Category Archives: R Package Into

R Packages – Intro

More than 4700 packages are available in R.  It keeps growing, whole bunch of functionalities are available, only thing is too choose correct package. R provides package to handle big data (ff), allow parallelism, plot graphs (ggplot2), analyze data through different algorithm available (ABCp2 etc etc..), develop GUI (shiny) and many more.

A3 A3: Accurate, Adaptable, and Accessible Error Metrics for Predictive Models
abc Tools for Approximate Bayesian Computation (ABC)
abcdeFBA ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package
ABCExtremes ABC Extremes
ABCp2 Approximate Bayesian Computational model for estimating P2
abctools Tools for ABC analyses
abd The Analysis of Biological Data
abf2 Load Axon ABF2 files (currently only in gap-free recording mode)
abind Combine multi-dimensional arrays
aBioMarVsuit A Biomarker Validation Suit for predicting Survival using gene signature
abn Data Modelling with Additive Bayesian Networks
abundant Abundant regression and high-dimensional principal fitted components
accelerometry Functions for processing uniaxial minute-to-minute accelerometer data
AcceptanceSampling Creation and evaluation of Acceptance Sampling Plans
ACCLMA ACC & LMA Graph Plotting
ACD Categorical data analisys with complete or missing responses
Ace Assay-based Cross-sectional Estimation of incidence rates
acepack ace() and avas() for selecting regression transformations
acer The ACER Method for Extreme Value Estimation
aCGH.Spline Robust spline interpolation for dual color array comparative genomic hybridisation data
ACNE Affymetrix SNP probe-summarization using non-negative matrix factorization
acopula Modelling dependence with multivariate Archimax (or any user-defined continuous) copulas
aCRM Convenience functions for analytical Customer Relationship Management
acs Download, manipulate, and present data from the US Census American Community Survey
Actigraphy Actigraphy Data Analysis
actuar Actuarial functions
ActuDistns Functions for actuarial scientists
ada ada: an R package for stochastic boosting
adabag Applies multiclass AdaBoost.M1, AdaBoost-SAMME and Bagging
adagio Discrete and Global Optimization Routines
AdaptFit Adaptive Semiparametic Regression
AdaptFitOS Adaptive Semiparametric Regression with Simultaneous Confidence Bands
adaptivetau Tau-leaping stochastic simulation
adaptMCMC Implementation of a generic adaptive Monte Carlo Markov Chain sampler
adaptsmoFMRI Adaptive Smoothing of FMRI Data
adaptTest Adaptive two-stage tests
ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences
ade4TkGUI ade4 Tcl/Tk Graphical User Interface
adegenet adegenet: an R package for the exploratory analysis of genetic and genomic data
adehabitat Analysis of habitat selection by animals
adehabitatHR Home range Estimation
adehabitatHS Analysis of habitat selection by animals
adehabitatLT Analysis of animal movements
adehabitatMA Tools to Deal with Raster Maps
adephylo adephylo: exploratory analyses for the phylogenetic comparative method
AdequacyModel Adequacy of probabilistic models and generation of pseudo-random numbers
ADGofTest Anderson-Darling GoF test
adimpro Adaptive Smoothing of Digital Images
adk Anderson-Darling K-Sample Test and Combinations of Such Tests
adlift An adaptive lifting scheme algorithm
ADM3 An Interpretation of the ADM method – automated detection algorithm
AdMit Adaptive Mixture of Student-t distributions
ads Spatial point patterns analysis
AER Applied Econometrics with R
afex Analysis of Factorial Experiments
aftgee Accelerated Failure Time Model with Generalized Estimating Equations
AGD Analysis of Growth Data
ageprior Prior distributions for molecular dating
aggrisk Estimate individual level risk using individual case data and spatially aggregated control data
agop Aggregation Operators and Preordered Sets
agRee Various Methods for Measuring Agreement
Agreement Statistical Tools for Measuring Agreement
agricolae Statistical Procedures for Agricultural Research
agridat Agricultural datasets
agrmt Calculate agreement
ahaz Regularization for semiparametric additive hazards regression
AICcmodavg Model selection and multimodel inference based on (Q)AIC(c)
AID An R Package to Estimate Box-Cox Power Transformation Parameter
AIM AIM: adaptive index model
akima Interpolation of irregularly spaced data
akmeans Adaptive Kmeans algorithm based on threshold
alabama Constrained nonlinear optimization
ALDqr Quantile Regression Using Asymmetric Laplace Distribution
AlgDesign Algorithmic Experimental Design
ALKr Generate Age-Length Keys for fish populations
allan Automated Large Linear Analysis Node
allanvar Allan Variance Analysis
allelematch Identifying unique multilocus genotypes where genotyping error and missing data may be present
AlleleRetain Allele Retention, Inbreeding, and Demography
allelic A fast, unbiased and exact allelic exact test
AllPossibleSpellings Computes all of a word’s possible spellings
alphahull Generalization of the convex hull of a sample of points in the plane
alphashape3d Implementation of the 3D alpha-shape for the reconstruction of 3D sets from a point cloud
alr3 Data to accompany Applied Linear Regression 3rd edition
alr4 Data to accompany Applied Linear Regression 4rd edition
ALS multivariate curve resolution alternating least squares (MCR-ALS)
amap Another Multidimensional Analysis Package
AMAP.Seq Compare Gene Expressions from 2-Treatment RNA-Seq Experiments
amei Adaptive Management of Epidemiological Interventions
Amelia Amelia II: A Program for Missing Data
amen Additive and multiplicative effects modeling of networks and relational data
AmericanCallOpt This package includes pricing function for selected American call options with underlying assets that generate payouts
AMGET Post-processing tool for ADAPT 5
AMORE A MORE flexible neural network package
anacor Simple and Canonical Correspondence Analysis
anaglyph 3D Anaglyph Plots
analogue Analogue and weighted averaging methods for palaeoecology
AnalyzeFMRI Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format
anametrix Bidirectional connector to Anametrix API
anapuce Tools for microarray data analysis
AncestryMapper Ancestry Mapper
AnDE An extended Bayesian Learning Technique developed by Dr. Geoff Webb
andrews Andrews curves
anesrake ANES Raking Implementation
Animal Analyze time-coded animal behavior data
animation A gallery of animations in statistics and utilities to create animations
ANN Feedforward Artificial Neural Network optimized by Genetic Algorithm
AnnotLists AnnotLists: A tool to annotate multiple lists from a specific annotation file
anoint Analysis of interactions
ant Version of ant specific to R
AnthropMMD A GUI for Mean Measures of Divergence
antitrust Antitrust Library
aod Analysis of Overdispersed Data
aods3 Analysis of Overdispersed Data using S3 methods
AOfamilies Aranda-Ordaz (AO) transformation families
apcluster Affinity Propagation Clustering
ape Analyses of Phylogenetics and Evolution
aplpack Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, and some slider functions
appell Compute Appell’s F1 hypergeometric function
apple Approximate Path for Penalized Likelihood Estimators
AppliedPredictiveModeling Functions and Data Sets for ‘Applied Predictive Modeling’
approximator Bayesian prediction of complex computer codes
APSIMBatch Analysis the output of Apsim software
apsrtable apsrtable model-output formatter for social science
apt Asymmetric Price Transmission (apt)
apTreeshape Analyses of Phylogenetic Treeshape
aqp Algorithms for Quantitative Pedology
aqr Interface methods to use with an ActiveQuant Master Server
AquaEnv AquaEnv – an integrated development toolbox for aquatic chemical model generation
ARAMIS A R Adaptive Multiple Importance Sampling
archetypes Archetypal Analysis
ArDec Time series autoregressive-based decomposition
arf3DS4 Activated Region Fitting, fMRI data analysis (3D)
arfima Fractional ARIMA Time Series Modeling
argosfilter Argos locations filter
argparse Command line optional and positional argument parser
arm Data Analysis Using Regression and Multilevel/Hierarchical Models
aroma.affymetrix Analysis of large Affymetrix microarray data sets
aroma.apd A probe-level data file format used by aroma.affymetrix [DEPRECATED] Copy-number analysis of large microarray data sets
aroma.core Core methods and classes used by aroma.* packages part of The Aroma Framework
ArrayBin Binarization of numeric data arrays
arrayhelpers Convenience functions for arrays
ars Adaptive Rejection Sampling
ARTIVA Infer a time-varying DBN network from time series data
ARTP Gene and Pathway p-values computed using the Adaptive Rank Truncated Product
arules Mining Association Rules and Frequent Itemsets
arulesNBMiner Mining NB-Frequent Itemsets and NB-Precise Rules
arulesSequences Mining frequent sequences
arulesViz Visualizing Association Rules and Frequent Itemsets
asbio A collection of statistical tools for biologists
ascii Export R objects to several markup languages
ascrda Augmented SCRDA
asd Simulations for adaptive seamless designs
ash David Scott’s ASH routines
aspace A collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns
aspect Aspects of Multivariables
assertive Readable check functions to ensure code integrity
AssetPricing Optimal pricing of assets with fixed expiry date
AssotesteR Statistical Tests for Genetic Association Studies
aster Aster Models
aster2 Aster Models
astro Astronomy Functions, Tools and Routines
astroFns Astronomy: time and position functions, misc. utilities
astsa Applied Statistical Time Series Analysis
asympTest Asymptotic statistic
asypow Calculate Power Utilizing Asymptotic Likelihood Ratio Methods
AtelieR A GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests
AtmRay Acoustic Traveltime Calculations for 1-D Atmospheric Models
attfad Evaluation and comparison of expression data and GRNs
AUC Threshold independent performance measures for probabilistic classifiers
AUCRF Variable Selection with Random Forest and the Area Under the Curve
audio Audio Interface for R
audiolyzR audiolyzR: Give your data a listen
audit Bounds for Accounting Populations
automap Automatic interpolation package
autopls pls regression with backward selection of predictors
AutoSEARCH General-to-Specific (GETS) Model Selection
aws Adaptive Weights Smoothing
awsMethods Class and Methods definitions for packages aws, adimpro, fmri, dwi R package to use Amazon Web Services
aylmer A generalization of Fisher’s exact test
B2Z Bayesian Two-Zone Model
b6e6rl Adaptive differential evolution, b6e6rl variant
BaBooN Bayesian Bootstrap Predictive Mean Matching – Multiple and single imputation for discrete data
BACCO Bayesian Analysis of Computer Code Output (BACCO)
backtest Exploring portfolio-based conjectures about financial instruments
BACprior Sensitivity of the Bayesian Adjustment for Confounding (BAC) algorithm to the choice of hyperparameter omega
BAEssd Bayesian Average Error approach to Sample Size Determination
bagRboostR Ensemble bagging and boosting classifiers
BaM Functions and datasets for books by Jeff Gill
bamdit Bayesian Meta-Analysis of diagnostic test data
bams Breakpoint annotation model smoothing
bandit Functions for simple A/B split test and multi-armed bandit analysis
barcode Barcode distribution plots
bark Bayesian Additive Regresssion Kernels
Barnard Barnard’s Unconditional Test
BAS Bayesian Model Averaging using Bayesian Adaptive Sampling
BaSAR Bayesian Spectrum Analysis in R
base64 Base 64 encoder/decoder
base64enc Tools for base64 encoding
baseline Baseline Correction of Spectra
basicspace A Package to Recover a Basic Space from Issue Scales
BaSTA A package for estimating age-specific survival from incomplete capture-recapture/recovery data
batade HTML reports and so on
batch Batching Routines in Parallel and Passing Command-Line Arguments to R
BatchExperiments Statistical experiments on batch computing clusters
BatchJobs Batch computing with R
batchmeans Consistent Batch Means Estimation of Monte Carlo Standard Errors
BayesBridge Bridge Regression
bayesclust Tests/Searches for significant clusters in genetic data
BayesComm Bayesian community ecology analysis
bayescount Power calculations and Bayesian analysis of count distributions and FECRT data using MCMC
BayesCR Bayesian analysis of censored linear regression models with scale mixtures of normal (SMN) distributions
BayesDA Functions and Datasets for the book “Bayesian Data Analysis”
bayesDem Graphical User Interface for bayesTFR, bayesLife and bayesPop
BayesFactor Computation of Bayes factors for common designs
bayesGARCH Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
bayesGDS Functions to implement Generalized Direct Sampling
BayesLCA Bayesian Latent Class Analysis
bayesLife Bayesian Projection of Life Expectancy
BayesLogit Logistic Regression
bayesm Bayesian Inference for Marketing/Micro-econometrics
bayesMCClust Mixtures-of-Experts Markov Chain Clustering and Dirichlet Multinomial Clustering
bayesmix Bayesian Mixture Models with JAGS
BayesNI BayesNI: Bayesian Testing Procedure for Noninferiority with Binary Endpoints
bayesPop Probabilistic Population Projection
bayespref Hierarchical Bayesian analysis of ecological count data
bayesQR Bayesian quantile regression
BayesQTLBIC Bayesian multi-locus QTL analysis based on the BIC criterion
bayess Bayesian Essentials with R
BayesSingleSub Computation of Bayes factors for interrupted time-series designs
bayesSurv Bayesian Survival Regression with Flexible Error and Random Effects Distributions
bayesTFR Bayesian Fertility Projection
Bayesthresh Bayesian thresholds mixed-effects models for categorical data
BayesTree Bayesian Methods for Tree Based Models
BayesValidate BayesValidate Package
BayesVarSel Bayesian Variable selection in Linear Models
BayesX R Utilities Accompanying the Software Package BayesX
BayesXsrc R Package Distribution of the BayesX C++ Sources
BayHap Bayesian analysis of haplotype association using Markov Chain Monte Carlo
BayHaz R Functions for Bayesian Hazard Rate Estimation
BaylorEdPsych R Package for Baylor University Educational Psychology Quantitative Courses
BaySIC Bayesian Analysis of Significantly Mutated Genes in Cancer
BB Solving and Optimizing Large-Scale Nonlinear Systems
bbemkr Bayesian bandwidth estimation for multivariate kernel regression with Gaussian error
BBmisc Miscellaneous helper functions for B. Bischl
bbmle Tools for general maximum likelihood estimation
BBMM Brownian bridge movement model
bbo Biogeography-Based Optimization
bc3net BC3NET
BCA Business and Customer Analytics
BCBCSF Bias-corrected Bayesian Classification with Selected Features
BCDating Business Cycle Dating and Plotting Tools – BCDating
BcDiag Diagnostics plots for Bicluster Data
BCE Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data
BCEA Bayesian Cost Effectiveness Analysis
BCEs0 Bayesian models for cost-effectiveness analysis in the presence of structural zero costs
Bchron Bayesian radiocarbon chronologies and relative sea level analysis
Bclim Bayesian Palaeoclimate Reconstruction from Pollen
bclust Bayesian clustering using spike-and-slab hierarchical model, suitable for clustering high-dimensional data
bcool Bringing to light significant Columns correlated with Organism Labels
bcp A Package for Performing a Bayesian Analysis of Change Point Problems
bcrm Bayesian continuous reassessment method (CRM) designs for Phase I dose-finding trials
bcv Cross-Validation for the SVD (Bi-Cross-Validation)
bda Density Estimation for Binned/Weighted Data
BDgraph Graph determination based on birth-death MCMC
bdoc Bayesian Discrete Ordered Classification of DNA Barcodes
bdpv Inference and design for predictive values in binary diagnostic tests
bdsmatrix Routines for Block Diagonal Symmetric matrices
bdynsys Bayesian Dynamical System Model
beadarrayFilter Bead filtering for Illumina bead arrays
beadarrayMSV Analysis of Illumina BeadArray SNP data including MSV markers
beanplot Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
bear Average bioequivalence and bioavailability data analysis tool
BEDASSLE Disentangles the effects of geographic and ecological isolation on genetic differentiation
beeswarm The bee swarm plot, an alternative to stripchart
benchden 28 benchmark densities from Berlinet/Devroye (1994)
benchmark Benchmark Experiments Toolbox
Benchmarking Benchmark and frontier analysis using DEA and SFA
BenfordTests Statistical Tests for Evaluating Conformity to Benford’s Law
bentcableAR Bent-Cable Regression for Independent Data or Autoregressive Time Series
ber Batch Effects Removal
Bergm Bayesian analysis for exponential random graph models
BerkeleyEarth Data Input for Berkeley Earth Surface Temperature
Bessel Bessel – Bessel Functions Computations and Approximations
BEST Bayesian Estimation Supersedes the t-Test
bestglm Best Subset GLM
betafam Detecting rare variants for quantitative traits using nuclear families
betapart Partitioning beta diversity into turnover and nestedness components
betaper Functions to incorporate taxonomic uncertainty on multivariate analyses of ecological data
betareg Beta Regression
betategarch Estimation and simulation of first-order Beta-t-EGARCH models
bethel Bethel’s algorithm
bfa Bayesian Factor Analysis
bfast Breaks For Additive Season and Trend (BFAST)
bfp Bayesian Fractional Polynomials
bgeva Binary Generalized Extreme Value Additive Models
bgmm Gaussian Mixture Modeling algorithms. Including the belief-based mixture modeling
BGSIMD Block Gibbs Sampler with Incomplete Multinomial Distribution
BH The Boost C++ Libraries
Bhat General likelihood exploration
BHH2 Useful Functions for Box, Hunter and Hunter II
biasbetareg Bias correction of the parameter estimates of the beta regression model
BiasedUrn Biased Urn model distributions
bibtex bibtex parser
biclust BiCluster Algorithms
BiDimRegression Calculates the bidimensional regression between two 2D configurations
bifactorial Inferences for bi- and trifactorial trial designs
biganalytics A library of utilities for big.matrix objects of package bigmemory
bigdata Big Data Analytics
bigGP Distributed Gaussian process calculations
biglars Scalable Least-Angle Regression and Lasso
biglm bounded memory linear and generalized linear models
bigmemory Manage massive matrices with shared memory and memory-mapped files
bigmemory.sri A shared resource interface for Bigmemory Project packages
bigml R bindings for the BigML API
bigrf Big Random Forests: Classification and Regression Forests for Large Data Sets
bigRR Generalized Ridge Regression (with special advantage for p >> n cases)
bigtabulate table-, tapply-, and split-like functionality for matrix and big.matrix objects
BigTSP Top Scoring Pair based methods for classification
bild bild: a package for BInary Longitudinal Data
bimetallic Power for SNP analyses using silver standard cases
binarySimCLF Simulates Correlated Binary Data
BINCO Bootstrap Inference for Network COstruction
bindata Generation of Artificial Binary Data
binGroup Evaluation and experimental design for binomial group testing
binMto Asymptotic simultaneous confidence intervals for many-to-one comparisons of proportions
BinNor Simultaneous generation of multivariate binary and normal variates
binom Binomial Confidence Intervals For Several Parameterizations
binomialcftp Generates binomial random numbers via the coupling from the past algorithm
binomlogit Efficient MCMC for Binomial Logit Models
binomTools Performing diagnostics on binomial regression models
binseqtest Exact Binary Sequential Designs and Analysis
Biodem Biodemography functions
BiodiversityR GUI for biodiversity, suitability and community ecology analysis
BioGeoBEARS BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
Biograph Explore life histories
bio.infer Predict environmental conditions from biological observations
biom An interface package (beta) for the BIOM file format
BioMark Find biomarkers in two-class discrimination problems
BiomarkeR Paired (pBI) and Unpaired Biomarker Identifier (uBI) including a method to infer networks
biomod2 Ensemble platform for species distribution modeling
bionetdata Biological and chemical data networks
biopara Self-contained parallel system for R
BioPhysConnectoR BioPhysConnectoR
biOps Image processing and analysis
biOpsGUI GUI for Basic image operations
bios2mds From BIOlogical Sequences to MultiDimensional Scaling
BioStatR Initiation à la Statistique avec R
bipartite Visualising bipartite networks and calculating some (ecological) indices
BiplotGUI Interactive Biplots in R
birch Dealing with very large datasets using BIRCH
bisectr Tools to find bad commits with git bisect
bisoreg Bayesian Isotonic Regression with Bernstein Polynomials
bit A class for vectors of 1-bit booleans
bit64 A S3 class for vectors of 64bit integers
bitops Bitwise Operations
bivarRIpower Sample size calculations for bivariate longitudinal data
biwavelet Conduct univariate and bivariate wavelet analyses
biwt Functions to compute the biweight mean vector and covariance & correlation matrices
BlakerCI Blaker’s binomial confidence limits
BLCOP Black-Litterman and copula-opinion pooling frameworks
blender Analyze biotic homogenization of landscapes
blighty United Kingdom coastlines
blm Binomial linear and linear-expit regression
blme Bayesian Linear Mixed-Effects models
blockcluster Co-Clustering package for Binary, Contingency and Continuous data-sets
BlockMessage Creates strings that show a text message in 8 by 8 block letters
blockmodeling An R package for Generalized and classical blockmodeling of valued networks
blockrand Randomization for block random clinical trials
blockTools Block, assign, and diagnose potential interference in randomized experiments
BLR Bayesian Linear Regression
BMA Bayesian Model Averaging
bmd Benchmark dose analysis for dose-response data
bmem Mediation analysis with missing data using bootstrap
Bmix Bayesian Sampling for Stick-breaking Mixtures
bmk MCMC diagnostics package
BMN The pseudo-likelihood method for pairwise binary markov networks
bmp Read Windows Bitmap (BMP) images
bmrm Bundle Methods for Regularized Risk Minimization Package
BMS Bayesian Model Averaging Library
bnlearn Bayesian network structure learning, parameter learning and inference
BNPdensity Ferguson-Klass type algorithm for posterior normalized random measures
bnpmr Bayesian monotonic nonparametric regression
boa Bayesian Output Analysis Program (BOA) for MCMC
BOG Bacterium and virus analysis of Orthologous Groups (BOG) is a package for identifying differentially regulated genes in the light of gene functions
boilerpipeR Interface to the boilerpipe Java library by Christian Kohlschutter (
Bolstad Bolstad functions
Bolstad2 Bolstad functions
boolfun Cryptographic Boolean Functions
BoolNet Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
boostSeq Optimized GWAS cohort subset selection for resequencing studies
boot Bootstrap Functions (originally by Angelo Canty for S)
bootES Bootstrap Effect Sizes
bootfs Use multiple feature selection algorithms to derive robust feature sets for two class classification problems
bootRes Bootstrapped Response and Correlation Functions
bootruin A bootstrap test for the probability of ruin in the classical risk process
bootspecdens Testing equality of spectral densities
bootStepAIC Bootstrap stepAIC
bootstrap Functions for the Book “An Introduction to the Bootstrap”
Boruta A wrapper algorithm for all-relevant feature selection
boss Boosted One-Step Statistics: Fast and accurate approximations for GLM, GEE and Mixed models for use in GWAS
BoSSA a Bunch of Structure and Sequence Analysis
boussinesq Analytic Solutions for (ground-water) Boussinesq Equation
bpca Biplot of Multivariate Data Based on Principal Components Analysis
bpcp Beta Product Confidence Procedure for Right Censored Data
bPeaks bPeaks: a simple and intuitive approach for detection of basic peaks (bPeaks) from ChIP-seq data
bpkde Back-Projected Kernel Density Estimation
bqtl Bayesian QTL mapping toolkit
BradleyTerry2 Bradley-Terry Models
BrailleR Improved access for blind useRs
brainwaver Basic wavelet analysis of multivariate time series with a visualisation and parametrisation using graph theory
branchLars Cost-efficient Variable Selection
breakage SICM pipette tip geometry estimation
bReeze Functions for wind resource assessment
brew Templating Framework for Report Generation
brglm Bias reduction in binomial-response generalized linear models
bride Brier score decomposition of probabilistic forecasts for binary events
brnn brnn (Bayesian regularization for feed-forward neural networks)
Brobdingnag Very large numbers in R
broman Karl Broman’s R code
Brq Bayesian analysis of quantile regression models
BRugs R interface to the OpenBUGS MCMC software
BSagri Statistical methods for safety assessment in agricultural field trials
bscr Bayesian parametric and semi-parametric analyses for semi-competing risks data
BSDA Basic Statistics and Data Analysis
BsMD Bayes Screening and Model Discrimination
bspec Bayesian spectral inference
bspmma bspmma: Bayesian Semiparametric Models for Meta-Analysis
BSquare Bayesian Simultaneous Quantile Regression
bst Gradient Boosting
bstats Basic statistical functions for R
BTSPAS Bayesian Time-Strat. Population Analysis
BTYD Implementing Buy ‘Til You Die Models
BurStFin Burns Statistics Financial
BurStMisc Burns Statistics miscellaneous
bursts Markov model for bursty behavior in streams
bvenn A Simple alternative to proportional Venn diagrams
bvls The Stark-Parker algorithm for bounded-variable least squares
bvpSolve Solvers for boundary value problems of ordinary differential equations
BVS Bayesian Variant Selection: Bayesian Model Uncertainty Techniques for Genetic Association Studies
c060 Additional variable selection, model validation and parameter tuning functions for glmnet models
