Corpus Plug-In
tm.plugin.factivaImport articles from Factiva using the tm text mining framework
tm.plugin.mailText Mining E-Mail Plug-In
tmleTargeted Maximum Likelihood Estimation
tmvtnormTruncated Multivariate Normal and Student t Distribution
tnettnet: Software for Analysis of Weighted, Two-mode, and Longitudinal networks
toleranceFunctions for calculating tolerance intervals
tonymiscFunctions for Econometrics Output
toolsTools for Package Development
topicmodelsTopic models
topmodelImplementation of the hydrological model TOPMODEL in R
topologyGSAtopologyGSA
tourrImplement tour methods in pure R code
tourrGuiA Tour GUI using gWidgets
ToxLimIncorporating Ecological Data and Associated Uncertainty in Bioaccumulation Modeling
TPAMTPAM
tpeTree preserving embedding
TPmsmEstimation of transitions probabilities in multistate models
tprTemporal Process Regression
trackTrack Objects
trackObjsTrack Objects
tractor.baseA package for reading, manipulating and visualising magnetic resonance images
TradeStrategyAnalyzerTrade Strategy Analyzer
traitrAn interface for creating GUIs modeled in part after traits UI module for python.
TraMineRTrajectory miner: a toolbox for exploring and rendering sequence data
TRAMPRTRFLP Analysis and Matching Package for R
trapezoidThe Trapezoidal Distribution
treeClassification and regression trees
treebaseAn R package for discovery, access and manipulation of online phylogenies
treecmCentre of mass assessment and consolidation of trees.
treeletTreelets - an adaptive multi-scale basis for high-dimensional, sparse and unordered data
treemapTreemap visualization
TreeParEstimating birth and death rates based on phylogenies
TreeSimSimulating trees under the birth-death model
treethreshMethods for Tree-based Local Adaptive Thresholding
trexTruncated exact test for two-stage case-control design for studying rare genetic variants
TrialSizeR functions in Chapter 3,4,6,7,9,10,11,12,14,15
TRIANGSymmetric discrete triangular distributions
TRIANGGGeneral discrete triangular distribution
triangleProvides the standard distribution functions for the triangle distribution
trifieldSome basic facilities for ternary fields and plots
trimclusterCluster analysis with trimming
triotrio package without Fortran code
tripSpatial analysis of animal track data
tripackTriangulation of irregularly spaced data
tripEstimationMetropolis sampler and supporting functions for estimating animal movement from archival tags and satellite fixes
TripleRSocial Relation Model (SRM) analyses for single or multiple round-robin groups
truncdistTruncated Random Variables
truncnormTruncated normal distribution
truncregTruncated Regression Models
truncSPSemi-parametric estimators of truncated regression models
trustTrust Region Optimization
TSATime Series Analysis
TSAggTime series Aggregation
TSdbiTime Series Database Interface
tsDynNonlinear time series models with regime switching
TSENTwo-dimensional peak sentinel tool for GC x GC-HRTOFMS
tseriesTime series analysis and computational finance
tseriesChaosAnalysis of nonlinear time series
tsfaTime Series Factor Analysis
TSfameTime Series Database Interface extensions for fame
TSgetSymbolTime Series Database Interface extension to connect with getSymbols
TShistQuoteTime Series Database Interface extensions for get.hist.quote
TSHRCTwo Stage Hazard Rate Comparison
tslarsLeast angle regression for time series analysis
tsModelTime Series Modeling for Air Pollution and Health
TSMySQLTime Series Database Interface extensions for MySQL
tsneT-distributed Stochastic Neighbor Embedding for R (t-SNE)
TSodbcTime Series Database Interface extensions for ODBC
TSPTraveling Salesperson Problem (TSP)
TSPCPrediction using time-course gene expression
TsphereTransposable Sphering for Large-Scale Inference with Correlated Data.
TSPostgreSQLTime Series Database Interface extensions for PostgreSQL
TSSQLiteTime Series Database Interface extentions for SQLite
TSxlsTime Series Database Interface extension to connect to spreadsheets
TSzipTime Series Database Interface extension to connect to zip files
TTAinterfaceTrendAnalysisTemporal Trend Analysis Graphical Interface
ttimeTranslate Neurodevelopmental Event Timing Across Species
TTRTechnical Trading Rules
ttrTestsStandard Backtests for Technical Trading Rules in Financial Data
ttutilsUtility functions
TukeyCConvencional Tukey Test
TuneParetoMulti-objective parameter tuning for classifiers
tuneRAnalysis of music and speech
turboEMA Suite of Convergence Acceleration Schemes for EM and MM algorithms
TUWmodelLumped hydrological model developed at the Vienna University of Technology for education purposes.