c3net Infering large-scale gene networks with C3NET
C50 C5.0 Decision Trees and Rule-Based Models
ca Simple, Multiple and Joint Correspondence Analysis
cabootcrs Bootstrap Confidence Regions for Correspondence Analysis
cacher Tools for caching and distributing statistical analyses
cacheSweave Tools for caching Sweave computations
cacIRT Classification accuracy and consistency under Item Response Theory
CaDENCE Conditional Density Estimation Network Construction and Evaluation
CADFtest This package performs the CADF unit root test proposed in Hansen (1995)
caGUI A Tcl/Tk GUI for the functions in the ca package
Cairo R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output
cairoDevice Cairo-based cross-platform antialiased graphics device driver
CalciOMatic Automatic Calcium Imaging Analysis
calibrate Calibration of Scatterplot and Biplot Axes
calibrator Bayesian calibration of complex computer codes
CALINE3 R interface to Fortran 77 implementation of CALINE3
calmate CalMaTe – Improved allele-specific copy number of SNP arrays for downstream segmentation
CAMAN Finite Mixture Models and meta-analysis tools – based on C.A.MAN
cancerTiming Estimation of temporal ordering of cancer abnormalities
candisc Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
cape Combined analysis of pleiotropy and epistasis
caper Comparative Analyses of Phylogenetics and Evolution in R
capme Covariate Adjusted Precision Matrix Estimation
capushe Capushe, data-driven slope estimation and dimension jump
capwire Estimates population size from non-invasive sampling
car Companion to Applied Regression
CARBayes Spatial areal unit modelling
carcass Estimation of the number of fatalities from carcass searches
cardidates Identification of cardinal dates in ecological time series
care High-Dimensional Regression and CAR Score Variable Selection
CARE1 Statistical package for population size estimation in capture-recapture models
caret Classification and Regression Training
caribou Estimation of caribou abundance based on large scale aggregations monitored by radio telemetry
CARramps Reparameterized and marginalized posterior sampling for conditional autoregressive models
CAscaling CA scaling in R
caschrono Séries temporelles avec R – Méthodes et cas
cat Analysis of categorical-variable datasets with missing values
catdata Categorical Data
CatDyn Fishery Stock Assessment by Catch Dynamic Models
catenary Fits a catenary to given points
catIrt An R Package for Simulating IRT-Based Computerized Adaptive Tests
catnet Categorical Bayesian Network Inference
caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc
catR Procedures to generate IRT adaptive tests (CAT)
catspec Special models for categorical variables
CausalGAM Estimation of Causal Effects with Generalized Additive Models
causalsens Selection Bias Approach to Sensitivity Analysis for Causal Effects
Causata Analysis utilities for binary classification and Causata users
cba Clustering for Business Analytics
CBPS R Package for Covariate Balancing Propensity Score
CCA Canonical correlation analysis
CCAGFA Bayesian canonical correlation analysis and group factor analysis
ccaPP (Robust) canonical correlation analysis via projection pursuit
cccd Class Cover Catch Digraphs
ccChooser Developing a core collections
cccrm CCC-RM
ccgarch Conditional Correlation GARCH models
cclust Convex Clustering Methods and Clustering Indexes
CCM Correlation classification method (CCM)
CCP Significance Tests for Canonical Correlation Analysis (CCA)
cda Coupled dipole approximation in electromagnetic scattering
cdb Reading and Writing Constant DataBases
CDFt Statistical downscaling through CDF-transform
CDLasso Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression
CDM Cognitive Diagnosis Modeling
CDNmoney Components of Canadian Monetary and Credit Aggregates
CDVine Statistical inference of C- and D-vine copulas
cec2005benchmark Benchmark for the CEC 2005 Special Session on Real-Parameter Optimization
cec2013 Benchmark functions for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013
celestial Collection of common astronomical conversion routines
CellularAutomaton One-Dimensional Cellular Automata
cellVolumeDist Functions to fit cell volume distributions and thereby estimate cell growth rates and division times
cem Coarsened Exact Matching
cems Conditional expectation manifolds
censReg Censored Regression (Tobit) Models
CensRegMod Fitting Normal and Student-t censored regression model
CePa Centrality-based pathway enrichment
cepp Context Driven Exploratory Projection Pursuit
cfa Analysis of configuration frequencies (CFA)
CfEstimateQuantiles Estimate quantiles using any order Cornish-Fisher expansion
CFL Compensatory Fuzzy Logic
cg Comparison of groups
cgAUC Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it
cgdsr R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)
cggd Continuous Generalized Gradient Descent
cgh Microarray CGH analysis using the Smith-Waterman algorithm
cghFLasso Detecting hot spot on CGH array data with fused lasso regression
cghseg Segmentation methods for array CGH analysis
CGP Composite Gaussian process models
ChainLadder Statistical methods for the calculation of outstanding claims reserves in general insurance
ChangeAnomalyDetection Change Anomaly Detection
changeLOS Change in LOS
changepoint An R package for changepoint analysis
charlson Converts listwise icd9 data into comorbidity count and Charlson Index
CHCN Canadian Historical Climate Network
cheb Discrete Linear Chebyshev Approximation
chebpol Multivariate Chebyshev interpolation
CheckDigit Calculate and verify check digits
cheddar Analysis and visualisation of ecological communities
chemCal Calibration functions for analytical chemistry
chemometrics Multivariate Statistical Analysis in Chemometrics
ChemometricsWithR Chemometrics with R – Multivariate Data Analysis in the Natural Sciences and Life Sciences
ChemometricsWithRData Data for package ChemometricsWithR
ChemoSpec Exploratory Chemometrics for Spectroscopy
cherry Multiple testing methods for exploratory research
chillR Statistical methods for phenology analysis in temperate fruit trees
CHNOSZ Chemical Thermodynamics and Activity Diagrams
ChoiceModelR Choice Modeling in R
choplump Choplump tests
chords Estimation in respondent driven samples
chron Chronological objects which can handle dates and times
CHsharp Choi and Hall Clustering in 3d
cimis R package for retrieving data from CIMIS
cin Causal Inference for Neuroscience
circlize Circular layout in R
CircNNTSR CircNNTSR: An R package for the statistical analysis of circular data using nonnegative trigonometric sums (NNTS) models
CircStats Circular Statistics, from “Topics in circular Statistics” (2001)
circular Circular Statistics
cit Causal Inference Test
CITAN CITation ANalysis toolpack
citbcmst Assigning tumor samples to CIT Breast Cancer Molecular Subtypes from gene expression data
citccmst CIT Colon Cancer Molecular SubTypes Prediction
CityPlot Visualization of structure and contents of a database
Ckmeans.1d.dp Optimal distance-based clustering for one-dimensional data
cladoRcpp C++ implementations of phylogenetic calculations
CLAG CLAG: an unsupervised non hierarchical clustering algorithm handling biological data
class Functions for Classification
classGraph Construct Graphs of S4 Class Hierarchies
classifly Explore classification models in high dimensions
classify Classification Accuracy and Consistency under IRT models
classInt Choose univariate class intervals
cldr Language Identifier based on CLD library
clhs Conditioned Latin Hypercube Sampling
climatol Some Tools for Climatology: series homogenization, plus windrose and Walter&Lieth diagrams
climdex.pcic PCIC implementation of Climdex routines
clime Constrained L1-minimization for Inverse (covariance) Matrix Estimation
clinfun Clinical Trial Design and Data Analysis Functions
ClinicalRobustPriors Robust Bayesian Priors in Clinical Trials: An R Package for Practitioners
clinsig Clinical significance functions
clinUtiDNA Clinical Utility of DNA Testing
clogitL1 Fitting exact conditional logistic regression with lasso and elastic net penalties
cloudUtil Cloud Util Plots
clpAPI R Interface to C API of COIN-OR Clp
CLSOCP A smoothing Newton method SOCP solver
clue Cluster ensembles
clues Clustering Method Based on Local Shrinking
cluster Cluster Analysis Extended Rousseeuw et al
clusterCrit Clustering Indices
clustergas A hierarchical clustering method based on genetic algorithms
clusterGeneration random cluster generation (with specified degree of separation)
clusterGenomics Identifying clusters in genomics data by recursive partitioning
clusterPower Power calculations for cluster-randomized and cluster-randomized crossover trials
clusterRepro Reproducibility of gene expression clusters
clusterSim Searching for optimal clustering procedure for a data set
clusteval Evaluation of Clustering Algorithms
clusthaplo Clustering of haplotypes
ClustOfVar Clustering of variables
clustsig Significant Cluster Analysis
clv Cluster Validation Techniques
clValid Validation of Clustering Results
cmaes Covariance Matrix Adapting Evolutionary Strategy
CMC Cronbach-Mesbah Curve
cmm Categorical Marginal Models
cmprsk Subdistribution Analysis of Competing Risks
cmrutils Misc Functions of the Center for the Mathematical Research
cncaGUI Canonical Non-symmetrical Correspondence Analysis in R
CNprep pre-process DNA copy number (CN) data for detection of CN events
CNVassoc Association analysis of CNV data
coalescentMCMC MCMC Algorithms for the Coalescent
coarseDataTools A collection of functions to help with analysis of coarsely observed data
COBRA Nonlinear Aggregation of Predictors
cobs COBS – Constrained B-splines (Sparse matrix based)
cobs99 Constrained B-splines – outdated 1999 version
CoClust Copula based cluster analysis
cocor Comparing correlations
cocorresp Co-correspondence analysis methods
cocron Statistical comparisons of two or more alpha coefficients
coda Output analysis and diagnostics for MCMC
codep Multiscale Codependence Analysis
codetools Code Analysis Tools for R
coefficientalpha Robust Cronbach’s alpha with missing and non-normal data
coefplot Plots Coefficients from Fitted Models
coexist Species coexistence modeling and analysis
coin Conditional Inference Procedures in a Permutation Test Framework
CoinMinD Simultaneous Confidence Interval for Multinomial Proportion
colbycol Read big text files column by column, sometimes much bigger than available RAM, into R
colcor Tests for column correlation in the presence of row correlation
cold cold: a package for Count Longitudinal Data
CollocInfer Collocation Inference for Dynamic Systems
coloc Colocalisation tests of two genetic traits
colorfulVennPlot Plot and add custom coloring to Venn diagrams for 2-dimensional, 3-dimensional and 4-dimensional data
colorRamps Builds color tables
colorspace Color Space Manipulation
colortools Tools for colors in an HSV color model
combinat combinatorics utilities
CombMSC Combined Model Selection Criteria
commandr Command pattern in R
CommonJavaJars Useful libraries for building a Java based GUI under R
CommonTrend Extract and plot common trends from a cointegration system. Calculate P-value for Johansen Statistics
comorbidities Categorizes ICD-9-CM codes based on published comorbidity indices
Comp2ROC Compare two ROC curves that intersect
compactr Creates empty plots with compact axis notation
compare Comparing Objects for Differences
compareGroups Descriptive analysis by groups
compareODM comparison of medical forms in CDISC ODM format
CompareTests Estimate diagnostic accuracy (sensitivity, specificity, etc) and agreement statistics when one test is conducted on only a subsample of specimens
comparison Multivariate likelihood ratio calculation and evaluation
compeir Event-specific incidence rates for competing risks data
compHclust Complementary Hierarchical Clustering
complex.surv.dat.sim Simulation of complex survival data
CompLognormal Functions for actuarial scientists
compoisson Conway-Maxwell-Poisson Distribution
COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression
compositions Compositional Data Analysis
compositionsGUI Graphical User Environment for Compositional Data Analysis
compound.Cox Regression estimation based on the compound shrinkage method under the Cox proportional hazard model
Compounding Computing Continuous Distributions
CompQuadForm Distribution function of quadratic forms in normal variables
CompRandFld Composite-likelihood based Analysis of Random Fields Compute Effect Sizes
ConConPiWiFun This package contains an implementation of continuous convex piecewise (linear and quadratic) functions
concor Concordance
concreg Concordance regression
condGEE Parameter estimation in conditional GEE for recurrent event gap times
condmixt Conditional Density Estimation with Neural Network Conditional Mixtures
CondReg Condition Number Regularized Covariance Estimation
coneproj Primal or Dual Cone Projections with Routines for Shape-restricted Regression Construction of factorial designs
confReg Confidence Estimators for Individual Regression Predictions
conics Plot Conics
conjoint Conjoint analysis package
ConjointChecks A package to check the cancellation axioms of conjoint measurement
constrainedKriging Constrained, covariance-matching constrained and universal point or block kriging
contfrac Continued fractions
conting Bayesian analysis of contingency tables
contrast A collection of contrast methods
ConvCalendar Converts dates between calendars
ConvergenceConcepts Seeing convergence concepts in action
convexHaz Nonparametric MLE/LSE of convex hazard
COP Variables selection for index models via correlation pursuit
copas Statistical methods to model and adjust for bias in meta-analysis
copBasic Basic Theoretical Copula, Empirical Copula, and Various Utility Functions
copula Multivariate Dependence with Copulas
copulaedas Estimation of Distribution Algorithms Based on Copulas
CopulaRegression Bivariate Copula Based Regression Models
CopyDetect An R Package for Computing Statistical Indices to Detect Answer Copying on Multiple-Choice Tests
corcounts Generate correlated count random variables
CORE Cores of Recurrent Events
CORElearn CORElearn – classification, regression, feature evaluation and ordinal evaluation
corHMM Analysis of binary character evolution
corpcor Efficient Estimation of Covariance and (Partial) Correlation
corpora Statistics and data sets for corpus frequency data
CorrBin Nonparametrics with clustered binary data
corrgram Plot a correlogram
corrperm Permutation Tests of Correlation with Repeated Measurements
corrplot Visualization of a correlation matrix
corrsieve CorrSieve
COSINE COndition SpecIfic sub-NEtwork
cosmoFns Functions for cosmological distances, times, luminosities, etc
cosso Fit Regularized Nonparametric Regression Models Using COSSO Penalty
costat Time series costationarity determination
cotrend Consistant Cotrend Rank Selection
COUNT Functions, data and code for count data
countrycode Convert country names and country codes
CountsEPPM Mean and variance modeling of count data
covLCA Latent Class Models with Covariate Effects on Underlying and Measured Variables
covRobust Robust Covariance Estimation via Nearest Neighbor Cleaning
covTest Computes covariance test for adaptive linear modelling
CoxBoost Cox models by likelihood based boosting for a single survival endpoint or competing risks
coxme Mixed Effects Cox Models
coxphf Cox regression with Firth’s penalized likelihood
coxphw Weighted Cox regression
CoxRidge Cox models with dynamic ridge penalties
coxrobust Robust Estimation in Cox Model
CPE Concordance Probability Estimates in Survival Analysis
CpGassoc Association between Methylation and a phenotype of interest
CPHshape Find the maximum likelihood estimator of the shape constrained hazard baseline and the effect parameters in the Cox proportional hazards model
cpk Clinical Pharmacokinetics
cplexAPI R Interface to C API of IBM ILOG CPLEX
cplm Compound Poisson linear models
cpm Sequential Parametric and Nonparametric Change Detection
CPMCGLM Correction of the pvalue after multiple coding
Cprob Conditional probability function of a competing event
CR Power Calculation for Weighted Log-Rank Tests in Cure Rate Models
cramer Multivariate nonparametric Cramer-Test for the two-sample-problem
crank Completing ranks
crantastic Various R tools for
crawl Fit continuous-time correlated random walk models to animal movement data
crblocks Categorical Randomized Block Data Analysis
CreditMetrics Functions for calculating the CreditMetrics risk model
crimCV Group-Based Modelling of Longitudinal Data
CRM Continual Reassessment Method (CRM) for Phase I Clinical Trials
crmn CCMN and other noRMalizatioN methods for metabolomics data
crn Downloads and Builds datasets for Climate Reference Network
crossdes Construction of Crossover Designs
crossmatch The Cross-match Test
crp.CSFP CreditRisk+ portfolio model
crrSC Competing risks regression for Stratified and Clustered data
crrstep Stepwise covariate selection for the Fine & Gray competing risks regression model
crs Categorical Regression Splines
CRTSize Sample Size Estimation Functions for Cluster Randomized Trials
CrypticIBDcheck Identifying cryptic relatedness in genetic association studies
cshapes CShapes Dataset and Utilities
cslogistic Conditionally Specified Logistic Regression
csound Accessing Csound functionality through R
CSS Extract information from an html document with CSS selectors
csSAM csSAM – cell-specific Significance Analysis of Microarrays
cts Continuous Time Autoregressive Models
CTT Classical Test Theory Functions
ctv CRAN Task Views
cubature Adaptive multivariate integration over hypercubes
Cubist Rule- and Instance-Based Regression Modeling
cudaBayesreg CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis
cudaBayesregData Data sets for the examples used in the package “cudaBayesreg”
cudia CUDIA Cross-level Imputation
CUMP Analyze Multivariate Phenotypes by Combining Univariate results
cumplyr Extends ddply to allow calculation of cumulative quantities
cumSeg Change point detection in genomic sequences
currentSurvival Estimation of CCI and CLFS Functions
curvetest The package will formally test two curves represented by discrete data sets to be statistically equal or not when the errors of the two curves were assumed either equal or not using the tube formula to calculate the tail probabilities
curvHDR curvHDR filtering of flow cytometry samples
cusp Cusp Catastrophe Model Fitting Using Maximum Likelihood
cvAUC Cross-Validated Area Under the ROC Curve Confidence Intervals
CvM2SL1Test L1-version of Cramer-von Mises Two Sample Tests
CvM2SL2Test Cramer-von Mises Two Sample Tests
cvplogistic Penalized Logistic Regression Model using Majorization Minimization by Coordinate Descent (MMCD) Algorithm
cvq2 Calculate the predictive squared correlation coefficient
CVST Fast Cross-Validation via Sequential Testing
CVThresh Level-Dependent Cross-Validation Thresholding
cvTools Cross-validation tools for regression models
cvxclustr Splitting methods for convex clustering
cwhmisc Miscellaneous Functions for math, plotting, printing, statistics, strings, and tools
cwm Cluster Weighted Models by EM algorithm
cxxfunplus extend cxxfunction by saving the dynamic shared objects
cyphid Cycle and Phase Identification for mastication data
cytoDiv Cytometric diversity indices
d3Network Tools for creating D3 JavaScript network and tree graphs from R
DAAG Data Analysis And Graphics data and functions
DAAGbio Data Sets and Functions, for demonstrations with expression arrays and gene sequences
DAAGxtras Data Sets and Functions, supplementary to DAAG
dae Functions useful in the design and ANOVA of experiments
daewr Design and Analysis of Experiments with R
dafs Data analysis for forensic scientists
DAGGER Consensus genetic maps
dagR R functions for directed acyclic graphs
DAKS Data Analysis and Knowledge Spaces
DALY DALY Calculator – A GUI for stochastic DALY calculation in R
DAMisc Dave Armstrong’s Miscellaneous Functions
DandEFA Dandelion Plot for R-mode Exploratory Factor Analysis
darts Statistical Tools to Analyze Your Darts Game
DatABEL file-based access to large matrices stored on HDD in binary format
datacheck Tools for checking data consistency
DataCombine R tools for making it easier to combine and clean data sets
DataFrameConstr Constrained data frames and homogenous list classes
dataframes2xls dataframes2xls writes data frames to xls files
datamap A system for mapping foreign objects to R variables and environments
datamart Unified access to your data sources
datamerge Merging of overlapping and inconsistent data
dataone DataONE R Client
dataonelibs DataONE R Client Libraries
data.table Extension of data.frame for fast indexing, fast ordered joins, fast assignment, fast grouping and list columns
datautils Support functions for packages VBmix, semisupKernelPCA, and patchPlot
dataview Human readable data presentation
date Functions for handling dates
DATforDCEMRI Deconvolution Analysis Tool for Dynamic Contrast Enhanced MRI
dave Functions for “Data Analysis in Vegetation Ecology”
Davies The Davies quantile function
dbConnect Provides a graphical user interface to connect with databases that use MySQL
dbEmpLikeGOF Goodness-of-fit and two sample comparison tests using sample entropy
dbEmpLikeNorm Test for joint assessment of normality
DBGSA methods of distance-based gene set functional enrichment analysis
DBI R Database Interface
DBKGrad Discrete Beta Kernel Graduation of mortality data
dblcens Compute the NPMLE of distribution from doubly censored data
dbmss Distance-based measures of spatial structures
dbstats Distance-based statistics (dbstats)
dcemriS4 A Package for Medical Image Analysis (S4 implementation)
DCGL Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
dclone Data Cloning and MCMC Tools for Maximum Likelihood Methods
DCluster Functions for the detection of spatial clusters of diseases
dcmle Hierarchical Models Made Easy with Data Cloning
dcv Conventional Cross-validation statistics for climate-growth model
ddalpha DDalpha-Classifier
DDD Diversity-dependent diversification
ddepn Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data
ddst Data driven smooth test
deal Learning Bayesian Networks with Mixed Variables
deamer Deconvolution density estimation with adaptive methods for a variable prone to measurement error
debug MVB’s debugger for R
decctools Get energy data from the UK Dept of Energy and Climate Change
DECIDE DEComposition of Indirect and Direct Effects
decon Deconvolution Estimation in Measurement Error Models
Deducer Deducer
DeducerExtras Additional dialogs and functions for Deducer
DeducerPlugInExample Deducer Plug-in Example
DeducerPlugInScaling Reliability and factor analysis plugin
DeducerSpatial Deducer for spatial data analysis
DeducerSurvival Add Survival Dialogue to Deducer
DeducerText Deducer GUI for Text Data
deducorrect deducorrect: Deductive correction, deductive imputation, and deterministic correction
Defaults Create Global Function Defaults
degenes Detection of differentially expressed genes
degreenet Models for Skewed Count Distributions Relevant to Networks
Delaporte Statistical functions for the Delaporte distribution
deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
deltaPlotR Identification of dichotomous differential item functioning (DIF) using Angoff’s Delta Plot method
Demerelate Functions to calculate relatedness on diploid genetic data
DEMEtics Evaluating the genetic differentiation between populations based on Gst and D values
demi Differential Expression from Multiple Indicators
demography Forecasting mortality, fertility, migration and population data
dendroextras Extra functions to cut, label and colour dendrogram clusters
DendSer Dendrogram seriation: ordering for visualisation
denstrip Density strips and other methods for compactly illustrating distributions
DEoptim Global optimization by Differential Evolution
depend.truncation Inference for parametric and semiparametric models based on dependent truncation data
depmix Dependent Mixture Models
depmixS4 Dependent Mixture Models – Hidden Markov Models of GLMs and Other Distributions in S4
depth Depth functions tools for multivariate analysis
depthTools Depth Tools Package
descr Descriptive statistics
DescribeDisplay R interface to DescribeDisplay (GGobi plugin)
deseasonalize Optimal deseasonalization for geophysical time series using AR fitting
designGG Computational tool for designing genetical genomics experiments
DesignPatterns Design Patterns in R to build reusable object-oriented software
desirability Desirabiliy Function Optimization and Ranking
desire Desirability functions in R
deSolve General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE), differential algebraic equations (DAE), and delay differential equations (DDE)
detect Analyzing Wildlife Data with Detection Error
deTestSet Testset for differential equations
detrendeR Start the detrendeR Graphical User Interface (GUI)
DetSel A computer program to detect markers responding to selection
devEMF EMF graphics output device
Devore6 Data sets from Devore’s “Prob and Stat for Eng (6th ed)”
Devore7 Data sets from Devore’s “Prob and Stat for Eng (7th ed)”
devtools Tools to make developing R code easier
df2json Convert a dataframe to JSON
dfcrm Dose-finding by the continual reassessment method
dfoptim Derivative-free Optimization
dglars Differential Geometric LARS (dgLARS) method
dglm Double generalized linear models
dgmb dgmb Simulating data for PLS structural models
dgof Discrete Goodness-of-Fit Tests
dhglm Double Hierarchical Generalized Linear Models
diagram Functions for visualising simple graphs (networks), plotting flow diagrams
DiagTest3Grp Diagnostic test summary measures for three ordinal groups