twangToolkit for Weighting and Analysis of Nonequivalent Groups
tweedieTweedie exponential family models
twiddlerInteractive manipulation of R expressions
twitteRR based Twitter client
TWIXTrees WIth eXtra splits
two.stage.bootTwo-stage cluster sample bootstrap algorithm
TwoStepCLogitConditional logistic regression: A two-step estimation method
twslmA two-way semilinear model for normalization and analysis of cDNA microarray data.
txtplotText based plots
ucminfGeneral-purpose unconstrained non-linear optimization
udunits2udunits-2 bindings for R
umpUniformly Most Powerful Tests
unbalhaarFunction estimation via Unbalanced Haar wavelets
uncompressUncompress
UnicodeUnicode data and utilities
uniCoxUnivarate shrinkage prediction in the Cox model
unknownRYou didn't know you didn't know?
unmarkedModels for Data from Unmarked Animals
untbecological drift under the UNTB
urcaUnit root and cointegration tests for time series data
UScensus2000US Census 2000 Suite of R Packages
UScensus2000addUS Census 2000 Suite of R Packages: Demographic Add
UScensus2000blkgrpUS Census 2000 Block Group Shapefiles and Additional Demographic Data
UScensus2000cdpUS Census 2000 Designated Places Shapefiles and Additional Demographic Data
UScensus2000tractUS Census 2000 Tract Level Shapefiles and Additional Demographic Data
UScensus2010US Census 2010 Suite of R Packages
usefulA collection of handy, useful functions
UsingRData sets for the text "Using R for Introductory Statistics"
USPSUnsupervised and Supervised methods of Propensity Score Adjustment for Bias
utilsThe R Utils Package
vacemVaccination Activities Coverage Estimation Model
validatorExternal and Internal Validation Indices
varbvsVariational inference for Bayesian variable selection
varcompciVARCOMPCI: A Package for Computation of Confidence Intervals for Variance Components of Mixed Models in R.
vardiagA package for variogram diagnostics
VarEffVariation of effective population size
VariABELTesting of genotypic variance heterogeneity to detect potentially interacting SNP.
VarianceGammaThe Variance Gamma Distribution
varsVAR Modelling
varSelectIPObjective Bayes Model Selection
varSelRFVariable selection using random forests
VarSwapPricePricing a variance swap on an equity index
VBLPCMVariational Bayes Latent Position Cluster Model for networks.
VBMA4hmmThe VBMA4hmm (Variational Bayesian Markov Model for hidden markov model) package
vcdVisualizing Categorical Data
vcdExtravcd additions
VdgraphThis package creates variance dispersion graphs for response surface designs
vec2dtransf2D Cartesian Coordinate Transformation
VecStatGraphs2DVector analysis using graphical and analytical methods in 2D
VecStatGraphs3DVector analysis using graphical and analytical methods in 3D
veganCommunity Ecology Package
vegclustFuzzy clustering of vegetation data
vegdataFunctions to access vegetation databases (Turboveg) and prepare vegetation data for analysis
vegetarianJost Diversity Measures for Community Data
VennDiagramGenerate high-resolution Venn and Euler plots
venneulerVenn and Euler Diagrams
verificationForecast verification utilities.
VGAMVector Generalized Linear and Additive Models
VHDClassificationDiscrimination/Classification in very high dimension with linear and quadratic rules.
VIFVIF Regression: A Fast Regression Algorithm For Large Data
VIMVisualization and Imputation of Missing Values
vimcomIntermediate the communication between Vim and R
VineCopulaStatistical inference of vine copulas
vinesMultivariate Dependence Modeling with Vines
violinmplotCombination of violin plot with mean and standard deviation.
vioplotViolin plot
viopoints1-D Scatter Plots with Jitter Using Kernel Density Estimates
VisCovVisualizing of distributions of covariance matrices
visregVisualization of regression functions
visualFieldsStatistical methods for visual fields
visualizationToolsPackage contains a few functions to visualize statistical circumstances.