dice Calculate probabilities of various dice-rolling events
DiceDesign Designs of Computer Experiments
DiceEval Construction and evaluation of metamodels
DiceKriging Kriging methods for computer experiments
DiceOptim Kriging-based optimization for computer experiments
DiceView Plot methods for computer experiments design and surrogate
dichromat Color Schemes for Dichromats
dicionariosIBGE Dictionaries for reading microdata surveys from IBGE
dielectric Defines some physical constants and dielectric functions commonly used in optics, plasmonics
DierckxSpline R companion to “Curve and Surface Fitting with Splines”
diffdepprop Calculates Confidence Intervals for two Dependent Proportions
diffEq Functions from the book Solving Differential Equations in R
diffractometry Baseline identification and peak decomposition for x-ray diffractograms
diffusionMap Diffusion map
difR Collection of methods to detect dichotomous differential item functioning (DIF) in psychometrics
digest Create cryptographic hash digests of R objects
Digiroo2 An application programming interface for generating null models of social contacts based on individuals’ space use
DIME DIME (Differential Identification using Mixture Ensemble)
dinamic DiNAMIC A Method To Analyze Recurrent DNA Copy Number Aberrations in Tumors
diptest Hartigan’s dip test statistic for unimodality – corrected code
DIRECT Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior
directlabels Direct labels for multicolor plots in lattice or ggplot2
DirichletReg Dirichlet Regression in R
dirmult Estimation in Dirichlet-Multinomial distribution
disclap Discrete Laplace Exponential Family
disclapmix Discrete Laplace mixture inference using the EM algorithm
DiscreteInverseWeibull Discrete inverse Weibull distribution
DiscreteLaplace Discrete Laplace distribution
discreteMTP Multiple testing procedures for discrete test statistics
discreteRV Functions to create and manipulate discrete random variables
DiscreteWeibull Discrete Weibull distribution
discretization Data preprocessing, discretization for classification
discrimARTs Discrimination of Alternative Reproductive Tactics (ARTs)
DiscriMiner Tools of the Trade for Discriminant Analysis
diseasemapping Calculate observed and expected disease incidence counts from a case file and population data
dismo Species distribution modeling
disp2D 2D Hausdorff and Simplex Dispersion Orderings
displayHTS displayHTS
dispmod Dispersion models
Distance A simple way to fit detection functions to distance sampling data and calculate abundance/density for biological populations
DistatisR DiSTATIS Three Way Metric Multidimensional Scaling Distribution-free confidence region (
distillery Method Functions for Confidence Intervals and to Distill Information from an Object
distory Distance Between Phylogenetic Histories
distr Object oriented implementation of distributions
distrDoc Documentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse
distrEllipse S4 classes for elliptically contoured distributions
distrEx Extensions of package distr
DistributionUtils Distribution Utilities
distrMod Object oriented implementation of probability models
distrRmetrics Package distr classes for distributions from Rmetrics
distrSim Simulation classes based on package distr
distrTeach Extensions of package distr for teaching Stochastics/Statistics in secondary school
distrTEst Estimation and Testing classes based on package distr
divagis Provides tools for quality checks of georeferenced plant species accessions
diveMove Dive analysis and calibration
diversitree diversitree: comparative phylogenetic analyses of diversification
diveRsity Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G’st and In
DiversitySampler Functions for re-sampling a community matrix to compute diversity indices at different sampling levels
DivMelt HRM Diversity Assay Analysis Tool
dixon Nearest Neighbour Contingency Table Analysis
dkDNA Diffusion kernels on a set of genotypes
dlm Bayesian and Likelihood Analysis of Dynamic Linear Models
dlmap Detection Localization Mapping for QTL
dlmodeler Generalized Dynamic Linear Modeler
dlnm Distributed Lag Non-linear Models
dma Dynamic model averaging
DMR Delete or Merge Regressors for linear model selection
dmt Dependency Modeling Toolkit
DMwR Functions and data for “Data Mining with R”
dna Differential Network Analysis
DNAtools Tools for analysing forensic genetic DNA data
DnE DnE(Distribution and Equation)
DOBAD Analysis of Discretely Observed linear Birth-And-Death(-and-immigration) Markov Chains
doBy doBy – Groupwise summary statistics, general linear contrasts, population means (least-squares-means), and other utilities
Dodge Functions for Acceptance Sampling Ideas originated by H.F. Dodge
DoE.base Full factorials, orthogonal arrays and base utilities for DoE packages
DoE.wrapper Wrapper package for design of experiments functionality
doMC Foreach parallel adaptor for the multicore package
Dominance ADI (average dominance index) and social network graphs with dual directions
doMPI Foreach parallel adaptor for the Rmpi package
doParallel Foreach parallel adaptor for the parallel package
doRedis Foreach parallel adapter for the rredis package
doRNG Generic Reproducible Parallel Backend for foreach Loops
DoseFinding Planning and Analyzing Dose Finding experiments
doSNOW Foreach parallel adaptor for the snow package
dostats Compute statistics helper functions
downloader A package for downloading files over http and https
dpa Dynamic Path Approach
dpglasso Primal Graphical Lasso
dplR Dendrochronology Program Library in R
DPM.GGM Dirichlet Process Mixtures (DPM) and related models using Gaussian Graphical Models (GGM) for Sparse covariance estimation in heterogeneous samples
dpmixsim Dirichlet Process Mixture model simulation for clustering and image segmentation
DPpackage Bayesian nonparametric modeling in R
DPw Semiparametric Bayesian procedure for selecting a subset containing the weakest species with an acceptably high probability
dr Methods for dimension reduction for regression
drawExpression Visualising R syntax through graphics
drc Analysis of dose-response curves
drfit Dose-response data evaluation
DRI DR-Integrator
driftsel Distinguishing drift and natural selection as causes of phenotypic differentiation
drm Regression and association models for repeated categorical data
ds Descriptive Statistics
dsample Discretization-based Direct Random Sample Generation
dse Dynamic Systems Estimation (time series package)
dse1 DSE (unbundled transition package)
dse2 DSE (unbundled transition package)
DSL Distributed Storage and List
dsm Density surface modelling of distance sampling data
DSpat Spatial modelling for distance sampling data
DTComPair Comparison of Binary Diagnostic Tests in a Paired Study Design
DTDA Doubly truncated data analysis
dti Analysis of diffusion weighted imaging (DWI) data
DTK Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes
DTMCPack Suite of functions related to discrete-time discrete-state Markov Chains
DTR Estimation and comparison of dynamic treatment regimes
dtw Dynamic time warping algorithms
dummies Create dummy/indicator variables flexibly and efficiently
dupiR Bayesian inference from count data using discrete uniform priors
dvfBm Discrete variations of a fractional Brownian motion
dvn Access to The Dataverse Network API
DWD DWD implementation based on A IPM SOCP solver
dyn Time Series Regression
dynamicGraph dynamicGraph
dynamicTreeCut Methods for detection of clusters in hierarchical clustering dendrograms
dynaTree Dynamic trees for learning and design
DynClust non-parametric denoising and clustering method of noisy images both indexed by time and space
dynCorr Dynamic Correlation Package
dynlm Dynamic Linear Regression
dynpred Companion package to “Dynamic Prediction in Clinical Survival Analysis”
dynsurv Dynamic models for survival data
e1071 Misc Functions of the Department of Statistics (e1071), TU Wien
eaf Plots of the Empirical Attainment Function
earlywarnings Early Warning Signals Toolbox for Detecting Critical Transitions in Timeseries
earth Multivariate Adaptive Regression Spline Models
easi EASI Demand System Estimation
EasyABC EasyABC: performing efficient approximate Bayesian computation sampling schemes
easyanova Analysis of variance and other important complementary analyzes
EasyHTMLReport Easy to send HTML reports
easystab Clustering Perturbation Stability Analysis
EasyUpliftTree Easy Uplift Tree Model
eba Elimination-by-Aspects (EBA) Models
ebal Entropy reweighting to create balanced samples
EbayesThresh Empirical Bayes Thresholding and Related Methods
ebdbNet Empirical Bayes Estimation of Dynamic Bayesian Networks
EBMAforecast Ensemble BMA Forecasting
EBS Exact Bayesian Segmentation
Ecdat Data sets for econometrics
ecespa Functions for spatial point pattern analysis
eco R Package for Ecological Inference in 2×2 Tables
ecodist Dissimilarity-based functions for ecological analysis
EcoHydRology A community modeling foundation for Eco-Hydrology
ecolMod “A practical guide to ecological modelling – using R as a simulation platform”
ecoreg Ecological regression using aggregate and individual data
ecosim Toolbox for Aquatic Ecosystem Modeling
EcoTroph EcoTroph modelling support
ecp Nonparametric Multiple Change Point Analysis of Multivariate Data
EDanalysis A R Package For Gene Enrichment Disequilibrium Analysis
edcc Economic Design of Control Charts
EDISON Software for network reconstruction and changepoint detection
editrules R package for parsing, applying, and manipulating data cleaning rules
EDR Estimation of the effective dimension reduction (EDR) space
edrGraphicalTools Provides tools for dimension reduction methods
eeptools Convenience functions for education data
effects Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models
EffectStars Visualization of Categorical Response Models
effsize Functions for computing effect sizes
egonet Tool for ego-centric measures in Social Network Analysis
eha Event History Analysis
eHOF Extended and enhanced Hierarchical Logistic Regression models (so called Huisman-Olff-Fresco models)
eigendog EigenDog
eigeninv Generates (dense) matrices that have a given set of eigenvalues
eigenmodel Semiparametric factor and regression models for symmetric relational data
eigenprcomp Computes confidence intervals for principal components
eiPack eiPack: Ecological Inference and Higher-Dimension Data Management
eive An algorithm for reducing errors-in-variable bias in simple linear regression
EL Two-sample Empirical Likelihood
elasticnet Elastic-Net for Sparse Estimation and Sparse PCA
el.convex empirical likelihood ratio tests for means
elec Collection of functions for statistical election audits
elec.strat Functions for election audits using stratified random samples
ElemStatLearn Data sets, functions and examples from the book: “The Elements of Statistical Learning, Data Mining, Inference, and Prediction” by Trevor Hastie, Robert Tibshirani and Jerome Friedman
ellipse Functions for drawing ellipses and ellipse-like confidence regions
elliptic elliptic functions
elmNN Implementation of ELM (Extreme Learning Machine ) algorithm for SLFN ( Single Hidden Layer Feedforward Neural Networks )
EMA Easy Microarray data Analysis
EMC Evolutionary Monte Carlo (EMC) algorithm
EMCC Evolutionary Monte Carlo (EMC) methods for clustering
EMCluster EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution
EMD Empirical Mode Decomposition and Hilbert Spectral Analysis
emdbook Ecological models and data (book support)
emdist Earth Mover’s Distance
emg Exponentially Modified Gaussian (EMG) Distribution
EMJumpDiffusion EM-Algorithm for Jump Diffusion processes
emma Evolutionary model-based multiresponse approach
EMMAgeo End-member modelling algorithm and supporting functions for grain-size analysis
emme2 Read and Write to an EMME/2 databank
emoa Evolutionary Multiobjective Optimization Algorithms
emplik Empirical likelihood ratio for censored/truncated data
emplik2 Empirical-likelihood test (two-sample, censored data)
EMT Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data
emulator Bayesian emulation of computer programs
ENA Ensemble Network Aggregation
enaR Tools for ecological network analysis (ena) in R
endogMNP R Package for Fitting Multinomial Probit Models with Endogenous Selection
endorse R Package for Analyzing Endorsement Experiments
energy E-statistics (energy statistics)
english Translate integers into English
EngrExpt Data sets from “Introductory Statistics for Engineering Experimentation”
ENmisc Neuwirth miscellaneous
EnQuireR A package dedicated to questionnaires
enRich An R package for analysis of multiple ChIP-seq data
enrichvs Enrichment assessment of virtual screening approaches
ensembleBMA Probabilistic Forecasting using Ensembles and Bayesian Model Averaging
ensembleMOS Ensemble Model Output Statistics
entropy Estimation of Entropy, Mutual Information and Related Quantities
enviPat Isotope pattern, profile and centroid calculation
EnvNicheR Environmental niche
epade Easy Plots
Epi A package for statistical analysis in epidemiology
epibase basic tools for the analysis of disease outbreaks
epibasix Elementary Epidemiological Functions for Epidemiology and Biostatistics
epicalc Epidemiological calculator
EpiContactTrace Epidemiological tool for contact tracing
EpiEstim EpiEstim: a package to estimate time varying reproduction numbers from epidemic curves
EpiModel Mathematical Modeling of Infectious Disease
epiR An R package for the analysis of epidemiological data
epitools Epidemiology Tools
epoc EPoC (Endogenous Perturbation analysis of Cancer)
epr Easy polynomial regression
EQL Extended-Quasi-Likelihood-Function (EQL)
eqs2lavaan EQS Output Conversion to lavaan Functions
eqtl Tools for analyzing eQTL experiments: A complementary to Karl Broman’s ‘qtl’ package for genome-wide analysis
equate Statistical Methods for Test Score Equating
equateIRT Direct, chain and average equating coefficients with standard errors using IRT methods
EquiNorm Normalize expression data using equivalently expressed genes
equivalence Provides tests and graphics for assessing tests of equivalence
erer Empirical Research in Economics with R
ergm Fit, Simulate and Diagnose Exponential-Family Models for Networks
ergm.count Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
ergmharris Local Health Department network data set
ergm.userterms User-specified terms for the statnet suite of packages
eRm Extended Rasch Modeling
ESG ESG – A package for asset projection
esotericR esotericR articles from
ESPRESSO Power Analysis and Sample Size Calculation
EstCRM Calibrating Parameters for the Samejima’s Continuous IRT Model
estout Estimates Output
EstSimPDMP Estimation of the jump rate and simulation for piecewise-deterministic Markov processes
etable Easy Table
ETAS Modeling earthquake data using Epidemic Type Aftershock Sequence model
ETC Equivalence to control
ETLUtils Utility functions to execute standard ETL operations (using package ff) on large data
etm Empirical Transition Matrix
EvalEst Dynamic Systems Estimation – extensions
evaluate Parsing and evaluation tools that provide more details than the default
evd Functions for extreme value distributions
evdbayes Bayesian Analysis in Extreme Value Theory
eVenn eVenn: A powerful tool to compare lists and draw Venn diagrams
events Store and manipulate event data
eventstudies Event study and extreme event analysis
EVER Estimation of Variance by Efficient Replication
evir Extreme Values in R
evmix Extreme Value Mixture Modelling and Threshold Estimation
evora Epigenetic Variable Outliers for Risk prediction Analysis
evtree Evolutionary Learning of Globally Optimal Trees
Exact Unconditional Exact Test
exact2x2 Exact Conditional Tests and Confidence Intervals for 2×2 tables
exactci Exact P-values and Matching Confidence Intervals for simple Discrete Parametric Cases
ExactCIdiff Inductive Confidence Intervals for the difference between two proportions
exactLoglinTest Monte Carlo Exact Tests for Log-linear models
ExactNumCI Exact Confidence Interval for binomial proportions
ExactPath Exact solution paths for regularized LASSO regressions with L_1 penalty
exactRankTests Exact Distributions for Rank and Permutation Tests
ExactSampling ExactSampling: risk evaluation using exact resampling methods for the k Nearest Neighbor algorithm
exams Automatic Generation of Exams in R
ExceedanceTools Confidence Regions for Exceedance Regions and Contour Lines Convenient way to work with data in Microsoft Excel
ExomeDepth Calls CNV from exome sequence data
ExpDes Experimental Designs package Pacote Experimental Designs (Portuguese)
expectreg Expectile and Quantile Regression
experiment experiment: R package for designing and analyzing randomized experiments
expert Modeling without data using expert opinion
expm Matrix exponential
expoRkit Expokit in R
ExPosition Exploratory analysis with the singular value decomposition
expoTree Calculate density dependent likelihood of a phylogenetic tree
expsmooth Data sets from “Forecasting with exponential smoothing”
exptest Tests for Exponentiality
exsic Convenience functions for botanist to create exsiccatae indices
extraBinomial Extra-binomial approach for pooled sequencing data
extracat Categorical Data Analysis and Visualization
extrafont Tools for using fonts
extrafontdb Package for holding the database for the extrafont package
extraTrees ExtraTrees method
extRemes Extreme value toolkit
extremevalues Univariate outlier detection
eyetracking Eyetracking Helper Functions
ez Easy analysis and visualization of factorial experiments
ezglm selects significant non-additive interaction between two variables using fast GLM implementation
ezsim provide an easy to use framework to conduct simulation
FacPad Bayesian Sparse Factor Analysis model for the inference of pathways responsive to drug treatment
factas Data Mining Methods
FactMixtAnalysis Factor Mixture Analysis with covariates
FactoClass Combination of Factorial Methods and Cluster Analysis
FactoMineR Multivariate Exploratory Data Analysis and Data Mining with R
factorQR Bayesian quantile regression factor models
factualR thin wrapper for the server API
FAdist Distributions that are sometimes used in hydrology
Fahrmeir Data from the book “Multivariate Statistical Modelling Based on Generalized Linear Models”, first edition, by Ludwig Fahrmeir and Gerhard Tutz
fail File Abstraction Interface Layer (FAIL) mimicking a key-value store
FAiR Factor Analysis in R
faisalconjoint Faisal Conjoint Model: A New Approach to Conjoint Analysis
fame Interface for FAME time series database
Familias Probabilities for Pedigrees given DNA data
FAMT Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data
fanc Penalized likelihood factor analysis via nonconvex penalty
fANCOVA Nonparametric Analysis of Covariance
fanovaGraph Building Kriging models from FANOVA graphs
fanplot Visualisation of sequential probability distributions using fan charts
FAOSTAT A complementary package to the FAOSTAT database and the Statistical Yearbook of the Food and Agricultural Organization of the United Nations
faoutlier Influential case detection methods for factor analysis and SEM
far Modelization for Functional AutoRegressive processes
faraway Functions and datasets for books by Julian Faraway
fArma ARMA Time Series Modelling
farsi Translate integers into persian
fAsianOptions EBM and Asian Option Valuation
fAssets Rmetrics – Assets Selection and Modelling
fast Implementation of the Fourier Amplitude Sensitivity Test (FAST)
fastclime A fast solver for parameterized lp problems and constrained l1 minimization approach to sparse precision matrix estimation
fastcluster Fast hierarchical clustering routines for R and Python
fastcox Lasso and elastic-net penalized Cox’s regression in high dimensions models using the cocktail algorithm
fastGHQuad Fast Rcpp implementation of Gauss-Hermite quadrature
fastICA FastICA Algorithms to perform ICA and Projection Pursuit
FastImputation Learn from training data then quickly fill in missing data
fastmatch Fast match() function
FastPCS R package to compute the FastPCS outlyingness index
fastR Data sets and utilities for Foundations and Applications of Statistics by R Pruim
FastRCS R package to compute the FastRCS Algorithm
FastRWeb Fast Interactive Framework for Web Scripting Using R
fastSOM Fast Calculation of Spillover Measures
FAwR Functions and Datasets for “Forest Analytics with R”
fBasics Rmetrics – Markets and Basic Statistics
fbati Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families
FBFsearch Algorithm for searching the space of Gaussian directed acyclic graphical models through moment fractional Bayes factors
FBN FISH Based Normalization and Copy Number inference of SNP microarray data
fBonds Bonds and Interest Rate Models
fbRanks Association Football (Soccer) Ranking via Poisson Regression
fCertificates fCertificates – Basics of Certificates and Structured Products Valuation
fclust Fuzzy clustering
fCopulae Rmetrics – Dependence Structures with Copulas
fcros FCROS for detecting differentially expressed genes
FD Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology
fda Functional Data Analysis
fdakma Clustering and alignment of a functional dataset
fdaMixed Functional data analysis in a mixed model framework
fdasrvf Elastic Functional Data Analysis
fdatest Interval Testing Procedure for functional data
fda.usc Functional Data Analysis and Utilities for Statistical Computing (fda.usc)
fdrci Permutation-based FDR Point and Confidence Interval Estimation
fdrtool Estimation of (Local) False Discovery Rates and Higher Criticism
fds Functional data sets
FeaLect Scores features for Feature seLection
feature Feature significance for multivariate kernel density estimation
features Feature Extraction for Discretely-Sampled Functional Data
fechner Fechnerian Scaling of Discrete Object Sets
fExoticOptions Exotic Option Valuation
fExtremes Rmetrics – Extreme Financial Market Data
ff memory-efficient storage of large data on disk and fast access functions
ffbase Basic statistical functions for package ff
FFD Freedom From Disease
FField Force field simulation for a set of points
ffmanova Fifty-fifty MANOVA
fftw Fast FFT and DCT based on FFTW
fftwtools Wrapper for fftw3: includes 1-D, univariate and multivariate, and 2-D transform
fgac Generalized Archimedean Copula
FGalgorithm Flury and Gautschi algorithms
fGarch Rmetrics – Autoregressive Conditional Heteroskedastic Modelling
FGN Fractional Gaussian Noise and hyperbolic decay time series model fitting
fgof Fast Goodness-of-fit Test
fgui Function GUI
FHtest Tests for right and interval-censored survival data based on the Fleming-Harrington class
FI Provide functions for forest inventory calculations
fields Tools for spatial data
FieldSim Random fields simulations
filehash Simple key-value database
filehashSQLite Simple key-value database using SQLite
fImport Rmetrics – Economic and Financial Data Import
FinancialInstrument Financial Instrument Model Infrastructure for R
FinAsym Classifies implicit trading activity from market quotes and computes the probability of informed trading
FinCal Time Value of Money Calculation and Computational Finance
FindAllRoots Find all root(s) of the equation and Find root(s) of the equation by dichotomy
FindIt R Package for Finding Heterogeneous Treatment Effects
fingerprint Functions to operate on binary fingerprint data
FinTS Companion to Tsay (2005) Analysis of Financial Time Series
FisherEM The Fisher-EM algorithm
fisheyeR Fisheye and Hyperbolic-space-alike Interactive Visualization Tools in R
fishmethods Fishery Science Methods and Models in R
fishmove Prediction of Fish Movement Parameters
fit4NM NONMEM platform
FitAR Subset AR Model Fitting
FitARMA FitARMA: Fit ARMA or ARIMA using fast MLE algorithm
fitdistrplus Help to fit of a parametric distribution to non-censored or censored data
fit.models fit.models
FITSio FITS (Flexible Image Transport System) utilities
fitTetra fitTetra is an R package for assigning tetraploid genotype scores
FKF Fast Kalman Filter
flare Family of Lasso Regression
flashClust Implementation of optimal hierarchical clustering
flexclust Flexible Cluster Algorithms
flexCWM Flexible Cluster-Weighted Modeling
flexmix Flexible Mixture Modeling
FlexParamCurve Tools to Fit Flexible Parametric Curves
flexsurv Flexible parametric survival models
flip Multivariate Permutation Tests
FLLat Fused Lasso Latent Feature Model
flora flora: taxonomical information on flowering species that occur in Brazil
flsa Path algorithm for the general Fused Lasso Signal Approximator
flubase Baseline of mortality free of influenza epidemics
FluOMatic Estimation of background-subtracted fluorescence data
Flury Data Sets from Flury, 1997
flux Flux rate calculation from dynamic closed chamber measurements
fma Data sets from “Forecasting: methods and applications” by Makridakis, Wheelwright & Hyndman (1998)
FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability, Monte Carlo Analysis
fmri Analysis of fMRI experiments
fmsb Functions for medical statistics book with some demographic data
FMStable Finite Moment Stable Distributions
fmt Variance estimation of FMT method (Fully Moderated t-statistic)
fMultivar Multivariate Market Analysis
FNN Fast Nearest Neighbor Search Algorithms and Applications
fNonlinear Nonlinear and Chaotic Time Series Modelling
foba greedy variable selection
fontcm Computer Modern font for use with extrafont package
foodweb visualisation and analysis of food web networks
fOptions Basics of Option Valuation
forams Foraminifera and Community Ecology Analyses
foreach Foreach looping construct for R
ForeCA ForeCA – Forecastable Component Analysis
forecast Forecasting functions for time series and linear models
foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ..
forensic Statistical Methods in Forensic Genetics
forensim Statistical tools for the interpretation of forensic DNA mixtures
ForImp Imputation of missing values through a forward imputation algorithm
fork R functions for handling multiple processes
FormalSeries Elementary arithemtic in formal series rings
formatR Format R Code Automatically
Formula Extended Model Formulas Utilities for working with formulas, expressions, calls and other R objects
fortunes R Fortunes
forward Forward search
fossil Palaeoecological and Palaeogeographical Analysis Tools
FourScores FourScores – A game for two players
fpc Flexible procedures for clustering
fpca Restricted MLE for Functional Principal Components Analysis
fPortfolio Rmetrics – Portfolio Selection and Optimization – ebook available at
fpow Computing the noncentrality parameter of the noncentral F distribution
fpp Data for “Forecasting: principles and practice”
fptdApprox Approximation of first-passage-time densities for diffusion processes
fracdiff Fractionally differenced ARIMA aka ARFIMA(p,d,q) models
fracprolif Fraction Proliferation via a quiescent growth model
fractaldim Estimation of fractal dimensions
fractalrock Generate fractal time series with non-normal returns distribution
FRACTION Numeric number into fraction
frailtyHL Frailty Models via H-likelihood
frailtypack General Frailty models: shared, joint and nested frailty models with prediction
FRAPO Financial Risk Modelling and Portfolio Optimisation with R
FRB Fast and Robust Bootstrap
FRBData Download interest rate data from FRB’s website
frbs Fuzzy Rule-based Systems for Classification and Regression Tasks
FRCC Fast Regularized Canonical Correlation Analysis
freeknotsplines Free-Knot Splines
fRegression Regression Based Decision and Prediction
freqMAP Frequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate
FrF2 Fractional Factorial designs with 2-level factors
FrF2.catlg128 Catalogues of resolution IV 128 run 2-level fractional factorials up to 33 factors that do have 5-letter words
frmqa The Generalized Hyperbolic Distribution, Related Distributions and Their Applications in Finance
frontier Stochastic Frontier Analysis
frontiles Partial frontier efficiency analysis
frt Full Randomization Test
fscaret Automated caret feature selection
FSelector Selecting attributes
fso Fuzzy Set Ordination
FTICRMS Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data
ftnonpar Features and Strings for Nonparametric Regression
fTrading Technical Trading Analysis
fts R interface to tslib (a time series library in c++)
ftsa Functional time series analysis
fugeR FUzzy GEnetic, a machine learning algorithm to construct prediction model based on fuzzy logic
fume FUME package
fun Use R for Fun
FunCluster Functional Profiling of Microarray Expression Data
FuncMap Hive Plots of R Package Function Calls
functional Curry, Compose, and other higher-order functions
fUnitRoots Trends and Unit Roots
FunNet Integrative Functional Analysis of Transcriptional Networks
futile.any Futile library to provide some polymorphic operations
futile.logger A logging library for R
futile.matrix Futile matrix utilities
futile.options Futile options management
futile.paradigm A framework for working in a functional programming paradigm in R
fuzzyFDR Exact calculation of fuzzy decision rules for multiple testing
FuzzyNumbers Tools to deal with fuzzy numbers
fuzzyRankTests Fuzzy Rank Tests and Confidence Intervals
FuzzyStatProb Fuzzy stationary probabilities from a sequence of observations of an unknown Markov chain
FuzzyToolkitUoN Type 1 Fuzzy Logic Toolkit
fwdmsa Forward search for Mokken scale analysis
FWDselect Selecting variables in regression models
fwi.fbp Fire Weather Index System and Fire Behaviour Prediction System Calculations
fwsim Fisher-Wright Population Simulation
fxregime Exchange Rate Regime Analysis
G1DBN A package performing Dynamic Bayesian Network inference
G2Sd Grain-size Statistics and Description of Sediment
GA Genetic Algorithms
GA4Stratification A genetic algorithm approach to determine stratum boundaries and sample sizes of each stratum in stratified sampling
GAD GAD: Analysis of variance from general principles
gains Gains Table Package
GAIPE Graphical Extension with Accuracy in Parameter Estimation (GAIPE)
galts Genetic algorithms and C-steps based LTS (Least Trimmed Squares) estimation
gam Generalized Additive Models
gamair Data for “GAMs: An Introduction with R”
GAMBoost Generalized linear and additive models by likelihood based boosting
gamboostLSS Boosting Methods for GAMLSS Models
gamclass Functions and data for a course on modern regression and classification
games Statistical Estimation of Game-Theoretic Models
gamesNws Playing games using a NWS Server
gamlr Gamma Lasso Regression
gamlss Generalised Additive Models for Location Scale and Shape
gamlss.add GAMLSS Additive
gamlss.cens Fitting an interval response variable using distributions GAMLSS Data
gamlss.demo Demos for GAMLSS
gamlss.dist Distributions to be used for GAMLSS modelling A GAMLSS add on package for fitting mixture distributions Fitting non linear parametric GAMLSS models Generating and fitting truncated ( distributions
gamlss.util GAMLSS Utilities
gamm4 Generalized additive mixed models using mgcv and lme4
gammSlice Generalized additive mixed model analysis via slice sampling
GANPA Gene Association Network-based Pathway Analysis
GANPAdata The GANPA Datasets Package
gaoptim Genetic Algorithm optimization for real-based and permutation-based problems
gap Genetic analysis package
gaussDiff Difference measures for multivariate Gaussian probability density functions
gaussquad Collection of functions for Gaussian quadrature
gazetools Gaze Tools
gb Generalize Lambda Distribution and Generalized Bootstrapping
GB2 Generalized Beta Distribution of the Second Kind: properties, likelihood, estimation
gbm Generalized Boosted Regression Models
gbRd Utilities for processing Rd objects and files
gbs Package for Generalized Birnbaum-Saunders Distributions
gcbd GPU/CPU Benchmarking in Debian-based systems
gcdnet A generalized coordinate descent (GCD) algorithm for computing the solution path of the hybrid Huberized support vector machine (HHSVM) and its generalization
gcExplorer Graphical Cluster Explorer
gclus Clustering Graphics
gcmr Gaussian Copula Marginal Regression
gcookbook Data for “R Graphics Cookbook”
gdata Various R programming tools for data manipulation Delayed-Data Packages
gdimap Generalized Diffusion Magnetic Resonance Imaging
gdistance distances and routes on geographical grids
gdsfmt CoreArray Genomic Data Structure (GDS) R Interface
gearman R interface to the Gearman Job Server
gee Generalized Estimation Equation solver
geeM Fit Generalized Estimating Equations
geepack Generalized Estimating Equation Package
geigen Calculate generalized eigenvalues of a matrix pair
geiger Analysis of evolutionary diversification
gems Generalized multistate simulation model
gemtc GeMTC network meta-analysis
gemtc.jar GeMTC Java binary
GenABEL genome-wide SNP association analysis
genalg R Based Genetic Algorithm
GENEAread Package For Reading Binary files
GeneCycle Identification of Periodically Expressed Genes
GeneF Package for Generalized F-statistics
Geneland Detection of structure from multilocus genetic data
geneListPie Profiling a gene list into GOslim or KEGG function pie
GeneNet Modeling and Inferring Gene Networks
genepi Genetic Epidemiology Design and Inference
GeneralizedHyperbolic The Generalized Hyperbolic Distribution
GeneReg Construct time delay gene regulatory network
geneSignatureFinder A Gene-signatures finder tools
genetics Population Genetics
GeneticTools Collection of Genetic Data Analysis Tools
GenKern Functions for generating and manipulating binned kernel density estimates
genlasso Path algorithm for generalized lasso problems
genMOSS An implementation of the MOSS algorithm for the analysis of GWAS data
genomicper Circular Genomic Permutation using GWAS p-values of association
genoPlotR Plot publication-grade gene and genome maps
GenOrd Simulation of ordinal and discrete variables with given correlation matrix and marginal distributions
genridge Generalized ridge trace plots for ridge regression
GenSA R functions for Generalized Simulated Annealing
gensemble generalized ensemble methods
genSurv Generating multi-state survival data
GeoLight Analysis of light based geolocator data
GEOmap Topographic and Geologic Mapping
geomapdata Data for topographic and Geologic Mapping
geometry Mesh generation and surface tesselation
geomorph Geometric morphometric analysis of 2d/3d landmark data
geonames Interface to web service
geophys Geophysics, Continuum Mechanics, Mogi Model
geoPlot Geocodes street or ip addresses and plots them on a map
geoR Analysis of geostatistical data
geoRglm geoRglm – a package for generalised linear spatial models
georob Robust Geostatistical Analysis of Spatial Data
geoscale Geological timescale plot
geospacom Helper package to facilitate the generation of distance matrices used in the package spacom
geosphere Spherical Trigonometry
geospt Spatial geostatistics; some geostatistical and radial basis functions, prediction and cross validation; design of optimal spatial sampling networks based on geostatistical modelling
geostatsp Geostatistics using SpatialPoints and rasters
geotools Geo tools
geotopbricks geotopbricks: Analyzes raster maps as input/output files from the Hydrological Distributed Model GEOtop
GeoXp Interactive exploratory spatial data analysis
geozoo Zoo of Geometric Objects
GESTr Gene Expression State Transformation
getopt C-like getopt behavior
GetR GetR: Calculate Guttman error trees in R
GEVcdn GEV conditional density estimation network
GExMap A visual, intuitive, easy to use software giving access to a new type of information buried into your microarray data
GGally Extension to ggplot2
ggdendro Tools for extracting dendrogram and tree diagram plot data for use with ggplot
GGEBiplotGUI GGEBiplotGUI: Interactive GGE Biplots in R
gglasso Group Lasso Penalized Learning Using A Unified BMD Algorithm
ggm A package for Graphical Markov Models
ggmap A package for spatial visualization with Google Maps and OpenStreetMap
ggmcmc Graphical tools for analyzing Markov Chain Monte Carlo simulations from Bayesian inference
GGMselect Gaussian Graphs Models selection
ggparallel Variations of Parallel Coordinate Plots for Categorical Data
ggplot2 An implementation of the Grammar of Graphics
ggROC package for roc curve plot with ggplot2
ggsubplot Explore complex data by embedding subplots within plots
ggthemes Extra themes, scales and geoms for ggplot
GhcnDaily Downloads and processes GHCN daily
ghyp A package on the generalized hyperbolic distribution and its special cases
GibbsACOV Gibbs Sampler for One-Way Mixed-Effects ANOVA and ANCOVA Models
gibbs.met Naive Gibbs Sampling with Metropolis Steps
GIGrvg Random variate generator for the GIG distribution
GillespieSSA Gillespie’s Stochastic Simulation Algorithm (SSA)
gIPFrm Generalized Iterative Proportional Fitting for Relational Models
giRaph The giRaph package for graph representation in R
GISTools Some further GIS capabilities for R
gitter Robust gridding and quantifying of pinned genetic screens
Giza Constructing panels of population pyramid plots based on lattice
glasso Graphical lasso- estimation of Gaussian graphical models
glassomix High dimensional Mixture Graph Models selection
gld Estimation and use of the generalised (Tukey) lambda distribution
GLDEX Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
gldist An Asymmetry-Steepness Parameterization of the Generalized Lambda Distribution
glm2 Fitting Generalized Linear Models
glmc Fitting Generalized Linear Models Subject to Constraints
glmdm R Code for Simulation of GLMDM
glmlep Fit GLM with LEP-based penalized maximum likelihood
glmmAK Generalized Linear Mixed Models
glmmBUGS Generalised Linear Mixed Models and Spatial Models with WinBUGS, BRugs, or OpenBUGS
glmmGS Gauss-Seidel Generalized Linear Mixed Model solver
glmmLasso Variable selection for generalized linear mixed models by L1-penalized estimation
glmmML Generalized linear models with clustering
glmnet Lasso and elastic-net regularized generalized linear models
glmnetcr Fit a penalized constrained continuation ratio model for predicting an ordinal response
glmpath L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
glmpathcr Fit a penalized continuation ratio model for predicting an ordinal response
glmperm Inference in Generalized Linear Models
glmulti Model selection and multimodel inference made easy
globalboosttest Testing the additional predictive value of high-dimensional data
glogis Fitting and Testing Generalized Logistic Distributions
glpkAPI R Interface to C API of GLPK
glrt Generalized Logrank Tests for Interval-censored Failure Time Data
gMCP Graph Based Multiple Comparison Procedures
GMD Generalized Minimum Distance of distributions
gmm Generalized Method of Moments and Generalized Empirical Likelihood
GMMBoost Likelihood-based Boosting for Generalized mixed models
gmodels Various R programming tools for model fitting
gmp Multiple Precision Arithmetic
gmt Interface between GMT Map-Making Software and R
gmvalid Validation of graphical models
gMWT Generalized Mann-Whitney Type Tests
gnm Generalized Nonlinear Models
gnmf Generalized Non-negative Matrix Factorization
gnumeric Read data from files readable by gnumeric
goalprog Weighted and lexicographical goal programming and optimization
gof Model-diagnostics based on cumulative residuals
GoFKernel GoFKernel: Testing Goodness-of-fit with the Kernel Density Estimator
GOFSN Goodness-of-fit tests for the family of skew-normal models
GOGANPA GO-Functional-Network-based Gene-Set-Analysis
gogarch Generalized Orthogonal GARCH (GO-GARCH) models
googlePublicData An R library to build Google’s Public Data Explorer DSPL Metadata files
googleVis Interface between R and the Google Chart Tools
gooJSON Google JSON Data Interpreter for R
goric Generalized Order-Restricted Information Criterion
GOSim Computation of functional similarities between GO terms and gene products; GO enrichment analysis
GOsummaries Word cloud summaries of GO enrichment analysis
govdat Interface to API methods for government data
govStatJPN functions to get public survey data in Japan
gpairs gpairs: The Generalized Pairs Plot
GPArotation GPA Factor Rotation
gPCA Batch Effect Detection via Guided Principal Components Analysis
gpclib General Polygon Clipping Library for R
gPdtest Bootstrap goodness-of-fit test for the generalized Pareto distribution
GPfit Gaussian Process Modeling
gpk 100 Data Sets for Statistics Education
gplm Generalized partial linear models (GPLM)
gplots Various R programming tools for plotting data
gppois Gaussian Processes for Poisson-noised Data
gProfileR g:ProfileR
GPseq gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
gptk Gaussian Processes Tool-Kit
gputools A few GPU enabled functions
GPvam Maximum Likelihood Estimation of the Multiple Membership Mixed Models Used in Value-Added Modeling
grade Provides functions for matching student-answers to teacher answers for a variety of data types
GRaF Species distribution modelling using latent Gaussian random fields
gRain Graphical Independence Networks
granova Graphical Analysis of Variance
granovaGG Graphical Analysis of Variance Using ggplot2
gRapHD Efficient selection of undirected graphical models for high-dimensional datasets
GrapheR A multi-platform GUI for drawing customizable graphs in R
graphicsQC Quality Control for Graphics in R
GrassmannOptim Grassmann Manifold Optimization
gRbase A package for graphical modelling in R
gRc Inference in Graphical Gaussian Models with Edge and Vertex Symmetries
gregmisc Greg’s Miscellaneous Functions
Grid2Polygons Convert Spatial Grids to Polygons
gridBase Integration of base and grid graphics
gridDebug Debugging Grid Graphics
gridExtra functions in Grid graphics
gridGraphviz Drawing Graphs with Grid
GridR Executes functions on remote hosts, clusters or grids
gridSVG Export grid graphics as SVG
GriegSmith Uses Grieg-Smith method on 2 dimentional spatial data
gRim Graphical Interaction Models
grImport Importing Vector Graphics
grnn General regression neural network
grofit The package was developed to fit fit many growth curves obtained under different conditions
grouped Regression Analysis of Grouped and Coarse Data
GroupSeq Performing computations related to group sequential designs
growcurves Bayesian semi and nonparametric growth curve models that additionally include multiple membership random effects
growthrate Bayesian reconstruction of growth velocity
grplasso Fitting user specified models with Group Lasso penalty
grpreg Regularization paths for regression models with grouped covariates
GRRGI Gauge R and R Confidence Intervals
grt General Recognition Theory
GRTo Tools for the analysis of Gutenberg-Richter distributions of earthquake magnitudes
GSA Gene set analysis
gsalib Utility functions for GATK
gsarima Two functions for Generalized SARIMA time series simulation
gsbDesign Group Sequential Bayes Design
gsDesign Group Sequential Design
GSE Robust Estimation of Multivariate Location and Scatter in the Presence of Missing Data
gsg Calculation of selection coefficients
GSIF Global Soil Information Facilities
gsl wrapper for the Gnu Scientific Library
GSM Gamma Shape Mixture
gsmaRt Gene Set Microarray Testing
gsmoothr Smoothing tools
gss General Smoothing Splines
gstat spatial and spatio-temporal geostatistical modelling, prediction and simulation
gstudio Spatial utility functions from the Dyer laboratory
gsubfn Utilities for strings and function arguments
gtable Arrange grobs in tables
gtcorr Calculate efficiencies of group testing algorithms with correlated responses
gte Generalized Turnbull’s estimator
gtools Various R programming tools
gtx Genetics ToolboX
GuardianR Guardian API Wrapper
Guerry Maps, data and methods related to Guerry (1833) “Moral Statistics of France”
GUIDE GUI for DErivatives in R
gumbel Gumbel copula
GUniFrac Generalized UniFrac distances
GUTS GUTS: Fast Calculation of the Likelihood of a Stochastic Survival Model Regularized Categorial Effects/Categorial Effect Modifiers/Continuous/Smooth effects in GLMs
gvlma Global Validation of Linear Models Assumptions
GWAF Genome-wide association/interaction analysis and rare variant analysis with family data
GWASExactHW Exact Hardy-Weinburg testing for Genome Wide Association Studies
GWAtoolbox GWAS Quality Control
gwerAM Controlling the genome-wide type I error rate in association mapping experiments
GWG Calculation of probabilities for inadequate and excessive gestational weight gain
gWidgets gWidgets API for building toolkit-independent, interactive GUIs
gWidgetsRGtk2 Toolkit implementation of gWidgets for RGtk2
gWidgetstcltk Toolkit implementation of gWidgets for tcltk package
gWidgetsWWW Toolkit implementation of the gWidgets API for use with web pages
GWmodel Geographically weighted models
gwrr Fits geographically weighted regression models with diagnostic tools
h5r Interface to HDF5 Files
haarfisz Software to perform Haar Fisz transforms
HAC Estimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC)
HadoopStreaming Utilities for using R scripts in Hadoop streaming
HandTill2001 Multiple Class Area under ROC Curve
hapassoc Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm
HapEstXXR Multi-locus stepwise regression (MSR)
Haplin Analyzing case-parent triad and/or case-control data with SNP haplotypes
haplo.ccs Estimate Haplotype Relative Risks in Case-Control Data
HaploSim HaploSim
haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
HAP.ROR Recursive Organizer (ROR)
hapsim Haplotype Data Simulation
HardyWeinberg Graphical tests for Hardy-Weinberg equilibrium
harvestr A Parallel Simulation Framework
hash Full feature implementation of hash/associated arrays/dictionaries
hashFunction A collection of non-cryptographic hash functions
hbim Hill/Bliss Independence Model for Combination Vaccines
hbmem Hierarchical Bayesian Analysis of Recognition Memory
hbsae Hierarchical Bayesian Small Area Estimation
hcc Hidden correlation check
hda Heteroscedastic Discriminant Analysis
HDclassif High Dimensional Supervised Classification and Clustering
hddplot Use known groups in high-dimensional data to derive scores for plots
hdeco Hierarchical DECOmposition of Entropy for Categorical Map Comparisons
hdlm Fitting High Dimensional Linear Models
HDMD Statistical Analysis Tools for High Dimension Molecular Data (HDMD)
hdrcde Highest density regions and conditional density estimation
HEAT Health Effects of Air Pollution and Temperature (HEAT)
heatex Heat exchange calculations during physical activity
heatmapFit Heatmap Fit Statistic For Binary Dependent Variable Models Heatmap with more sensible behavior
heavy Package for outliers accommodation using heavy-tailed distributions
helloJavaWorld Hello Java World
heplots Visualizing Hypothesis Tests in Multivariate Linear Models
hergm Hierarchical Exponential-Family Random Graph Models with Local Dependence
hett Heteroscedastic t-regression
het.test White’s Test for Heteroskedasticity
hexbin Hexagonal Binning Routines
hexView Viewing Binary Files
hgam High-dimensional Additive Modelling
hglm Hierarchical Generalized Linear Models
HGLMMM Hierarchical Generalized Linear Models
HGNChelper Handy functions for working with HGNC gene symbols and Affymetrix probeset identifiers
HH Statistical Analysis and Data Display: Heiberger and Holland
HHG Heller-Heller-Gorfine Tests of Independence
hht The Hilbert-Huang Transform: Tools and Methods
HI Simulation from distributions supported by nested hyperplanes
HIBAG HIBAG – HLA Genotype Imputation with Attribute Bagging
HiddenMarkov Hidden Markov Models
HiDimDA High Dimensional Discriminant Analysis
hierarchicalDS Functions for performing hierarchical analysis of distance sampling data
hierfstat Estimation and tests of hierarchical F-statistics
hierNet A Lasso for Hierarchical Interactions
hier.part Hierarchical Partitioning
HIest Hybrid index estimation
highfrequency highfrequency
highlight Syntax highlighter
highr Syntax highlighting for R
highriskzone Determining and evaluating high-risk zones
hint Tools for hypothesis testing based on Hypergeometric Intersection distributions
hints Provide hints on what to do next
HiPLARM High Performance Linear Algebra in R
hiPOD hierarchical Pooled Optimal Design
hisemi Hierarchical Semiparametric Regression of Test Statistics
HistData Data sets from the history of statistics and data visualization
histogram Construction of regular and irregular histograms with different options for automatic choice of bins
hitandrun “Hit and Run” method for sampling uniformly from convex shapes
hive Hadoop InteractiVE
HiveR 2D and 3D Hive Plots for R
HLMdiag Diagnostic tools for hierarchical (multilevel) linear models
hlr Hidden Logistic Regression
hmeasure The H-measure and other scalar classification performance metrics
Hmisc Harrell Miscellaneous
HMM HMM – Hidden Markov Models
hmm.discnp Hidden Markov models with discrete non-parametric observation distributions
hmmm hierarchical multinomial marginal models
HMMmix The HMMmixture package
HMP Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
HMPTrees Statistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data: Modeling, Visualization, and Two-Group Comparison
HMR Flux estimation with static chamber data
hof More higher order functions for R
holdem Texas Holdem simulator
Holidays Holiday and halfday data, for use with the TimeWarp package
homals Gifi Methods for Optimal Scaling
homeR Functions useful for building physics
homtest Homogeneity tests for Regional Frequency Analysis
Hotelling Hotelling’s T-squared test and variants
hotspots Hot spots
howmany A lower bound for the number of correct rejections
HPbayes Heligman Pollard mortality model parameter estimation using Bayesian Melding with Incremental Mixture Importance Sampling
HPO.db A set of annotation maps describing the Human Phenotype Ontology
HPOSim Analysis similarities between HPO terms and phenotypic similarity between genes and between diseases
HSAUR A Handbook of Statistical Analyses Using R
HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition)
hSDM hierarchical Bayesian species distribution models
hsicCCA Canonical Correlation Analysis based on Kernel Independence Measures
hsmm Hidden Semi Markov Models
HSROC Joint meta-analysis of diagnostic test sensitivity and specificity with or without a gold standard reference test
HTMLUtils Facilitates automated HTML report creation
hts Hierarchical and grouped time series
HTSCluster Clustering high throughput sequencing (HTS) data
httpRequest Basic HTTP Request
httpuv HTTP and WebSocket server library
httr Tools for working with URLs and HTTP
huge High-dimensional Undirected Graph Estimation
hwde Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci
HWEBayes Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing
HWEintrinsic Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem
HW.pval Testing Hardy-Weinberg Equilibrium for Multiallelic Genes
hwriter HTML Writer – Outputs R objects in HTML format
hwriterPlus hwriterPlus: Extending the hwriter Package
hybridHclust Hybrid hierarchical clustering
HybridMC Implementation of the Hybrid Monte Carlo and Multipoint Hybrid Monte Carlo sampling techniques
hydroGOF Goodness-of-fit functions for comparison of simulated and observed hydrological time series
HydroMe R codes for estimating water retention and infiltration model parameters using experimental data
hydroPSO Particle Swarm Optimisation, with focus on Environmental Models
hydroTSM Time series management, analysis and interpolation for hydrological modelling
HyperbolicDist The hyperbolic distribution