VizCompXVisualisation of Computer Models
VLMCVLMC -- Variable Length Markov Chains
vmvVisualization of Missing Values
voronoiMethods and applications related to Voronoi tessellations
VossGeneric Voss algorithm (random sequential additions)
vowelsVowel Manipulation, Normalization, and Plotting
VPdtwVariable Penalty Dynamic Time Warping
vrmlgenGenerate 3D visualizations for data exploration on the web
vrtestVariance Ratio tests and other tests for Martigale Difference Hypothesis
vwrUseful functions for visual word recognition research
waffectA package to simulate constrained phenotypes under a disease model H1
walkscoreAPIWalk Score and Transit Score API
wasimVisualisation and analysis of output files of the hydrological model WASIM
waterfallWaterfall Charts in R
wavebandComputes credible intervals for Bayesian wavelet shrinkage
WaveCDWavelet change point detection for array CGH data
waveclockTime-frequency analysis of cycling cell luminescence data
wavedWavelet Deconvolution
WaveletCoWavelet Coherence Analysis
waveletsA package of funtions for computing wavelet filters, wavelet transforms and multiresolution analyses
wavemulcorWavelet routine for multiple correlation
waveslimBasic wavelet routines for one-, two- and three-dimensional signal processing
wavethreshWavelets statistics and transforms.
wccsomSOM networks for comparing patterns with peak shifts
WCQWCQ: QTL Mapping with Small Sample Size
WDIWorld Development Indicators (World Bank)
weathermetricsFunctions to convert between weather metrics
websocketsHTML 5 Websocket Interface for R
webvisCreate graphics for the web from R.
weightedKmeansWeighted KMeans Clustering
WeightedPortTestWeighted Portmanteau Tests for Time Series Goodness-of-fit
weightedScoresWeighted scores method for regression with dependent data
weightsWeighting and Weighted Statistics
weirsA Hydraulics Package to Compute Open-Channel Flow over Weirs
wfeWeighted Linear Fixed Effects Estimators for Causal Inference
wgaimWhole Genome Average Interval Mapping for QTL detection using mixed models
WGCNAWeighted Correlation Network Analysis
WhatIfWhatIf: Software for Evaluating Counterfactuals
whisker{{mustache}} for R, logicless templating
wikibooksFunctions and datasets of the german WikiBook "GNU R"
WilcoxCVWilcoxon-based variable selection in cross-validation
wild1R Tools for Wildlife Research and Management
wleWeighted Likelihood Estimation
WMBrukerParserWilliam and Mary Parser For Bruker-Ultraflex Mass Spec Data
WMCapacityGUI implementing Bayesian working memory models
WMDBDiscriminant Analysis Methods by Weight Mahalanobis Distance and bayes
WMTregionsExact Calculation of WMTR
wmtsaWavelet Methods for Time Series Analysis
wnominateWNOMINATE Roll Call Analysis Software.
wombsoftWombling Computation
wordcloudWord Clouds
wordnetWordNet Interface
wqExploring water quality monitoring data
write.snnsFunction for exporting data to SNNS pattern files.
WriteXLSCross-platform Perl based R function to create Excel 2003 (XLS) files
wSVMWeighted SVM with boosting algorithm for improving accuracy
wvioplotWeighted violin plot
WWGbookFunctions and datasets for WWGbook.
x12X12 - wrapper function and structure for batch processing
x12GUIX12 - Graphical User Interface
xgridAccess Apple Xgrid using R
XLConnectExcel Connector for R
XLConnectJarsJAR dependencies for the XLConnect package
xlsReadWriteRead and write Excel files (.xls)
xlsxRead, write, format Excel 2007 and Excel 97/2000/XP/2003 files
xlsxjarsPackage required jars for the xlsx package
xpose4Xpose 4
xpose4classicXpose 4 Classic Menu System
xpose4dataXpose 4 Data Functions Package
xpose4genericXpose 4 Generic Functions Package
xpose4specificXpose 4 Specific Functions Package
xtableExport tables to LaTeX or HTML
xtermStyleBasic text formatting using xterm escape sequences
xtseXtensible Time Series
yaccaYet Another Canonical Correlation Analysis Package
yaImputeyaImpute: An R Package for k-NN Imputation
YaleToolkitData exploration tools from Yale University.
yamlMethods to convert R data to YAML and back
yhatInterpreting Regression Effects
YieldCurveModelling and estimation of the yield curve
YjdnJlpText Analysis by Yahoo! Japan Develper Network
YourCastForecasting age-sex-country-cause mortality rates
ZeligEveryone's Statistical Software
zendeskRZendesk API Wrapper
zicBayesian Inference for Zero-Inflated Count Models
zipcodeU.S. ZIP Code database for geocoding
zipfRStatistical models for word frequency distributions
zoeppritzZoeppritz Equations
zooS3 Infrastructure for Regular and Irregular Time Series (Z's ordered observations)
zypZhang + Yue-Pilon trends package