hyperdirichlet A generalization of the Dirichlet distribution
hypergeo The hypergeometric function
hyperSpec Interface for hyperspectral data, i.e. spectra + meta info (spatial, time, concentration, …)
HyPhy Macroevolutionary phylogentic analysis of species trees and gene trees
hypothesestest Confidence Intervals and Tests of Statistical Hypotheses
hypred Simulation of genomic data in applied genetics
hzar Hybrid Zone Analysis using R
IASD Model selection for index of asymmetry distribution
IBDhaploRtools Functions for the Analysis of IBD Haplo output
ibdreg Regression Methods for IBD Linkage With Covariates
IBDsim Simulation of chromosomal regions shared by family members
IBHM Approximation using the IBHM method
Iboot Iboot: iterated bootstrap tests and confidence sets
ibr Iterative Bias Reduction
IBrokers R API to Interactive Brokers Trader Workstation
iBUGS An Interface to WinBUGS/OpenBUGS/JAGS by gWidgets
IC2 Inequality and Concentration Indices and Curves
ic50 Standardized high-throughput evaluation of cell-based compound screens
icaOcularCorrection Independent Components Analysis (ICA) based artifact correction
ICC Functions facilitating the estimation of the Intraclass Correlation Coefficient
ICE Iterated Conditional Expectation
ICEinfer Incremental Cost-Effectiveness (ICE) Statistical Inference from Two Unbiased Samples
icensmis Study Design and Data Analysis in the presence of error-prone diagnostic tests and self-reported outcomes
ic.infer Inequality constrained inference in linear normal situations
iCluster Integrative clustering of multiple genomic data types
icomp ICOMP criterion
ICS Tools for Exploring Multivariate Data via ICS/ICA
ICSNP Tools for Multivariate Nonparametrics
idbg R debugger
identity Jacquard Condensed Coefficients of Identity
IDPmisc Utilities of Institute of Data Analyses and Process Design (
idr Irreproducible discovery rate
ieeeround Functions to set and get the IEEE rounding mode
ifa Independent Factor Analysis
iFad An integrative factor analysis model for drug-pathway association inference
ifs Iterated Function Systems
ifultools Insightful Research Tools
iGasso Genetic association tests and utilities
IgorR Read binary files saved by Igor Pro (including Neuromatic data)
igraph Network analysis and visualization
igraph0 Network analysis and visualization, old, deprecated package
igraphdata A collection of network data sets for the igraph package
igraphtosonia Convert iGraph graps to SoNIA .son files
IM Orthogonal Moment Analysis
Imap Interactive Mapping
imguR Share plots using the image hosting service
IMIS Increamental Mixture Importance Sampling
ImpactIV Identifying Causal Effect for Multi-Component Intervention Using Instrumental Variable Method
imprProbEst Minimum distance estimation in an imprecise probability model
imputation imputation
imputeMDR The Multifactor Dimensionality Reduction (MDR) Analysis for Incomplete Data
imputeYn Imputing the last largest censored observation/observations under weighted least squares
inarmix Mixture models for longitudinal count data
IndependenceTests Nonparametric tests of independence between random vectors
indicspecies Studying the statistical relationship between species and groups of sites
ineq Measuring Inequality, Concentration, and Poverty
InfDim Infine-dimensional model (IDM) to analyse phenotypic variation in growth trajectories
inference Functions to extract inferential values of a fitted model object
InferenceSMR Inference about the standardized mortality ratio when evaluating the effect of a screening program on survival
inflection Finds the inflection point of a curve
influence.ME Tools for detecting influential data in mixed effects models
infoDecompuTE Information Decomposition of Two-phase Experiments
informR R Tools for Creating Sequence Statistics
infotheo Information-Theoretic Measures
infutil Information Utility
inline Inline C, C++, Fortran function calls from R
inlinedocs Convert inline comments to documentation
InPosition Inference Tests for ExPosition
insideRODE insideRODE includes buildin functions with deSolve solver and C/FORTRAN interfaces to nlme, together with compiled codes
insol Solar Radiation
installr Functions for updating and installing a new version of R and other software – from R
int64 64 bit integer types
intamap procedures for automated interpolation
intamapInteractive procedures for automated interpolation – methods only to be used interactively, not included in intamap package
intcox Iterated Convex Minorant Algorithm for interval censored event data
integrOmics end of integrOmics package
Interact Tests for marginal interactions in a 2 class response model
InteractiveIGraph interactive network analysis and visualization
interactivity toggle R interactive mode
intergraph Coercion routines for network data objects in R
Interpol Interpolation of amino acid sequences
Interpol.T Hourly interpolation of multiple temperature daily series
interval Weighted Logrank Tests and NPMLE for interval censored data
intervals Tools for working with points and intervals
intpoint linear programming solver by the interior point method and graphically (two dimensions)
intReg Interval Regression
intRegGOF Integrated Regression Goodness of Fit
introgress methods for analyzing introgression between divergent lineages
intsvy International Assessment Data Manager
ipdmeta Tools for subgroup analyses with multiple trial data using aggregate statistics
ipfp Fast implementation of the iterative proportional fitting procedure in C
iplots iPlots – interactive graphics for R
IPMpack Builds and analyses Integral Projection Models (IPMs)
ipred Improved Predictors
IPSUR Introduction to Probability and Statistics Using R
ipw Estimate inverse probability weights
IQCC Improved Quality Control Charts
irace Iterated Racing Procedures
iRefR iRefIndex Manager
iRegression Regression methods for interval-valued variables
irlba Fast partial SVD by implicitly-restarted Lanczos bidiagonalization
irr Various Coefficients of Interrater Reliability and Agreement
irtoys Simple interface to the estimation and plotting of IRT models
irtProb Utilities and Probability Distributions Related to Multidimensional Person Item Response Models (IRT)
irtrees Estimation of Tree-Based Item Response Models
isa2 The Iterative Signature Algorithm
ISBF Iterative Selection of Blocks of Features – ISBF
isdals Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences
ISDA.R interval symbolic data analysis for R
ISIPTA ISIPTA network analysis
ISLR Data for An Introduction to Statistical Learning with Applications in R
ismev An Introduction to Statistical Modeling of Extreme Values
Iso Functions to perform isotonic regression
isocir Isotonic Inference for Circular data
ISOcodes Selected ISO codes
IsoGene Testing for monotonic relationship between gene expression and doses in a microarray experiment
isopam Isopam (Clustering)
isopat Calculation of isotopic pattern for a given molecular formula
isotone Active set and generalized PAVA for isotone optimization
IsotopeR Stable isotope analysis
ISOweek Week of the year and weekday according to ISO 8601
iSubpathwayMiner The package can implement the graph-based reconstruction and analyses of the KEGG pathways
isva Independent Surrogate Variable Analysis
ISwR Introductory Statistics with R
iteRates Parametric rate comparison
iterators Iterator construct for R
iterLap Approximate probability densities by iterated Laplace Approximations
itertools Iterator Tools
itree Tools for classification and regression trees, with an emphasis on interpretability
its Irregular Time Series
itsmr Time series analysis package for students
IUPS Incorporating Uncertainties in Propensity Scores
ivbma Bayesian Instrumental Variable Estimation and Model Determination via Conditional Bayes Factors
ivivc A data analysis tool for in vitro-in vivo correlation (IVIVC)
iWebPlots Interactive web-based plots
iWeigReg Improved methods for causal inference and missing data problems
iwtp Numerical evaluation willingness to pay based on interval data
jaatha A Fast Parameter Estimation Method for Evolutionary Biology
jackknifeKME Jackknife estimates of Kaplan-Meier estimators or integrals
JADE JADE and other BSS methods as well as some BSS performance criteria
JASPAR R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices
JavaGD Java Graphics Device
JGL Performs the Joint Graphical Lasso for sparse inverse covariance estimation on multiple classes
JGR JGR – Java GUI for R
JJcorr Calculates polychorical correlations for several copula families
JM Joint Modeling of Longitudinal and Survival Data
JMbayes Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
jmec Fit joint model for event and censoring with cluster-level frailties
Jmisc Julian Miscellaneous Function
JMLSD Joint Modeling of Longitudinal and Survival Data – Power Calculation
Johnson Johnson Transformation
JohnsonDistribution Johnson Distribution
joineR Joint modelling of repeated measurements and time-to-event data
jointDiag Joint Approximate Diagonalization of a set of square matrices
JointRegBC Joint Modelling of Mixed Correlated Binary and Continuous Responses : A Latent Variable Approach
JOP Joint Optimization Plot
JoSAE Functions for unit-level small area estimators and their variances
jpeg Read and write JPEG images
JPSurv Methods for population-based cancer survival analysis
jtrans Johnson transformation for normality
JudgeIt JudgeIt: A Program for Evaluating Electoral Systems and Redistricting Plans
Julia Fractal Image Data Generator
jvmr Integration of R, Java, and Scala
KappaGUI GUI for Cohen’s and Fleiss’ Kappa
kappalab Non-additive measure and integral manipulation functions
kappaSize Sample Size Estimation Functions for Studies of Interobserver Agreement
kaps K Adaptive Partitioning for Survival data
kdetrees Nonparametric method for identifying discordant trees
kelvin Calculate solutions to Kelvin differential equation using Bessel functions
Kendall Kendall rank correlation and Mann-Kendall trend test
kequate The kernel method of test equating
kerdiest Nonparametric kernel estimation of the distribution function. Bandwidth selection and estimation of related functions
kernelFactory Kernel Factory: An ensemble of kernel Machines
kernlab Kernel-based Machine Learning Lab
KernSmooth Functions for kernel smoothing for Wand & Jones (1995)
KernSmoothIRT Nonparametric Item Response Theory
KFAS Kalman Filter and Smoother for Exponential Family State Space Models
kin.cohort Analysis of kin-cohort studies
kinfit Routines for fitting kinetic models to chemical degradation data
kinship2 Pedigree functions
kitagawa Model the spectral response of a closed water-well to harmonic strains at seismic frequencies
kknn Weighted k-Nearest Neighbors
klaR Classification and visualization
klausuR Multiple Choice Test Evaluation
klin Linear equations with Kronecker structure Confidence intervals for the Kaplan-Meier estimator
kmi Kaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting
Kmisc Miscellaneous functions intended to improve the R coding experience
kml K-means for Longitudinal data
kml3d K-means for joint Longitudinal data
KMsurv Data sets from Klein and Moeschberger (1997), Survival Analysis
knitcitations Citations for knitr markdown files
knitr A general-purpose package for dynamic report generation in R
knitrBootstrap Knitr Bootstrap framework
knnGarden Multi-distance based k-Nearest Neighbors
knorm Microarray Data From Multiple Biologically Interrelated Experiments
kobe Tools for providing advice for the Tuna Regional Fisheries Management Organisations
kohonen Supervised and unsupervised self-organising maps
kolmim An improved evaluation of Kolmogorov’s distribution
KoNLP Korean NLP Package
koRpus An R Package for Text Analysis
Kpart Spline Fitting
kriging Ordinary Kriging
KrigInv Kriging-based Inversion for Deterministic and Noisy Computer Experiments
KRLS Kernel-based Regularized Least Squares (KRLS)
ks Kernel smoothing
kSamples K-Sample Rank Tests and their Combinations
KsPlot Check the power of seveal statistical models
kst Knowledge Space Theory
ktspair k-Top Scoring Pairs for Microarray Classification
kulife Datasets and functions from the Faculty of Life Sciences, University of Copenhagen
kza Kolmogorov-Zurbenko Adaptive Filters
kzft Kolmogorov-Zurbenko Fourier Transform and Applications
kzs Kolmogorov-Zurbenko Spatial Smoothing and Applications
l2boost l2boost – Friedman’s boosting algorithm for regularized linear regression
labdsv Ordination and Multivariate Analysis for Ecology
labeledLoop Labeled Loop
labeling Axis Labeling
labeltodendro Convert labels or tables to a dendrogram
labstatR Libreria del Laboratorio di Statistica con R
laeken Estimation of indicators on social exclusion and poverty
laercio Duncan test, Tukey test and Scott-Knott test
LaF Fast access to large ASCII files
Lahman Sean Lahman’s Baseball Database
Lambda4 Collection of Internal Consistency Reliability Coefficients
lambda.r Functional programming in R
LambertW Analyze and Gaussianize skewed, heavy-tailed data
lancet.iraqmortality Surveys of Iraq Mortality Published in The Lancet
landsat Radiometric and topographic correction of satellite imagery
languageR Data sets and functions with “Analyzing Linguistic Data: A practical introduction to statistics”
LARF LARF: Local Average Response Functions for Estimating Treatment Effects
LargeRegression Large Regressions
lars Least Angle Regression, Lasso and Forward Stagewise
lasso2 L1 constrained estimation aka ‘lasso’
lassoshooting L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting
latdiag Draws diagrams useful for checking latent scales
latentnet Latent position and cluster models for statistical networks
Laterality Functions to calculate common laterality statistics in primatology
lattice Lattice Graphics
latticeDensity Density estimation and nonparametric regression on irregular regions
latticeExtra Extra Graphical Utilities Based on Lattice
LatticeKrig Multiresolution Kriging based on Markov random fields
latticist A graphical user interface for exploratory visualisation
lava Linear Latent Variable Models
lavaan Latent Variable Analysis
lavaan.survey Complex survey structural equation modeling (SEM)
lava.tobit LVM with censored and binary outcomes
lawstat An R package for biostatistics, public policy, and law
lazyData A LazyData Facility
lazyWeave LaTeX Wrappers for R Users
lbiassurv Length-biased correction to survival curve estimation
LCAextend Latent Class Analysis (LCA) with familial dependence in extended pedigrees
lcd Learn Chain graphs via Decomposition
lcda Latent Class Discriminant Analysis
LCFdata Data sets for package “LMERConvenienceFunctions”
lcmm Estimation of latent class mixed models, joint latent class mixed models and mixed models for curvilinear outcomes
lcmr lcmr package
lda Collapsed Gibbs sampling methods for topic models
ldbounds Lan-DeMets Method for Group Sequential Boundaries
LDcorSV Linkage disequilibrium corrected by the structure and the relatedness
ldDesign Design of experiments for detection of linkage disequilibrium
LDExplorer Efficient Whole-Genome LD Based Haplotpe Block Recognition
LDheatmap Graphical display of pairwise linkage disequilibria between SNPs
ldlasso LD LASSO Regression for SNP Association Study
LDOD Finding Locally D-optimal optimal designs for some nonlinear and generalized linear models
ldr Methods for likelihood-based dimension reduction in regression
LDtests Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium
LeafAngle Fits, plots, and summarizes leaf angle distributions
LEAPFrOG Likelihood Estimation of Admixture in Parents From Offspring Genotypes
leapp latent effect adjustment after primary projection
leaps regression subset selection
LearnBayes Functions for Learning Bayesian Inference
LearnEDA Functions for Learning Exploratory Data Analysis
leiv Bivariate linear errors-in-variables estimation
LeLogicielR Functions and datasets to accompany the book “Le logiciel R: Maitriser le langage, Effectuer des analyses statistiques” (french)
lemma Laplace approximated EM Microarray Analysis
lessR Less Code, More Results
lestat A package for LEarning STATistics
lfe Linear Group Fixed Effects
lfstat Calculation of Low Flow Statistics for daily stream flow data
lga Tools for linear grouping analysis (LGA)
lgcp Log-Gaussian Cox Process
LGS simulating Linkage Group Selection (LGS)
lgtdl A set of methods for longitudinal data objects
lhs Latin Hypercube Samples
libamtrack Computational routines for proton and ion radiotherapy
LiblineaR Linear Predictive Models Based On The Liblinear C/C++ Library
LICurvature Sensitivity Analysis for Case Weight in Normal Linear Regression
lifecontingencies A package to perform actuarial mathematics for life contingencies insurances
LifeTables A package to implement HMD model life table system
LIHNPSD Poisson Subordinated Distribution
likelihood Methods for maximum likelihood estimation
LIM Linear Inverse Model examples and solution methods
limitplot Jitter/CI Plot with Ordered Points Below the Limit of Detection
limSolve Solving Linear Inverse Models
LinearizedSVR Linearized Support Vector Regression
lineup Lining up two sets of measurements
linkcomm Tools for Generating, Visualizing, and Analysing Link Communities in Networks
linLIR linear Likelihood-based Imprecise Regression
linprog Linear Programming / Optimization
lint Tools to check R code style
liso Fitting lasso penalised additive isotone models
lisp List-processing à la SRFI-1
lisrelToR Import output from LISREL into R
list Statistical Methods for the Item Count Technique and List Experiment
LIStest Longest Increasing Subsequence Independence Test
ljr Logistic Joinpoint Regression
llama Leveraging Learning to Automatically Manage Algorithms
lle Locally linear embedding
lmbc Linear Model Bias Correction for RNA-Seq Data
lme4 Linear mixed-effects models using S4 classes
lmec Linear Mixed-Effects Models with Censored Responses
lmeNB Fit negative binomial mixed-effect regression model
lmeNBBayes Sample from the posterior of the negative binomial mixed-effect regression model. The random effect is modeled with DP mixture of beta distributions
LMERConvenienceFunctions A suite of functions to back-fit fixed effects and forward-fit random effects, as well as other miscellaneous functions
lmeSplines Add smoothing spline modelling capability to nlme
LMest Fit Latent Markov models in basic versions
lmf Functions for estimation and inference of selection in age-structured populations
lmm Linear mixed models
lmmfit Goodness-of-fit-measures for linear mixed models with one-level-grouping
lmmlasso Linear mixed-effects models with Lasso
lmodel2 Model II Regression
lmom L-moments
lmomco L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
Lmoments L-moments and quantile mixtures
lmomRFA Regional frequency analysis using L-moments
lmPerm Permutation tests for linear models
lmSupport Support for Linear Models
lmtest Testing Linear Regression Models
localdepth Local Depth
localgauss Estimating local Gaussian parameters
locfdr Computes local false discovery rates
locfit Local Regression, Likelihood and Density Estimation
Lock5Data Datasets for “Statistics: UnLocking the Power of Data”
locpol Kernel local polynomial regression
log4r A simple logging system for R, based on log4j
LogConcDEAD Log-concave Density Estimation in Arbitrary Dimensions
logconcens Maximum likelihood estimation of a log-concave density based on censored data
logcondens Estimate a Log-Concave Probability Density from iid Observations
logcondens.mode Compute MLE of Log-Concave Density on R with Fixed Mode, and Perform Inference for the Mode
logcondiscr Estimate a Log-Concave Probability Mass function from Discrete i.i.d. Observations
logging R logging package
LogicReg Logic Regression
logistf Firth’s bias reduced logistic regression
logistiX Exact logistic regression including Firth correction
LogitNet Infer network based on binary arrays using regularized logistic regression
logitnorm Functions for the logitnormal distribution
loglognorm Double log normal distribution functions
logmult Log-multiplicative models, including association models
LogrankA Logrank Test for Aggregated Survival Data
logregperm Inference in Logistic Regression
logspline Logspline density estimation routines
lokern Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
longCatEDA Package for Plotting Categorical Longitudinal and Time-Series Data
longclust Model-Based Clustering and Classification for Longitudinal Data
longitudinal Analysis of Multiple Time Course Data
longitudinalData Longitudinal Data
longmemo Statistics for Long-Memory Processes (Jan Beran) – Data and Functions
longpower Sample size calculations for longitudinal data
loop loop decomposition of weighted directed graphs for life cycle analysis, providing flexbile network plotting methods, and analyzing food chain properties in ecology
LoopAnalyst A collection of tools to conduct Levins’ Loop Analysis
lordif Logistic Regression Differential Item Functioning using IRT
lorec LOw Rand and sparsE Covariance matrix estimation
lossDev Robust Loss Development Using MCMC
LOST Missing morphometric data simulation and estimation
LowRankQP Low Rank Quadratic Programming
lpc Lassoed principal components for testing significance of features
LPCM Local principal curve methods
lpint Local polynomial esitmators of intensity function or its derivatives
LPmerge Merging linkage maps by linear programming
lpridge Local Polynomial (Ridge) Regression
lpSolve Interface to Lp_solve v. 5.5 to solve linear/integer programs
lpSolveAPI R Interface for lp_solve version
lqa Penalized Likelihood Inference for GLMs
lqmm Linear Quantile Mixed Models
LS2W Locally stationary two-dimensional wavelet process estimation scheme
lsa Latent Semantic Analysis
LSD Lots of Superior Depictions
lsdv Fixed effect panel data regression
lshorth The Length of the Shorth
lsmeans Least-squares means
lspls LS-PLS Models
lsr Companion package to “Learning Statistics with R”
lss the accelerated failure time model to right censored data based on least-squares principle
ltm Latent Trait Models under IRT
ltmle Longitudinal Targeted Maximum Likelihood Estimation
LTPDvar LTPD and AOQL plans for acceptance sampling inspection by variables
LTR Perform LTR analysis on microarray data
ltsa Linear time series analysis
ltsbase Ridge and Liu Estimates based on LTS (Least Trimmed Squares) Method
lubridate Make dealing with dates a little easier
luca Likelihood inference from case-control data Under Covariate Assumptions (LUCA)
Luminescence Package for Luminescence Dating data analysis
LVMMCOR A Latent Variable Model for Mixed Continuous and Ordinal Responses
LVQTools Learning Vector Quantization Tools
lxb Fast LXB file reader
lymphclon Accurate Estimation of Clonal Coincidences and Abundances from Biological Replicates
M3 Reading M3 files
MAc Meta-Analysis with Correlations
MAclinical Class prediction based on microarray data and clinical parameters
MAd Meta-Analysis with Mean Differences
mada Meta-Analysis of Diagnostic Accuracy (mada)
MADAM This package provides some basic methods for meta-analysis
madsim A Flexible Microarray Data Simulation Model
Maeswrap Wrapper functions for MAESTRA/MAESPA
magic create and investigate magic squares
magicaxis Pretty scientific plotting with minor-tick and log minor-tick support
magma Matrix Algebra on GPU and Multicore Architectures
magnets Simulate micro-magnets dynamics
mail Sending Email Notifications from R
MAINT.Data Model and Analize Interval Data
makeProject Creates an empty package framework for the LCFD format
makeR Package for managing projects with multiple versions derived from a single source repository
malaria.em EM Estimation of Malaria Haplotype Probabilities from Multiply Infected Human Blood Samples
MALDIquant Quantitative Analysis of Mass Spectrometry Data
MALDIquantForeign Import/Export routines for MALDIquant
MAMA Meta-Analysis of MicroArray
MAMS Designing Multi-Arm Multi-Stage Studies
MAMSE Calculation of Minimum Averaged Mean Squared Error (MAMSE) weights
Mangrove Risk prediction on trees
mapdata Extra Map Databases
MapGAM Mapping Smoothed Odds Ratios from Individual-Level Data
MAPLES Smoothed age profile estimation
mapplots Data visualisation on maps
mapproj Map Projections
maps Draw Geographical Maps
maptools Tools for reading and handling spatial objects
maptree Mapping, pruning, and graphing tree models
mAr Multivariate AutoRegressive analysis
1-Mar Multivariate Autoregressive Modeling for Analysis of Community Time-Series Data
mar1s Multiplicative AR(1) with Seasonal Processes
marelac Tools for Aquatic Sciences
margie Log Marginal Likelihood of Gaussian Mixture
marginalmodelplots Marginal Mean Model Plots
markdown Markdown rendering for R
marked R Code for mark-recapture analysis
MarkedPointProcess Analysis of Marks of Marked Point Processes
maRketSim Market simulator for R
marmap Import, plot and analyze bathymetric and topographic data
marqLevAlg An algorithm for least-squares curve fitting
MARSS Multivariate Autoregressive State-Space Modeling
MASS Support Functions and Datasets for Venables and Ripley’s MASS
MASSTIMATE Body Mass Estimation Equations for Vertebrates
MasterBayes ML and MCMC Methods for Pedigree Reconstruction and Analysis
MAT Multidimensional Adaptive Testing (MAT)
Matching Multivariate and Propensity Score Matching with Balance Optimization
MatchIt MatchIt: Nonparametric Preprocessing for Parametric Casual Inference
mathgraph Directed and undirected graphs
maticce Mapping Transitions in Continuous Character Evolution
matie Measuring Association and Testing Independence Efficiently
matlab MATLAB emulation package
Matrix Sparse and Dense Matrix Classes and Methods
matrixcalc Collection of functions for matrix calculations
MatrixEQTL Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
MatrixModels Modelling with Sparse And Dense Matrices
matrixStats Methods that apply to rows and columns of a matrix
MATTOOLS Modern Calibration Functions for the Modern Analog Technique (MAT)
MAVTgsa Ordinary least square test and Multivariate Analysis Of Variance test with n contrasts
MaXact Exact max-type Cochran-Armitage trend test(CATT)
maxent Low-memory Multinomial Logistic Regression with Support for Text Classification
maxLik Maximum Likelihood Estimation
maxlike Model species distributions by estimating the probability of occurrence using presence-only data
maxstat Maximally Selected Rank Statistics
MBA Multilevel B-spline Approximation
MBCluster.Seq Model-Based Clustering for RNA-seq Data
MBI (M)ultiple-site (B)iodiversity (I)ndices Calculator
MBmca Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R
mbmdr Model Based Multifactor Dimensionality Reduction
mboost Model-Based Boosting
mc2d Tools for Two-Dimensional Monte-Carlo Simulations
MCAPS MCAPS data and results
mcbiopi Matrix Computation Based Identification Of Prime Implicants
mcclust Process an MCMC Sample of Clusterings
mcga Machine coded genetic algorithms for real-valued optimization problems
mcgibbsit Warnes and Raftery’s MCGibbsit MCMC diagnostic
mchof multicore higher-order functions
MChtest Monte Carlo hypothesis tests with Sequential Stopping
mcIRT IRT models for multiple choice items (mcIRT)
mcll Monte Carlo Local Likelihood Estimation
mclogit Mixed Conditional Logit
mclust Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation
mcmc Markov Chain Monte Carlo
MCMCglmm MCMC Generalised Linear Mixed Models
MCMChybridGP Hybrid Markov chain Monte Carlo using Gaussian Processes
MCMCpack Markov chain Monte Carlo (MCMC) Package
mcmcplots Create Plots from MCMC Output
MCMC.qpcr Bayesian analysis of qRT-PCR data
mcmcse Monte Carlo Standard Errors for MCMC
mco Multi criteria optimization algorithms and related functions
Mcomp Data from the M-competitions
MConjoint Conjoint Analysis through Averaging of Multiple Analyses
MCPAN Multiple comparisons using normal approximation
McParre Run a Regenerative Markov chain in Parallel on a Cluster
MCPerm A Monte Carlo permutation method for multiple test correlation
MCPMod Design and Analysis of Dose-Finding Studies (see also DoseFinding package)
mcprofile Multiple Contrast Profiles
mcr Method Comparison Regression
mcsm Functions for Monte Carlo Methods with R
McSpatial Nonparametric spatial data analysis
MCUSUM Multivariate Cumulative Sum (MCUSUM) Control Chart
mda Mixture and flexible discriminant analysis
mded Measuring the difference between two empirical distributions
MDM Multinomial Diversity Model
MDPtoolbox Markov Decision Processes toolbox
MDR Detect gene-gene interactions using multifactor dimensionality reduction
MDSGUI A GUI for interactive MDS in R
meboot Maximum Entropy Bootstrap for Time Series
mederrRank Bayesian Methods for Identifying the Most Harmful Medication Errors
mediation R Package for Causal Mediation Analysis
MedOr Median Ordering Statistical R package
medSTC A max-margin supervised Sparse Topical Coding Model
MEET MEET: Motif Elements Estimation Toolkit
mefa Multivariate Data Handling in Ecology and Biogeography
mefa4 Multivariate Data Handling with S4 Classes and Sparse Matrices
meifly Interactive model exploration using GGobi
mem Moving Epidemics Method R Package
memisc Tools for Management of Survey Data, Graphics, Programming, Statistics, and Simulation
memoise Memoise functions
MEMSS Data sets from Mixed-effects Models in S
memuse Estimate the memory usage of dense, in-core, numeric objects
MergeGUI A GUI for Merging Datasets in R
merror Accuracy and Precision of Measurements
MESS Miscellaneous esoteric statistical scripts
meta Meta-Analysis with R
MetABEL meta-analysis of genome-wide SNP association results
MetabolAnalyze Probabilistic latent variable models for metabolomic data
metabolomics A collection of functions for analysing metabolomics data
metacom Analysis of the ‘elements of metacommunity structure’
metacor Meta-analysis of correlation coefficients
Metadata Collates Metadata for Climate Surface Stations
MetaDE MetaDE: Microarray meta-analysis for differentially expressed gene detection
metafor Meta-Analysis Package for R
metagen Generalised Inference in the Random Effects Meta Regression Model
metaLik Likelihood inference in meta-analysis and meta-regression models
metaMA Meta-analysis for MicroArrays
metamisc Diagnostic and prognostic meta analysis (metamisc)
MetaPath Perform the Meta-Analysis for Pathway Enrichment analysis (MAPE)
MetaPCA MetaPCA: Meta-analysis in the Dimension Reduction of Genomic data
MetaQC MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis
MetaSKAT Meta analysis for SNP-set (Sequence) Kernel Association Test
metatest Fit and test metaregression models
meteogRam Tools for plotting meteograms
Meth27QC Meth27QC: sample quality analysis, and sample control analysis
MethComp Functions for analysis of agreement in method comparison studies
Metrics Evaluation metrics for machine learning
metRology Support for metrological applications
metrumrg Pharmacometric tools for data preparation, modeling, simulation, and reporting
mets Analysis of Multivariate Event Times
MEWMA Multivariate Exponentially Weighted Moving Average (MEWMA) Control Chart
MExPosition Multi-table ExPosition
MFDA Model Based Functional Data Analysis
mFilter Miscellaneous time series filters
mfp Multivariable Fractional Polynomials
mfr Minimal Free Resolutions of Graph Edge Ideals
MFSAS Creation and Evaluation of Multilevel Fixed and Sequential Sampling Plans
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
mgpd mgpd: Functions for multivariate generalized Pareto distribution (MGPD of Type II)
mgraph Graphing map attributes and non-map variables in R
MHadaptive General Markov Chain Monte Carlo for Bayesian Inference using adaptive Metropolis-Hastings sampling
mhsmm Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences
mht Multiple Hypotheses Testing For Variable Selection
mhurdle Estimation of models with limited dependent variables
mi Missing Data Imputation and Model Checking
mice Multivariate Imputation by Chained Equations
micEcon Microeconomic Analysis and Modelling
micEconAids Demand Analysis with the Almost Ideal Demand System (AIDS)
micEconCES Analysis with the Constant Elasticity of Scale (CES) function
micEconSNQP Symmetric Normalized Quadratic Profit Function
MiClip A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
microbenchmark Sub microsecond accurate timing functions
micromap Linked Micromap Plots
micromapST Linked Micromap Plots for U. S. States
MicroStrategyR MicroStrategyR Package
MIfuns Pharmacometric tools for data preparation, modeling, simulation, and reporting
MigClim Implementing dispersal into species distribution models
migest Useful R code for the Estimation of Migration
migration.indices Migration indices
migui Graphical User Interface of the mi Package
MImix Mixture summary method for multiple imputation
MindOnStats Data sets included in Utts and Heckard’s Mind on Statistics
minerva minerva: Maximal Information-Based Nonparametric Exploration R package for Variable Analysis
Miney Implementation of the Well-Known Game to Clear Bombs from a Given Field (Matrix)
miniGUI tktcl quick and simple function GUI
minimax Minimax distribution family
minpack.lm R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK, plus support for bounds
minPtest Gene region-level testing procedure for SNP data, using the min P test resampling approach
minqa Derivative-free optimization algorithms by quadratic approximation
minxent Entropy Optimization Distributions
miP Multiple Imputation Plots
MIPHENO Mutant Identification through Probabilistic High throughput Enabled NOrmalization
miRada MicroRNA Microarray Data Analysis
mirt Multidimensional Item Response Theory
miRtest combined miRNA- and mRNA-testing
misc3d Miscellaneous 3D Plots
miscF Miscellaneous Functions
miscFuncs Miscellaneous Useful Functions
MiscPsycho Miscellaneous Psychometric Analyses
miscTools Miscellaneous Tools and Utilities
missForest Nonparametric Missing Value Imputation using Random Forest
MissingDataGUI A GUI for Missing Data Exploration
missMDA Handling missing values with/in multivariate data analysis (principal component methods)
MissMech Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random
MiST Mixed effects Score Test for continuous outcomes
mistral Methods in Structural Reliability
MitISEM Mixture of Student t Distributions using Importance Sampling and Expectation Maximization
mitools Tools for multiple imputation of missing data
mix Estimation/multiple Imputation for Mixed Categorical and Continuous Data
mixAK Multivariate normal mixture models and mixtures of generalized linear mixed models including model based clustering
mixcat Mixed effects cumulative link and logistic regression models
mixdist Finite Mixture Distribution Models
mixedQF Estimator with Qudratics Forms in Mixeds Models
mixer Random graph clustering
mixexp Design and analysis of mixture experiments
mixfdr Computes false discovery rates and effect sizes using normal mixtures
mixlow mixlow method for assessing drug synergism
MixMAP Implements the MixMAP algorithm
mixOmics Omics Data Integration Project
mixPHM Mixtures of proportional hazard models
mixRasch Mixture Rasch Models with JMLE
mixreg Functions to fit mixtures of regressions
mixsep Forensic Genetics DNA Mixture Separation
MixSim Simulating Data to Study Performance of Clustering Algorithms
mixsmsn Fitting finite mixture of scale mixture of skew-normal distributions
mixstock functions for mixed stock analysis
mixtools Tools for analyzing finite mixture models
mixture Mixture Models for Clustering and Classification
MixtureInf Inference for Finite Mixture Models
mkin Routines for fitting kinetic models with one or more state variables to chemical degradation data
MKLE Maximum kernel likelihood estimation
MKmisc Miscellaneous Functions from M. Kohl
mkssd Efficient multi-level k-circulant supersaturated designs
mlbench Machine Learning Benchmark Problems
MLCM Maximum Likelihood Conjoint Measurement
MLDA Methylation Linear Discriminant Analysis (MLDA)
mlDNA Machine Learning-based Differential Network Analysis of Transcriptome Data
MLDS Maximum Likelihood Difference Scaling
mlearning Machine learning algorithms with unified interface and confusion matrices
MLEcens Computation of the MLE for bivariate (interval) censored data
mlegp Maximum Likelihood Estimates of Gaussian Processes
MLEP Maximum likelihood estimate of penetrance parameters
mleur Maximum likelihood unit root test
mlgt Multi-Locus Geno-Typing
mlica2 Independent Component Analysis using Maximum Likelihood
mlmmm ML estimation under multivariate linear mixed models with missing values
mlmRev Examples from Multilevel Modelling Software Review
mlogit multinomial logit model
mlogitBMA Bayesian Model Averaging for Multinomial Logit Models
MLPAstats MLPA analysis to detect gains and loses in genes
mlPhaser Multi-Locus Haplotype Phasing
MM The multiplicative multinomial distribution
mmand Mathematical Morphology in Any Number of Dimensions
mmap Map Pages of Memory
mmcm Modified Maximum Contrast Method
mmds Mixture Model Distance Sampling (mmds)
mmeln MMELN : Estimation of multinormal mixture distribution
mmeta Multivariate Meta-Analysis Using Sarmanov Beta Prior Distributions
MMIX Model selection uncertainty and model mixing
mmm an R package for analyzing multivariate longitudinal data with multivariate marginal models
mmm2 Multivariate marginal models with shared regression parameters
mmod Modern measures of population differentiation
MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks
mnormt The multivariate normal and t distributions
MNP R Package for Fitting the Multinomial Probit Model
mobForest Model based Random Forest analysis
Mobilize Mobilize plots and functions
MOCCA Multi-objective optimization for collecting cluster alternatives
Modalclust Hierarchical Modal Clustering
modeest Mode Estimation
modehunt Multiscale Analysis for Density Functions
modelcf Modeling physical computer codes with functional outputs using clustering and dimensionality reduction
modelfree Model-free estimation of a psychometric function
ModelGood Validation of risk prediction models
ModelMap Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps
modeltools Tools and Classes for Statistical Models
modiscloud R tools for processing Level 2 Cloud Mask products from MODIS
MODISTools MODIS Subsetting Tools
modTempEff Modelling temperature effects using time series data
moduleColor Basic module functions
MOJOV Mojo Variants: Rare Variants analysis
mokken Mokken Scale Analysis in R
mombf Moment and Inverse Moment Bayes factors
moments Moments, cumulants, skewness, kurtosis and related tests
Momocs Shape Analysis of Outlines
mondate Keep track of dates in terms of months
MonetDB.R Connect MonetDB to R
monmlp Monotone multi-layer perceptron neural network
monomvn Estimation for multivariate normal and Student-t data with monotone missingness
MonoPoly Functions to fit monotone polynomials
monreg Nonparametric monotone regression
moonsun Basic astronomical calculations with R
mopsocd MOPSOCD: Multi-objective Particle Swarm Optimization with Crowding Distance
Morpho Calculations and visualisations related to Geometric Morphometrics
MorseGen Simple raw data generator based on user-specified summary statistics
MortalitySmooth Smoothing and forecasting Poisson counts with P-splines
mosaic Project MOSAIC ( statistics and mathematics teaching utilities
moult Models for Analysing Moult in Birds
move Visualizing and analyzing animal track data
movMF Mixtures of von Mises-Fisher Distributions
mpa CoWords Method
MPCI Multivariate Process Capability Indices (MPCI)
MPDiR Data sets and scripts for Modeling Psychophysical Data in R
MPINet The package can implement the network-based metabolite pathway identification of pathways
MplusAutomation Automating Mplus Model Estimation and Interpretation
mpm Multivariate Projection Methods
mpMap Multi-parent RIL genetic analysis
mpmcorrelogram Multivariate Partial Mantel Correlogram
mpoly Symbolic computation and more with multivariate polynomials
mpt Multinomial Processing Tree (MPT) Models
MPTinR Analyze Multinomial Processing Tree Models
MPV Data Sets from Montgomery, Peck and Vining’s Book
mra Analysis of Mark-Recapture data
mratios Inferences for ratios of coefficients in the general linear model
MRCE Multivariate regression with covariance estimation
MRCV Methods for Analyzing Multiple Response Categorical Variables (MRCVs)
mrdrc Model-robust concentration-response analysis
mrds Mark-Recapture Distance Sampling (mrds)
mritc MRI tissue classification
mRm An R package for conditional maximum likelihood estimation in mixed Rasch models
mRMRe R package for parallelized mRMR ensemble feature selection
msap Statistical analysis for Methylation-sensitive Amplification Polymorphism data
msarc Draws diagrams (mis)representing the results of mass spec experiments
MsatAllele Visualizes the scoring and binning of microsatellite fragment sizes
MSBVAR Markov-Switching, Bayesian, Vector Autoregression Models
mseapca Metabolite set enrichment analysis for factor loading in principal component analysis
MSeasy Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS) data
MSeasyTkGUI MSeasy Tcl/Tk Graphical User Interface
mseq Modeling non-uniformity in short-read rates in RNA-Seq data
MSG Data and functions for the book Modern Statistical Graphics
msgl High dimensional multiclass classification using sparse group lasso
msgpackR A library to serialize or unserialize data in MessagePack format
msgps Degrees of freedom of elastic net, adaptive lasso and generalized elastic net
msir Model-based Sliced Inverse Regression
msm Multi-state Markov and hidden Markov models in continuous time
msme Functions and Datasets for “Methods of Statistical Model Estimation”
MSQC Multivariate Statistical Quality Control
msr Morse-Smale approximation, regression and visualization
msSurv Nonparametric Estimation for Multistate Models
mstate Data preparation, estimation and prediction in multi-state models
MSwM Fitting Markov Switching Models
mtcreator Creating MAGE-TAB files using mtcreator
mtsdi Multivariate time series data imputation
MTSKNN Multivariate two-sample tests based on K-nearest-neighbors
MTurkR Access to Amazon Mechanical Turk Requester API via R
MUCflights Munich Franz-Josef-Strauss Airport Pattern Analysis
MuFiCokriging Multi-Fidelity Cokriging models
mugnet Mixture of Gaussian Bayesian Network Model
muhaz Hazard Function Estimation in Survival Analysis
multcomp Simultaneous Inference in General Parametric Models
multcompView Visualizations of Paired Comparisons
MultEq Multiple Equivalence Tests and Simultaneous Confidence Intervals
multgee GEE Solver for Correlated Nominal or Ordinal Multinomial Responses
multibiplotGUI Multibiplot Analysis in R
multic Quantitative linkage analysis tools using the variance components approach
MultiChIPmixHMM MultiChIPmixHMM, an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates
Multiclasstesting Performance of N-ary classification testing
multicool Permutations of multisets in cool-lex order
multicore Parallel processing of R code on machines with multiple cores or CPUs
MultiLCIRT Multidimensional latent class Item Response Theory models
multilevel Multilevel Functions
multilevelPSA Multilevel Propensity Score Analysis
MultinomialCI Simultaneous confidence intervals for multinomial proportions according to the method by Sison and Glaz
multinomRob Robust Estimation of Overdispersed Multinomial Regression Models
MultiOrd Generation of multivariate ordinal variates
MultiPhen MultiPhen, a package for the genetic association testing of multiple phenotypes
multiPIM Variable Importance Analysis with Population Intervention Models
multipol multivariate polynomials
multisensi Multivariate Sensitivity Analysis
multitable Simultaneous manipulation of multiple arrays of data, with data.list objects
multitaper Multitaper spectral analysis tools
multivator A multivariate emulator
multmod Testing of multiple outcomes
multxpert Common Multiple Testing Procedures and Gatekeeping Procedures
muma Metabolomics Univariate and Multivariate Analysis
MuMIn Multi-model inference
munfold Metric Unfolding
munsell Munsell colour system
muRL Mailmerge using R, LaTeX, and the Web
muscle Multiple Sequence Alignment
muStat Prentice Rank Sum Test and McNemar Test
mutatr Mutable objects for R
mutoss Unified multiple testing procedures
mutossGUI A graphical user interface for the MuToss Project
MVA An Introduction to Applied Multivariate Analysis with R
mvabund statistical methods for analysing multivariate abundance data
MVB Mutivariate Bernoulli log-linear model
mvbutils Workspace organization, code and documentation editing, package prep and editing, etc
mvc Multi-View Clustering
mvinfluence Influence Measures and Diagnostic Plots for Multivariate Linear Models
mvmeta Multivariate meta-analysis and meta-regression
MVN Multivariate Normality Tests
mvna Nelson-Aalen estimator of the cumulative hazard in multistate models
mvngGrAd Software for moving grid adjustment in plant breeding field trials
mvnmle ML estimation for multivariate normal data with missing values
mvnormtest Normality test for multivariate variables
mvoutlier Multivariate outlier detection based on robust methods
mvpart Multivariate partitioning
MVPARTwrap MVPARTwrap: Additional functionnalities for package mvpart
MVpower Give power for a given effect size using multivariate classification methods
mvProbit Multivariate Probit Models
MVR Mean-Variance Regularization
mvsf Shapiro-Francia Multivariate Normality Test
mvShapiroTest Generalized Shapiro-Wilk test for multivariate normality
mvtBinaryEP Generates Correlated Binary Data
mvtmeta Multivariate meta-analysis
mvtnorm Multivariate Normal and t Distributions
mvtsplot Multivariate Time Series Plot
mxkssd Efficient mixed-level k-circulant supersaturated designs
myepisodes MyEpisodes RSS/API functions
Myrrix Interface to Myrrix. Myrrix is a complete, real-time, scalable clustering and recommender system, evolved from Apache Mahout
Myrrixjars External jars required for package Myrrix
nacopula Nested Archimedean Copulas
NADA Nondetects And Data Analysis for environmental data
nadiv Functions to construct (non)additive genetic relatedness matrices and facilitate animal model analyses
namespace Provide namespace managment functions not (yet) present in base R
nanop tools for nanoparticle simulation and PDF calculation
NanoStringNorm Normalize NanoString miRNA and mRNA data
naturalsort Natural Ordering
NBDdirichlet NBD-Dirichlet model of consumer buying behavior for marketing research
nbpMatching functions for non-bipartite optimal matching
NBPSeq Negative Binomial Models for RNA-Sequencing Data
nCal Nonlinear Calibration
NCBI2R NCBI2R-An R package to navigate and annotate genes and SNPs
ncbit retrieve and build NBCI taxonomic data
ncdf Interface to Unidata netCDF data files
ncdf4 Interface to Unidata netCDF (version 4 or earlier) format data files
nCDunnett Noncentral Dunnett’s test distribution
ncf spatial nonparametric covariance functions
ncg Computes the noncentral gamma function
NCmisc Miscellaneous general purpose functions
ncvreg Regularization paths for SCAD- and MCP-penalized regression models
ndl Naive Discriminative Learning
ndtv Network Dynamic Temporal Visualizations
ndvits NDVI Time series extraction and analysis
neariso Near-Isotonic Regression
NeatMap Non-clustered heatmap alternatives
needy needy
negenes Estimating the number of essential genes in a genome
neldermead R port of the Scilab neldermead module
nephro Biostatistics utilities for nephrology
NestedCohort Survival Analysis for Cohorts with Missing Covariate Information
netClass netClass: An R Package for Network-Based Biomarker Discovery
NetCluster Clustering for networks
NetComp Network Generation and Comparison
NetData Network Data for McFarland’s SNA R labs
NetIndices Estimating network indices, including trophic structure of foodwebs in R
netmeta Network meta-analysis with R
NetPreProc NetPreProc: Network Pre-Processing and normalization
nets Network Estimation for Time Series
netweavers NetWeAvers: Weighted Averages for Networks
network Classes for Relational Data
NetworkAnalysis Statistical inference on populations of weighted or unweighted networks
networkDynamic Dynamic Extensions for Network Objects
networksis Simulate bipartite graphs with fixed marginals through sequential importance sampling
networkTomography Tools for network tomography
neuralnet Training of neural networks
neuroblastoma Neuroblastoma copy number profiles
neuRosim Functions to generate fMRI data including activated data, noise data and resting state data
nFactors Parallel Analysis and Non Graphical Solutions to the Cattell Scree Test
nga NGA Earthquake Ground Motion Prediction Equations
ngramr Retrieve and plot Google n-gram data
ngspatial Classes for Spatial Data
NHEMOtree Non-hierarchical evolutionary multi-objective tree learner to perform cost-sensitive classification
nhlscrapr Compiling the NHL Real Time Scoring System Database for easy use in R
NHPoisson Modelling and validation of non homogeneous Poisson processes
nice Get or Set UNIX Niceness
NightDay Night and Day Boundary Plot Funtion
Nippon Japanese utility functions and data
NISTnls Nonlinear least squares examples from NIST
nlADG Regression in the Normal Linear ADG Model
nleqslv Solve systems of non linear equations
nlme Linear and Nonlinear Mixed Effects Models
nlmeODE Non-linear mixed-effects modelling in nlme using differential equations
nlmeU Datasets and utility functions enhancing functionality of nlme package
nlmrt Functions for nonlinear least squares solutions
nloptr R interface to NLopt
nloptwrap Wrapper for Package nloptr
NLRoot searching for the root of equation
nlrwr Nonlinear regression with R
nls2 Non-linear regression with brute force
nlsmsn Fitting nonlinear models with scale mixture of skew-normal distributions
nlstools Tools for nonlinear regression diagnostics
NlsyLinks Utilities and kinship information for Behavior Genetics and Developmental research using the NLSY
nlt A nondecimated lifting transform for signal denoising
nlts (non)linear time series analysis
NMF Algorithms and framework for Nonnegative Matrix Factorization (NMF)
NMFN Non-negative Matrix Factorization
NMOF Numerical Methods and Optimization in Finance
NMRS NMR Spectroscopy
nnclust Nearest-neighbour tools for clustering
nnet Feed-forward Neural Networks and Multinomial Log-Linear Models
nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS)
nodeHarvest Node Harvest for regression and classification
noia Implementation of the Natural and Orthogonal InterAction (NOIA) model
nonparaeff Nonparametric Methods for Measuring Efficiency and Productivity
NonpModelCheck Model Checking and Variable Selection in Nonparametric Regression
nontarget Detecting, combining and filtering isotope, adduct and homologue series relations in high-resolution mass spectrometry (HRMS) data
nopp Nash Optimal Party Positions
nor1mix Normal (1-d) Mixture Models (S3 Classes and Methods)
nordklimdata1 Dataset for climate analysis with data from the Nordic region
norm Analysis of multivariate normal datasets with missing values
NormalGamma Normal-gamma convolution model
normalp Package for exponential power distributions (EPD)
NORMT3 Evaluates complex erf, erfc, Faddeeva, and density of sum of Gaussian and Student’s t
normwhn.test Normality and White Noise Testing
nortest Tests for Normality
nose nose Package for R
notifyR Send push notifications to your smartphone via (ACCOUNT REQUIRED!)
noweb Noweb system for R
Nozzle.R1 Nozzle Reports
np Nonparametric kernel smoothing methods for mixed data types
nparcomp Perform multiple comparisons and compute simultaneous confidence intervals for the nonparametric relative contrast effects
nparLD Nonparametric Analysis of Longitudinal Data in Factorial Experiments
NPCD Nonparametric Methods for Cognitive Diagnosis
NPCirc Nonparametric Circular Methods
npde Normalised prediction distribution errors for nonlinear mixed-effect models
NPHMC Sample Size Calculation for the Proportional Hazards Mixture Cure Model
nplplot Plotting non-parametric linkage results
npmlreg Nonparametric maximum likelihood estimation for random effect models
NPMPM tertiary probabilistic model in predictive microbiology for use in food manufacture
npmv Nonparametric Comparison of Multivariate Samples
NPMVCP Nonparametric Multivariate Change Point Model
nppbib Nonparametric Partially-Balanced Incomplete Block Design Analysis
npRmpi Parallel nonparametric kernel smoothing methods for mixed data types
NPsimex Nonparametric Smoothing for contaminated data using Simulation-Extrapolation
NRAIA Data sets from “Nonlinear Regression Analysis and Its Applications”
nricens NRI for risk prediction models with time to event and binary response data
NSA Post-normalization of total copy numbers
NScluster Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models
nsga2R Elitist Non-dominated Sorting Genetic Algorithm based on R
nsprcomp Non-Negative Sparse PCA
nsRFA Non-supervised Regional Frequency Analysis
nullabor Tools for graphical inference
numbers Number-theoretic Functions
numConversion Test of accuracy of formatting numbers
numDeriv Accurate Numerical Derivatives
nutshell Data for “R in a Nutshell”
nutshell.audioscrobbler Audioscrobbler data for “R in a Nutshell”
nutshell.bbdb Baseball Database for “R in a Nutshell”
nws R functions for NetWorkSpaces and Sleigh
OAIHarvester Harvest Metadata Using OAI-PMH v2.0
Oarray Arrays with arbitrary offsets
objectProperties A factory of self-describing properties
objectSignals objectSignals
obliclus Cluster-based factor rotation
obliqueRF Oblique Random Forests from Recursive Linear Model Splits
oblique.tree Oblique Trees for Classification Data
obsSens Sensitivity analysis for Observational studies
oc OC Roll Call Analysis Software
occ Estimates PET neuroreceptor occupancies
oce Analysis of Oceanographic data
ODB Open Document Databases (.odb) management
odfWeave Sweave processing of Open Document Format (ODF) files
odfWeave.survey Support for odfWeave on the survey package
ODMconverter tools to convert ODM files
odprism Optimal design and performance of random intercept and slope models
oem Orthogonalizing Expectation maximization
Ohmage R Client for Mobilize/Andwellness server
OIdata Data sets and supplements (OpenIntro)
OIsurv Survival analysis supplement to OpenIntro guide
OjaNP Multivariate Methods Based on the Oja Median and Related Concepts
okmesonet Retrieve Oklahoma Mesonet climatological data
OligoSpecificitySystem Oligo Specificity System
OLScurve OLS growth curve trajectories
omd filter the molecular descriptors for QSAR
OmicKriging OmicKriging for Phenotypic Prediction
oncomodel Maximum likelihood tree models for oncogenesis
Oncotree Estimating oncogenetic trees
OneHandClapping Prediction of condition-specific transcription factor interactions
onemap Software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses
OneTwoSamples Deal with one and two (normal) samples
onion octonions and quaternions
OOmisc Ozgur-Ozlem Miscellaneous
OpasnetUtils Utility functions for dealing with data in Opasnet ( environment
OPDOE OPtimal Design Of Experiments
OPE Outer-product emulator
opefimor Option Pricing and Estimation of Financial Models in R
openair Tools for the analysis of air pollution data
OpenCL Interface allowing R to use OpenCL
opencpu.demo OpenCPU Demo apps
opencpu.encode opencpu object encoder/decoder
openintro OpenIntro data sets and supplemental functions
OpenMPController Control number of OpenMP threads dynamically
openNLP openNLP Interface
openNLPmodels.en openNLP Models for English openNLP Models for Spanish
OpenRepGrid Tools to analyse repertory grid data
OpenStreetMap Access to open street map raster images
operators Additional binary operators for the R language Utilities for working with R’s operators
OPI Open Perimetry Interface
opm Tools for analysing OmniLog(R) Phenotype Microarray data
opmdata Example data for analyzing OmniLog(R) Phenotype Microarray data
oposSOM Package for analysis and visualization of metagenes
ops Optimal Power Space Transformation
optAUC Optimal Combinations of Diagnostic Tests Based on AUC
optBiomarker Estimation of optimal number of biomarkers for two-group microarray based classifications at a given error tolerance level for various classification rules
OptimalCutpoints Computing optimal cutpoints in diagnostic tests
optimbase R port of the Scilab optimbase module
optimsimplex R port of the Scilab optimsimplex module
optimx A Replacement and Extension of the optim() Function
OptInterim Optimal Two and Three Stage Designs for Single-Arm and Two-Arm Randomized Controlled Trials with a Long-Term Binary Endpoint
optmatch Functions for optimal matching
optparse Command line option parser
ora Convenient Tools for Working with Oracle Databases
orclus ORCLUS subspace clustering
ORCME Order Restricted Clustering for Microarray Experiments
orcutt Estimate procedure in case of first order autocorrelation
orddom Ordinal Dominance Statistics
ORDER2PARENT Estimate parent distributions with data of several order statistics
orderbook Orderbook visualization/Charting software
OrdFacReg Least squares, logistic, and Cox-regression with ordered predictors
ordinal Regression Models for Ordinal Data
OrdMonReg Compute least squares estimates of one bounded or two ordered isotonic regression curves
ordPens Selection and/or Smoothing of Ordinal Predictors
OrgMassSpecR Organic Mass Spectrometry
ORIClust Order-restricted Information Criterion-based Clustering Algorithm
orientlib Support for orientation data
orloca The package deals with Operations Research LOCational Analysis models Spanish version of orloca package
oro.dicom Rigorous – DICOM Input / Output
oro.nifti Rigorous – NIfTI+ANALYZE+AFNI Input / Output Rigorous – Positron Emission Tomography
orQA Order Restricted Assessment Of Microarray Titration Experiments
orsk Converting Odds Ratio to Relative Risk in Cohort Studies with Partial Data Information
orth Multivariate Logistic Regressions Using Orthogonalized Residuals
orthogonalsplinebasis Orthogonal Bspline Basis Functions
orthopolynom Collection of functions for orthogonal and orthonormal polynomials
osDesign Design and analysis of observational studies
osmar OpenStreetMap and R
ouch Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses
outbreaker Bayesian inference of outbreak dynamics based on epidemiological and genetic information
OutlierDC Outlier Detection using Quantile Regression for Censored Data
outliers Tests for outliers
OUwie Analysis of evolutionary rates in an OU framework
overlap Estimates of coefficient of overlapping for animal activity patterns
oz Plot the Australian coastline and states
p2distance Welfare’s Synthetic Indicator
p3state.msm Analyzing survival data
pa Performance Attribution for Equity Portfolios
pacbpred PAC-Bayesian Estimation and Prediction in Sparse Additive Models
pack Convert values to/from raw vectors
packClassic Toy example of Pack Classic
packdep Mapping dependencies among R packages
packHV A few useful functions for statisticians
packS4 Toy example of S4 package
pacose iPACOSE, PACOSE and other methods for covariance selection
PAGI The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways
pairedCI Confidence intervals for the ratio of locations and for the ratio of scales of two paired samples
PairedData Paired Data Analysis
pairheatmap A tool for comparing heatmaps
PairViz Visualization using Eulerian tours and Hamiltonian decompositions
pairwise Rasch Model Parameters by Pairwise Algorithm
pairwiseCI Confidence intervals for two sample comparisons
palaeoSig Significance tests for palaeoenvironmental reconstructions
paleoMAS Paleoecological Analysis
paleotree Paleontological and Phylogenetic Analyses of Evolution
paleoTS Analyze paleontological time-series
PamGeneMixed Preprocessing and Modeling Kinase Activity Profiles in PamChip Data
pamm Power analysis for random effects in mixed models
pamr Pam: prediction analysis for microarrays
pan Multiple imputation for multivariate panel or clustered data
pander An R pandoc writer
papeR A toolbox for writing Sweave or other LaTeX-based papers and reports
parallelize.dynamic Automate parallelization of function calls by means of dynamic code analysis
ParamHelpers Helpers for parameters in black-optimization, tuning and maching learning
paramlink Parametric linkage analysis in R
paran Horn’s Test of Principal Components/Factors
parcor Regularized estimation of partial correlation matrices
ParDNAcopy parallel implementation of the “segment” function of package “DNAcopy”
parfm Parametric Frailty Models
parfossil Parallelized functions for palaeoecological and palaeogeographical analysis
parma Portfolio Allocation and Risk Management Applications
parmigene Parallel Mutual Information estimation for Gene Network reconstruction
parspatstat Parallel spatial statistics
partDSA Partitioning using deletion, substitution, and addition moves
partialOR Partial Odds Ratio
partitionMap Partition Maps
partitionMetric Compute a distance metric between two partitions of a set
partitions Additive partitions of integers
partsm Periodic Autoregressive Time Series Models
party A Laboratory for Recursive Partytioning
partykit A Toolkit for Recursive Partytioning
parviol Parviol
PAS Polygenic Analysis System (PAS)
pass Prediction and Stability Selection of Tuning Parameters
pastecs Package for Analysis of Space-Time Ecological Series
pastis Phylogenetic Assembly with Soft Taxonomic Inferences
patchDVI Package to patch .dvi files
patchPlot Scatterplots of image patches
pathClass Classification using biological pathways as prior knowledge
pathdiagram Basic functions for drawing path diagrams
pathmox Segmentation Trees in Partial Least Squares Path Modeling
PatternClass Class-focused pattern metric comparisons using simulation
pavo Perceptual analysis, visualization and organization of spectral color data in R
PAWL Implementation of the PAWL algorithm
pbapply Adding Progress Bar to ‘*apply’ Functions
pbatR P2BAT
pbdBASE Programming with Big Data – Base Wrappers for Distributed Matrices
pbdDEMO Programming with Big Data – Demonstrations of pbd Packages
pbdDMAT Programming with Big Data – Distributed Matrix Methods
pbdMPI Programming with Big Data – Interface to MPI
pbdNCDF4 Programming with Big Data – Interface to Parallel Unidata NetCDF4 Format Data Files
pbdPROF Programming with Big Data — MPI Profiling Tools
pbdSLAP Programming with Big Data – Scalable Linear Algebra Packages
PBImisc A set of datasets used in my classes or in the book ,,Modele liniowe i mieszane w R, wraz z przykladami w analizie danych”
pbivnorm Vectorized Bivariate Normal CDF
pbkrtest Parametric bootstrap and Kenward Roger based methods for mixed model comparison
pbs Periodic B Splines
PBSadmb ADMB for R Using Scripts or GUI
PBSddesolve Solver for Delay Differential Equations
PBSmapping Mapping Fisheries Data and Spatial Analysis Tools
PBSmodelling GUI Tools Made Easy: Interact with Models, Explore Data, Give Dynamic Presentations
pca3d Three dimensional PCA plots
pcaL1 Three L1-Norm PCA Methods
pcalg Estimation of CPDAG/PAG and causal inference using the IDA algorithm
pcaPP Robust PCA by Projection Pursuit
pcenum Permutations and Combinations Enumeration
PCICt Implementation of POSIXct work-alike for 365 and 360 day calendars
PCIT PCIT algorithm – Partial Correlation Coefficient with Information Theory
PCovR Principal Covariates Regression
pcrcoal A package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997)
pcrsim Simulation of the forensic DNA process
PCS Calculate the probability of correct selection (PCS)
pcse Panel-Corrected Standard Error Estimation in R
pcurve Principal curve analysis
pdc Permutation Distribution Clustering
pdfCluster Cluster analysis via nonparametric density estimation
pdist Partitioned Distance Function
PDSCE Positive definite sparse covariance estimators
Peak2Trough Estimation of the peak-to-trough ratio of a seasonal variation component
Peaks Peaks
pear Package for Periodic Autoregression Analysis
pearson7 Maximum Likelihood Inference for the Pearson VII Distribution with Shape Parameter 3/2
PearsonDS Pearson Distribution System
PearsonICA Independent component analysis using score functions from the Pearson system
pec Prediction Error Curves for Survival Models
pedantics Functions to facilitate power and sensitivity analyses for genetic studies of natural populations
pedigree Pedigree functions
pedigreemm Pedigree-based mixed-effects models
pegas Population and Evolutionary Genetics Analysis System
PEIP Functions for Aster Book on Inverse Theory
penalized L1 (lasso and fused lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model
penalizedLDA Penalized classification using Fisher’s linear discriminant
penalizedSVM Feature Selection SVM using penalty functions
pencopula Flexible Copula Density Estimation with Penalized Hierarchical B-Splines
pendensity Density Estimation with a Penalized Mixture Approach
penDvine Flexible Pair-Copula Estimation in D-vines using Bivariate Penalized Splines
PenLNM Group l1 penalized logistic normal multinomial (LNM) regression model
pensim Simulation of high-dimensional data and parallelized repeated penalized regression
peperr Parallelised Estimation of Prediction Error
peplib Peptide Library Analysis Methods
pequod Moderated regression package
perARMA Package for Periodic Time Series Analysis
PerfMeas PerfMeas: Performance Measures for ranking and classification tasks
PerformanceAnalytics Econometric tools for performance and risk analysis
perm Exact or Asymptotic permutation tests
PermAlgo Permutational algorithm to simulate survival data
permGPU permPGU: Using GPUs in Statistical Genomics
permtest Permutation test to compare variability within and distance between two groups
permute Functions for generating restricted permutations of data
PERregress Regression Functions and Datasets
perry Resampling-based prediction error estimation for regression models
persiandictionary English to Persian dictionary
perturb Tools for evaluating collinearity
pesticides Analysis of single serving and composite pesticide residue measurements
PET Simulation and Reconstruction of PET Images
PF Functions related to prevented fraction
pfa Estimates False Discovery Proportion Under Arbitrary Covariance Dependence
pgam Poisson-Gamma Additive Models
pgirmess Data analysis in ecology
pglm panel generalized linear model
pGLS Generalized Least Square in comparative Phylogenetics
pgmm Parsimonious Gaussian mixture models
pgnorm The p-generalized normal distribution
pgs Precision of Geometric Sampling
phangorn Phylogenetic analysis in R
PhaseType Inference for Phase-type Distributions
phcfM Modelling anthropogenic deforestation
pheatmap Pretty Heatmaps
phenex Auxiliary functions for phenological data analysis
pheno Auxiliary functions for phenological data analysis
pheno2geno Pheno2Geno – Generating genetic markers and maps from molecular phenotypes
phenology Tools to manage a parametric function that describes phenology
phia Post-Hoc Interaction Analysis
phmm Proportional Hazards Mixed-effects Model (PHMM)
phom Persistent Homology in R
phonR R tools for phoneticians and phonologists
phonTools Functions for phonetics in R
phtt Panel Data Analysis with Heterogeneous Time Trends
PhViD PhViD: an R package for PharmacoVigilance signal Detection
phyclust Phylogenetic Clustering (Phyloclustering)
phyext An extension of some of the classes in phylobase. Tree objects now support subnodes on branches
phylobase Base package for phylogenetic structures and comparative data
phyloclim Integrating Phylogenetics and Climatic Niche Modeling
phylolm Phylogenetic Linear Regression
phylosim R package for simulating biological sequence evolution
phylotools Phylogenetic tools for Eco-phylogenetics
phyloTop Phylogenetic Tree Topological Properties Evaluator
PhysicalActivity Process Physical Activity Accelerometer Data
phytools Phylogenetic Tools for comparative biology (and other things)
pi0 Estimating the proportion of true null hypotheses for FDR
picante R tools for integrating phylogenies and ecology
PIN Estimates the parameters of a trading-tree model for the computation of the probability of informed trading
PIPS Predicted Interval Plots
pitchRx Tools for Collecting and Visualizing Major League Baseball PITCHfx Data
PivotalR R front-end to PostgreSQL and Pivotal (Greenplum) database, wrapper for MADlib
pixmap Bitmap Images (“Pixel Maps”)
PK Basic Non-Compartmental Pharmacokinetics
PKfit A Data Analysis Tool for Pharmacokinetics
pkgmaker Package development utilities
PKgraph Model diagnostics for population pharmacokinetic models
pkgutils pkgutils – Utilities for creating R packages
PKI Public Key Infrastucture for R based on the X.509 standard
PKmodelFinder Software for Pharmacokinetic model
PKPDmodels Pharmacokinetic/pharmacodynamic models
PKreport A reporting pipeline for checking population pharmacokinetic model assumption
pks Probabilistic Knowledge Structures
PKtools unified computational interfaces for pop PK
plan Tools for project planning
planar Multilayer optics
planor Generation of regular factorial designs
PlayerRatings Dynamic Updating Methods For Player Ratings Estimation
playitbyr Representing and exploring data through sound
playwith A GUI for interactive plots using GTK+
plfm Probabilistic latent feature analysis of two-way two-mode frequency data
plgp Particle Learning of Gaussian Processes
plink IRT Separate Calibration Linking Methods
PLIS Multiplicity control using Pooled LIS statistic
plm Linear Models for Panel Data
plmDE Additive partially linear models for differential gene expression analysis
plmm Partially Linear Mixed Effects Model
pln Polytomous logit-normit (graded logistic) model estimation
plotGoogleMaps Plot SP or SPT(STDIF,STFDF) data as HTML map mashup over Google Maps
plotKML Visualization of spatial and spatio-temporal objects in Google Earth
plotmo Plot a model’s response while varying the values of the predictors
plotpc Plot principal component histograms around a scatter plot
PlotRegionHighlighter Creates an envelope that surrounds a set of points plotted in a two dimensional space
plotrix Various plotting functions
plotSEMM Graphing nonlinear latent variable interactions in SEMM
PL.popN Population Size Estimation
plRasch Log Linear by Linear Asscociation models
PLRModels Statistical inference in partial linear regression models
pls Partial Least Squares and Principal Component regression
plsdepot Partial Least Squares (PLS) Data Analysis Methods
plsdof Degrees of Freedom and Statistical Inference for Partial Least Squares Regression
plsgenomics PLS analyses for genomics
plspm Tools for Partial Least Squares Path Modeling
plsRbeta Partial least squares Regression for beta regression models
plsRcox Partial least squares Regression for Cox models and related techniques
plsRglm Partial least squares Regression for generalized linear models
plugdensity Plug-in Kernel Density Estimation
plumbr Mutable and dynamic data models
plus Penalized Linear Unbiased Selection
plyr Tools for splitting, applying and combining data
PMA Penalized Multivariate Analysis
pmclust Parallel Model-Based Clustering
pmg Poor Man’s GUI
pmlr Penalized Multinomial Logistic Regression
pmml Generate PMML for various models
pmmlTransformations Transforms input data from a PMML perspective
pmr Probability Models for Ranking Data
png Read and write PNG images
pnmtrem Probit-Normal Marginalized Transition Random Effects Models
pnn Probabilistic neural networks
pocrm Dose-finding in drug combination Phase I trials using the partial order continual reassessment method (PO-CRM)
POET Principal Orthogonal ComplEment Thresholding (POET) method
poibin The Poisson Binomial Distribution
PoiClaClu Classification and clustering of sequencing data based on a Poisson model
poilog Poisson lognormal and bivariate Poisson lognormal distribution
poisson.glm.mix Fit high dimensional mixtures of Poisson GLMs
PoissonSeq Significance analysis of sequencing data based on a Poisson log linear model
poistweedie Poisson-Tweedie exponential family models
poLCA Polytomous variable Latent Class Analysis
polspline Polynomial spline routines
polyapost Simulating from the Polya posterior
polycor Polychoric and Polyserial Correlations
polyCub Cubature over Polygonal Domains
polynom A collection of functions to implement a class for univariate polynomial manipulations
PolynomF Polynomials in R
polysat Tools for Polyploid Microsatellite Analysis
polySegratio Simulate and test marker dosage for dominant markers in autopolyploids
polySegratioMM Bayesian mixture models for marker dosage in autopolyploids
polytomous Polytomous logistic regression for fixed and mixed effects
polywog Bootstrapped Basis Regression with Oracle Model Selection
pom POM – Patch Occupancy Models
Pomic Pattern Oriented Modelling Information Criterion
PoMoS Polynomial (ordinary differential equation) Model Search
pomp Statistical inference for partially observed Markov processes
pooh Partial Orders and Relations
popbio Construction and analysis of matrix population models
popdemo Provides Tools For Demographic Modelling Using Projection Matrices
popgen Statistical and Population Genetics
PopGenKit Useful functions for (batch) file conversion and data resampling in microsatellite datasets
PopGenome A swiss army knife for population genetic & genomic analysis
PopGenReport PopGen: A simple way to analyse and visualize population genetic data
popgraph This is an R package that constructs and manipulates population graphs
popPK Summary of Population Pharmacokinetic Analysis
poppr an R package for genetic analysis of populations with mixed reproduction
popReconstruct Reconstruct population counts, fertility, mortality and migration rates of human populations of the recent past
portes Portmanteau Tests for Univariate and Multivariate Time Series Models
portfolio Analysing equity portfolios
portfolioSim Framework for simulating equity portfolio strategies
postCP A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM
postgwas GWAS Post-Processing Utilities
POT Generalized Pareto Distribution and Peaks Over Threshold
potts Markov Chain Monte Carlo for Potts Models
PottsUtils Utility Functions of the Potts Models
powell Powell’s UObyQA algorithm
powerGWASinteraction Power Calculations for Interactions for GWAS
poweRlaw Fitting heavy tailed distributions: the poweRlaw package
powerMediation Power/Sample size calculation for mediation analysis
powerpkg Power analyses for the affected sib pair and the TDT design
powerSurvEpi Power and sample size calculation for survival analysis of epidemiological studies
PowerTOST Power and Sample size based on two one-sided t-tests (TOST) for (bio)equivalence studies
PP Person Parameter estimation
ppcor Partial and Semi-partial (Part) correlation
ppiPre Predict protein-protein interactions based on functional and topological similarities
ppls Penalized Partial Least Squares
ppMeasures Point pattern distances and prototypes
pps Functions for PPS sampling
ppstat Point Process Statistics
PPtree Projection pursuit classification tree
prabclus Functions for clustering of presence-absence, abundance and multilocus genetic data
pracma Practical Numerical Math Functions
PracTools Tools for Designing and Weighting Survey Samples
pragma Provides a pragma / directive / keyword syntax for R
PredictABEL Assessment of risk prediction models
PredictiveRegression Prediction Intervals for Three Basic Statistical Models
predmixcor Classification rule based on Bayesian mixture models with feature selection bias corrected
prefmod Utilities to fit paired comparison models for preferences
PReMiuM Dirichlet Process Bayesian Clustering, Profile Regression
PresenceAbsence Presence-Absence Model Evaluation
PResiduals Probability scale residuals and residual correlations
prettyGraphs publication-quality graphics
prettyR Pretty descriptive stats
prevalence The prevalence package
prevR Estimating regional trends of a prevalence from a DHS
prim Patient Rule Induction Method (PRIM)
primer Functions and data for A Primer of Ecology with R
princurve Fits a Principal Curve in Arbitrary Dimension
PRISMA Protocol Inspection and State Machine Analysis
PrivateLR Differentially private regularized logistic regression
prLogistic Estimation of Prevalence Ratios using Logistic Models
prob Elementary Probability on Finite Sample Spaces
probemapper Connects to QBRC’s ProbeMapper platform
ProbForecastGOP Probabilistic weather forecast using the GOP method
probsvm probsvm: Class probability estimation for Support Vector Machines
pROC display and analyze ROC curves
processdata Process Data
ProDenICA Product Density Estimation for ICA using tilted Gaussian density estimates
prodlim Product Limit Estimation for event history and survival analysis
profanal Implements profile analysis described in Davison & Davenport (2002)
PROFANCY The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
profdpm Profile Dirichlet Process Mixtures
ProfessR Grades Setting and Exam Maker
ProfileLikelihood Profile Likelihood for a Parameter in Commonly Used Statistical Models
profileModel Tools for profiling inference functions for various model classes
profr An alternative display for profiling information
proftools Profile Output Processing Tools for R
ProgGUIinR support package for “Programming Graphical User Interfaces in R”
proj4 A simple interface to the PROJ.4 cartographic projections library
ProjectTemplate Automates the creation of new statistical analysis projects
PropCIs Various confidence interval methods for proportions
PropClust Propensity Clustering and Decomposition
PropScrRand Propensity score methods for assigning treatment in randomized trials
proteomicdesign Optimization of a multi-stage proteomic study
protiq Protein (identification and) quantification based on peptide evidence
proto Prototype object-based programming
protoclass Interpretable classification with prototypes
protoclust Hierarchical clustering with prototypes
PROTOLIDAR PRocess TOol LIdar DAta in R
protr Protein Sequence Feature Extraction with R
protViz Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
proxy Distance and Similarity Measures
PSAgraphics Propensity Score Analysis Graphics
psbcGroup Penalized semi-parametric Bayesian Cox (PSBC) models with shrinkage and grouping priors
PSCBS Analysis of Parent-Specific DNA Copy Numbers
pscl Political Science Computational Laboratory, Stanford University
psd Adaptive, sine-multitaper power spectral density estimation
pseudo Pseudo – observations
psgp Projected Spatial Gaussian Process (psgp) methods
psidR Build panel data sets from PSID raw data
PSM Non-Linear Mixed-Effects modelling using Stochastic Differential Equations
pso Particle Swarm Optimization
pspearman Spearman’s rank correlation test
pspline Penalized Smoothing Splines
PST Probabilistic Suffix Trees
psy Various procedures used in psychometry
psych Procedures for Psychological, Psychometric, and Personality Research
psychometric Applied Psychometric Theory
psychomix Psychometric Mixture Models
psychotools Infrastructure for Psychometric Modeling
psychotree Recursive Partitioning Based on Psychometric Models
psyphy Functions for analyzing psychophysical data in R
psytabs Produce well-formatted tables for psychological research
PTAk Principal Tensor Analysis on k modes
ptinpoly Point-In-Polyhedron Test (2D and 3D)
PtProcess Time Dependent Point Process Modelling
ptw Parametric Time Warping
pumilioR Pumilio in R
PurBayes Bayesian Estimation of Tumor Purity and Clonality
PVAClone Population Viability Analysis with Data Cloning
pvar p-variation
pvclass P-values for Classification
pvclust Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
PVR Computes phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation curve (PSR) (with null and Brownian expectations)
pvsR An R package to interact with the Project Vote Smart API for scientific research
pwr Basic functions for power analysis
PwrGSD Power in a Group Sequential Design
pwt Penn World Table (Versions 5.6, 6.x, 7.x)
pwt8 Penn World Table (Version 8.0)
pxR PC-Axis with R
pycno Pycnophylactic Interpolation
pyramid Functions to draw population pyramid
qat Quality Assurance Toolkit
QCA Qualitative Comparative Analysis
QCA3 Yet another package for Qualitative Comparative Analysis
QCAGUI QCA Graphical User Interface
qcc Quality Control Charts
qdap Bridging the gap between qualitative data and quantitative analysis
qfa Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA)
qgraph Network representations of relationships in data
qLearn Estimation and inference for Q-learning
qlspack Quasi Least Square Package
QLSpline QLSpline
qmap Statistical transformations for post-processing climate model output
qmrparser Parser combinator in R
qp q-order partial correlation graph search algorithm
qpcR Modelling and analysis of real-time PCR data
qPCR.CT qPCR data analysis and plot package
qrfactor Simultaneous simulation of Q and R mode factor analyses with Spatial data
QRM Provides R-language code to examine Quantitative Risk Management concepts
qrnn Quantile regression neural network
QSARdata Quantitative Structure Activity Relationship (QSAR) Data Sets
QT QT Knowledge Management System
qtbase Interface between R and Qt
qtl Tools for analyzing QTL experiments
qtlbim QTL Bayesian Interval Mapping
qtlbook Datasets for the R/qtl book
qtlDesign Design of QTL experiments
qtlhot Inference for QTL Hotspots
qtlmt Tools for mapping multiple complex traits
qtlnet Causal Inference of QTL Networks
QTLRel Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree
qtpaint Qt-based painting infrastructure
qtutils Miscellaneous Qt-based utilities
QuACN QuACN: Quantitative Analysis of Complex Networks
quadprog Functions to solve Quadratic Programming Problems
quadrupen Sparsity by Worst-Case Quadratic Penalties
qualityTools Statistical Methods for Quality Science
qualV Qualitative Validation Methods
Quandl Quandl Data Connection
quantchem Quantitative chemical analysis: calibration and evaluation of results
quantmod Quantitative Financial Modelling Framework
QuantPsyc Quantitative Psychology Tools
quantreg Quantile Regression
quantregForest Quantile Regression Forests
quantregGrowth Growth charts via regression quantiles
quantspec Quantile-based Spectral Analysis of Time Series
QuasiSeq QuasiSeq
questionr Functions to make surveys processing easier
queueing Analysis of Queueing Networks and Models
QUIC Regularized sparse inverse covariance matrix estimation
qvcalc Quasi variances for factor effects in statistical models
QZ Generalized Eigenvalues and QZ Decomposition
R0 Estimation of R0 and real-time reproduction number from epidemics
R1magic Compressive Sampling: Sparse signal recovery utilities
R2admb ADMB to R interface functions
R2BayesX Estimate Structured Additive Regression Models with BayesX
R2Cuba Multidimensional Numerical Integration
r2dRue 2d Rain Use Efficience model
R2G2 Converting R CRAN outputs into Google Earth
R2HTML HTML exportation for R objects
R2jags A Package for Running jags from R
r2lh R to LaTeX and HTML
R2MLwiN Running MLwiN from within R
R2OpenBUGS Running OpenBUGS from R
R2PPT Simple R Interface to Microsoft PowerPoint using rcom or RDCOMClient
R2STATS A GTK GUI for fitting and comparing GLM and GLMM in R
r2stl r2stl, R package for visualizing data using a 3D printer
R2SWF Convert R Graphics to Flash Animations
R2wd Write MS-Word documents from R
R2WinBUGS Running WinBUGS and OpenBUGS from R / S-PLUS
R330 An R package for Stats 330
r4ss R code for Stock Synthesis
race Racing methods for the selection of the best
RAD Fit RAD models to biological data
RadialPlotter Package for statistical age models analysis in optically stimulated luminescence dating
RadioSonde Tools for plotting skew-T diagrams and wind profiles
RadOnc Analytical Tools for Radiation Oncology
RAFM Admixture F-model
rainbow Rainbow plots, bagplots and boxplots for functional data
rAltmetric Retrieves altmerics data for any published paper from
Rambo The Random Subgraph Model
RAMpath Structural Equation Modeling using RAM Notation
ramps Bayesian Geostatistical Modeling with RAMPS
randaes Random number generator based on AES cipher
random True random numbers using
RandomFields Simulation and Analysis of Random Fields
randomForest Breiman and Cutler’s random forests for classification and regression
randomForestSRC Random Forests for Survival, Regression and Classification (RF-SRC)
randomGLM Random General Linear Model Prediction
randomizeBE Function to create a random list for crossover studies
randomLCA Random Effects Latent Class Analysis
randomNames Random name generating function and data set A Parallel Analysis With Polychoric Correlation Matrices
randomSurvivalForest Random Survival Forests
randtoolbox toolbox for pseudo and quasi random number generation and RNG tests
RandVar Implementation of random variables
rangeMapper A platform for the study of macroecology of life history traits
RankAggreg Weighted rank aggregation
rankhazard Rank-hazard plots
RANN Fast Nearest Neighbour Search (wraps Arya and Mount’s ANN library)
RAP Reversal Association Pattern
RAppArmor RAppArmor
rapport A report templating system
RArcInfo Functions to import data from Arc/Info V7.x binary coverages
Rarity Calculation of rarity indices for species and assemblages of species
RaschSampler Rasch Sampler
rasclass Supervised Raster Image Classification
raster raster: Geographic data analysis and modeling
rasterVis Visualization methods for the raster package
rateratio.test Exact rate ratio test
rationalfun Manipulation of Rational Functions
RAtmosphere Standard Atmosperic profiles
rattle Graphical user interface for data mining in R
rAverage Parameter estimation for the averaging model of Information Integration Theory
rawFasta Memory efficient handling of FASTA sequence files, a pure R implementation
rbamtools Reading, manipulation and writing BAM (Binary alignment) files
rbefdata BEFdata R package
rbenchmark Benchmarking routine for R
RBerkeley R API to Oracle Berkeley DB
rBeta2009 The Beta Random Number and Dirichlet Random Vector Generating Functions
RbioRXN RbioRXN – process Rhea and MetaCyc (BioCyc, EcoCyc) biochemical reaction data
rbmn Handling Linear Gaussian Bayesian Networks
rbounds Perform Rosenbaum bounds sensitivity tests for matched and unmatched data
rbugs Fusing R and OpenBugs and Beyond
rbundler Rbundler manages an application’s dependencies systematically and repeatedly
RC Reproducible Computing
R.cache Fast and light-weight caching (memoization) of objects and results to speed up computations
RCALI Calculation of the Integrated Flow of Particles between Polygons
Rcapture Loglinear Models for Capture-Recapture Experiments
rCarto This package builds maps with a full cartographic layout
RCassandra R/Cassandra interface
rcdd rcdd (Computational Geometry)
rcdk rcdk – Interface to the CDK Libraries
rcdklibs rcdklib – CDK libraries packaged for R
Rcell Microscopy Based Cytometry Data Analysis Package
Rcgmin Conjugate gradient minimization of nonlinear functions with box constraints
rChoiceDialogs rChoiceDialogs collection
RCircos Circos 2D Track Plot
RClimMAWGEN RClimMAWGEN (R Climate Index Multi-site Auto-regressive Weather GENeretor): a package to generate time series of climate indices from RMAWGEN generations
rCMA CMA-ES R-to-Java interface
Rcmdr R Commander
RcmdrPlugin.BCA Rcmdr Plug-In for Business and Customer Analytics
RcmdrPlugin.coin Rcmdr Coin Plug-In
RcmdrPlugin.depthTools R commander Depth Tools Plug-In
RcmdrPlugin.doBy Rcmdr doBy Plug-In
RcmdrPlugin.DoE R Commander Plugin for (industrial) Design of Experiments
RcmdrPlugin.doex Rcmdr plugin for Stat 4309 course
RcmdrPlugin.EACSPIR Plugin de R-Commander para el manual EACSPIR
RcmdrPlugin.EBM Rcmdr Evidence Based Medicine Plug-In package
RcmdrPlugin.epack Rcmdr plugin for time series
RcmdrPlugin.EZR R Commander Plug-in for the EZR (Easy R) Package
RcmdrPlugin.HH Rcmdr support for the HH package
RcmdrPlugin.IPSUR An IPSUR Plugin for the R Commander
RcmdrPlugin.KMggplot2 An Rcmdr Plug-In for Kaplan-Meier Plots and Other Plots by Using the ggplot2 Package
RcmdrPlugin.lfstat Rcmdr Plug-In for low flow analysis
RcmdrPlugin.MA Graphical User Interface for Conducting Meta-Analyses in R
RcmdrPlugin.mosaic Adds menu items to produce mosaic plots and assoc plots to Rcmdr
RcmdrPlugin.MPAStats R Commander Plug-in for MPA Statistics
RcmdrPlugin.orloca orloca Rcmdr Plug-in
RcmdrPlugin.plotByGroup Rcmdr plots by group using lattice
RcmdrPlugin.qcc Rcmdr qcc Plug-In
RcmdrPlugin.qual Rcmdr plugin for quality control course
RcmdrPlugin.sampling Tools for sampling in Official Statistical Surveys
RcmdrPlugin.SCDA Rcmdr plugin for designing and analyzing single-case experiments
RcmdrPlugin.seeg Rcmdr Plugin for seeg
RcmdrPlugin.SLC SLC Rcmdr Plug-in
RcmdrPlugin.SM Rcmdr Sport Management Plug-In
RcmdrPlugin.StatisticalURV Statistical URV Rcmdr Plug-In
RcmdrPlugin.survival R Commander Plug-in for the survival Package
RcmdrPlugin.TeachingDemos Rcmdr Teaching Demos Plug-In
RcmdrPlugin.temis Graphical Integrated Text Mining Solution
RcmdrPlugin.UCA UCA Rcmdr Plug-in
Rcolombos Interface to Colombos Compendia using the exposed REST API
RColorBrewer ColorBrewer palettes
Rcplex R interface to CPLEX
Rcpp Seamless R and C++ Integration
RcppArmadillo Rcpp integration for Armadillo templated linear algebra library
RcppBDT Rcpp bindings for the Boost Date_Time library
rcppbugs R binding for cppbugs
RcppClassic Deprecated ‘classic’ Rcpp API
RcppClassicExamples Examples using RcppClassic to interface R and C++
RcppCNPy Rcpp bindings for NumPy files
RcppDE Global optimization by differential evolution in C++
RcppEigen Rcpp integration for the Eigen templated linear algebra library
RcppExamples Examples using Rcpp to interface R and C++
RcppGSL Rcpp integration for GNU GSL vectors and matrices
RcppOctave Seamless Interface to Octave – and Matlab
RcppProgress An interruptible progress bar with OpenMP support for c++ in R packages
RcppRoll Fast rolling functions through Rcpp and RcppArmadillo
RcppSMC Rcpp bindings for Sequential Monte Carlo
RcppXts Interface the xts API via Rcpp
rcqp Interface to the Corpus Query Protocol
Rcsdp R interface to the CSDP semidefinite programming library
rCUR CUR decomposition package
RCurl General network (HTTP/FTP/…) client interface for R
Rd2roxygen Convert Rd to roxygen documentation and utilities to improve documentation
rda Shrunken Centroids Regularized Discriminant Analysis
rdatamarket Data access API for
rdd Regression Discontinuity Estimation
rdetools Relevant Dimension Estimation (RDE) in Feature Spaces
R.devices Unified handling of graphics devices
RDIDQ It perform Quality check on data
RDieHarder R interface to the dieharder RNG test suite
Rdistance Distance sampling analyses
rDNA R Bindings for the Discourse Network Analyzer
Rdpack Update and manipulate Rd documentation objects
Rdrools A rules engine for R based on Drools
Rdroolsjars Rdrools jars
rdryad Dryad API interface
RDS R Functions for Respondent-Driven Sampling
Rdsm Threads Environment for R
RDSTK An R wrapper for the Data Science Toolkit API
rdyncall Improved Foreign Function Interface (FFI) and Dynamic Bindings to C Libraries (e.g. OpenGL)
ReacTran Reactive transport modelling in 1D, 2D and 3D
readbitmap Read bitmap images (BMP,JPEG,PNG) without external dependencies
readBrukerFlexData Reads mass spectrometry data in Bruker *flex format
Read.isi Automated access to old World Fertility Survey data saved in fixed-width format based on ISI-formatted codebooks
readMETEO Weather Data Download from WWW.METEOGALICIA.COM
readMLData Reading machine learning benchmark data sets from different sources in their original format
readMzXmlData Reads mass spectrometry data in mzXML format
reams Resampling-Based Adaptive Model Selection
Rearrangement Monotonize point and interval functional estimates by rearrangement
REBayes Empirical Bayes Estimation and Inference in R
rebird Interface to eBird
rebmix The Rebmix Package
reccsim Simulation of Rare Events Case-Control Studies
ReCiPa Redundancy Control in Pathways databases
recluster Ordination methods for the analysis of beta-diversity indices
recommenderlab Lab for Developing and Testing Recommender Algorithms
recommenderlabBX Book-Crossing Dataset (BX) for recommenderlab
recommenderlabJester Jester Dataset for recommenderlab
RecordLinkage Record Linkage in R
Records Record Values and Record Times
REEMtree Regression Trees with Random Effects for Longitudinal (Panel) Data
ref References for R
refGenome Managing data from Ensembl and UCSC genome browsers
refund refund: Regression with Functional Data
REGENT REGENT: Risk Estimation for Genetic and Environmental Traits
registry Registry infrastructure
reglogit Simulation-based Regularized Logistic Regression
regress Gaussian linear models with linear covariance structure
regsubseq Detect and Test Regular Sequences and Subsequences
regtest Regression testing
rehh Searching for footprints of selection using Haplotype Homozygosity based tests
rela Item Analysis Package with Standard Errors
relaimpo Relative importance of regressors in linear models
relations Data Structures and Algorithms for Relations
RelativeRisk Relative Risk
relax relax – R Editor for Literate Analysis and lateX
relaxnet Relaxation of glmnet models (as in relaxed lasso, Meinshausen 2007)
relaxo Relaxed Lasso
reldist Relative Distribution Methods
relevent Relational Event Models
Reliability Functions for estimating parameters in software reliability models
ReliabilityTheory Tools for structural reliability analysis
reliaR Package for some probability distributions
relimp Relative Contribution of Effects in a Regression Model
relSim Relative Simulator
relsurv Relative survival
remix Remix your data
rEMM Extensible Markov Model (EMM) for Data Stream Clustering in R
remMap Regularized Multivariate Regression for Identifying Master Predictors
Renext Renewal method for extreme values extrapolation
RenextGUI GUI for Renext
rentrez Entrez in R
Reol R interface to the Encyclopedia of Life
RepeatedHighDim Detection of global group effect in microarrays data
repmis A collection of miscellaneous tools for reproducible research with R
repolr Repeated measures proportional odds logistic regression
reportr A general message and error reporting system
reports An R package to assist in the workflow of writing academic articles and other reports
reporttools Generate LaTeX tables of descriptive statistics
REPPlab R interface to EPP-lab, a Java program for exploratory projection pursuit
represent Determine the representativity of two multidimensional data sets
REQS R/EQS Interface
reshape Flexibly reshape data
reshape2 Flexibly reshape data: a reboot of the reshape package
reshapeGUI A GUI for the reshape2 and plyr packages
ResistorArray electrical properties of resistor networks
ResourceSelection Resource Selection (Probability) Functions for Use-Availability Data
restlos Robust estimation of location and scatter
restorepoint Debugging with restore points
retimes Reaction Time Analysis
review Manage Review Logs
reweight Adjustment of Survey Respondent Weights
rexpokit R wrappers for EXPOKIT; other matrix functions
rFerns Random ferns classifier
RFGLS a family GWAS data-analysis tool that uses a generalized least squares method to perform single-marker association analysis
rfigshare an R interface to
R.filesets Easy handling of and access to files organized in structured directories
rfishbase R Interface to FishBASE
rfisheries R interface for fisheries data
Rfit Rank Estimation for Linear Models
RFLPtools Tools to analyse RFLP data
RfmriVC Varying stimulus coefficient fMRI models in R
RFOC Graphics for Spherical Distributions and Earthquake Focal Mechanisms
RForcecom RForcecom provides the connection to and from R
rforensicbatwing BATWING for calculating forensic trace-suspect match probabilities
rfPermute Estimate permutation p-values for Random Forest importance metrics
rgam Robust Generalized Additive Model
rGammaGamma Gamma convolutions for methylation array background correction
rgbif Interface to the Global Biodiversity Information Facility API methods
Rgbp Bayesian Hierarchical Modeling and Frequentist Method Check
RGCCA RGCCA and Sparse GCCA for multi-block data analysis
rgcvpack R Interface for GCVPACK Fortran Package
rgdal Bindings for the Geospatial Data Abstraction Library
rgenoud R version of GENetic Optimization Using Derivatives
rgeos Interface to Geometry Engine – Open Source (GEOS)
rgexf An R package to build GEXF graph files
rggobi Interface between R and GGobi
RghcnV3 Global Historical Climate Network Version 3
RGIFT Create quizzes in GIFT Format
rgl 3D visualization device system (OpenGL)
Rglpk R/GNU Linear Programming Kit Interface
Rgnuplot Rgnuplot, R interface for gnuplot
RgoogleMaps Overlays on Google map tiles in R
rgp R genetic programming framework
rgr The GSC Applied Geochemistry EDA Package
RGraphics Data and Functions from the book R Graphics, Second Edition
rgrs Functions to make R usage in social sciences easier (in french)
RGtk2 R bindings for Gtk 2.8.0 and above
RGtk2Extras Data frame editor and dialog making wrapper for RGtk2
RH2 DBI/RJDBC interface to h2 Database
rHadoopClient hadoop client interface for R
Rhh Calculating multilocus heterozygosity and heterozygosity-heterozygosity correlation
RHmm Hidden Markov Models simulations and estimations
rhosp Side effect risks in hospital : simulation and estimation
rHpcc Interface between HPCC and R
RHRV Heart rate variability analysis of ECG data
RHT Regularized Hotelling’s T-square Test for Pathway (Gene Set) Analysis
R.huge Methods for accessing huge amounts of data [DEPRECATED]
ri ri: R package for performing randomization-based inference for experiments
rich Computes and compares species richnesses
ridge Ridge Regression with automatic selection of the penalty parameter
Ridit Ridit Analysis (An extension of the Kruskal-Wallis Test.)
RiDMC R interface to the idmclib library
RIFS Random Iterated Function System (RIFS)
rImpactStory Retrieves altmetrics from ImpactStory. See for more about the metrics
rindex Indexing for R
ringbuffer Ring buffer (circular buffer) data structure
ringscale Ringscale
RInside C++ classes to embed R in C++ applications
RInSp R Individual Specialization (RInSp) package
rioja Analysis of Quaternary Science Data
risaac A fast cryptographic random number generator using ISAAC by Robert Jenkins
riskRegression Risk regression for survival analysis
risksetROC Riskset ROC curve estimation from censored survival data
RISmed Download content from NCBI databases
Ritc Isothermal Titration Calorimetry (ITC) Data Analysis
rite The Right Editor to Write R
RItools Randomization inference tools
riv Robust instrumental variables estimator
Rivivc In vitro in vivo correlation linear level A
RJaCGH Reversible Jump MCMC for the analysis of CGH arrays
rjags Bayesian graphical models using MCMC
rJava Low-level R to Java interface
rJavax rJava extensions
RJDBC Provides access to databases through the JDBC interface
rje Miscellaneous useful functions
Rjms R messaging using ActiveMQ and jms
Rjmsjars Rjms jars
rJPSGCS R-interface to gene drop Java Programs for Statistical Genetics and Computational Statistics (JPSGCS)
rjson JSON for R
RJSONIO Serialize R objects to JSON, JavaScript Object Notation
rJython R interface to Python via Jython
RKEA R/KEA interface
Rknots Rknots
rkt Mann-Kendall test, Seasonal and Regional Kendall Tests
Rlab Functions and Datasets Required for ST370 class
Rlabkey Data exchange between R and LabKey Server
rlandscape Generates random landscapes with specifiable spatial characteristics
RLastFM R interface to API
rlecuyer R interface to RNG with multiple streams
rlme Rank-based Estimation and Prediction in Random Effects Nested Models
RLRsim Exact (Restricted) Likelihood Ratio tests for mixed and additive models
RM2 Revenue Management and Pricing Package
rmac calculate RMAC or FMAC agreement coefficients
RMallow Fit Multi-Modal Mallows’ Models to ranking data
Rmalschains Continuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains) in R
RMark R Code for MARK Analysis
R.matlab Read and write of MAT files together with R-to-MATLAB connectivity
RMAWGEN RMAWGEN (R Multi-site Auto-regressive Weather GENerator), a package to generate daily time series of precipitation and temperature from monthly mean values
RMC Functions for fitting Markov models
RMendeley Interface to Mendeley API methods
RMessenger IM Client for R
rmeta Meta-analysis
R.methodsS3 Utility function for defining S3 methods
rmgarch Multivariate GARCH models
rminer Simpler use of data mining methods (e.g. NN and SVM) in classification and regression
Rmisc Rmisc: Ryan Miscellaneous
Rmixmod An interface of MIXMOD
rmmseg4j R interface to the Java Chinese word segmentation system of mmseg4j
RMongo MongoDB Client for R
rmongodb R-MongoDB driver
Rmosek The R-to-MOSEK Optimization Interface
rmp Rounded Mixture Package. Performs probability mass function estimation with Dirichlet process mixtures of rounded kernels
Rmpfr R MPFR – Multiple Precision Floating-Point Reliable
Rmpi Interface (Wrapper) to MPI (Message-Passing Interface)
rms Regression Modeling Strategies
rms.gof Root-mean-square goodness-of-fit test for simple null hypothesis
RMTstat Distributions, Statistics and Tests derived from Random Matrix Theory
RMySQL R interface to the MySQL database
RnavGraph Using graphs as a navigational infrastructure
RnavGraphImageData Some image data used in the RnavGraph package demos
RNCBI The java ncbi interface to R
RNCBIAxis2Libs Axis2 libraries for use in the R environment
RNCBIEUtilsLibs EUtils libraries for use in the R environment
RNCEP Obtain, organize, and visualize NCEP weather data
RND Risk Neutral Density
rneos rneos: XML-RPC Interface to NEOS
RNetCDF R Interface to NetCDF Datasets
RNetLogo Provides an interface to the agent-based modelling platform NetLogo
rngSetSeed Initialization of the R base random number generator Mersenne-Twister with a vector of an arbitrary length
rngtools Utility functions for working with Random Number Generators
rngWELL toolbox for WELL random number generators
rngwell19937 WELL19937a random number generator implemented with 53 bit output
Rniftilib Rniftilib – R Interface to NIFTICLIB (V2.0.0: 2010-07-20)
RNiftyReg Medical image registration using the NiftyReg library
ROAuth R interface for OAuth
RobAStBase Robust Asymptotic Statistics
robCompositions Robust Estimation for Compositional Data
robeth R functions for robust statistics
robfilter Robust Time Series Filters
RobLox Optimally robust influence curves and estimators for location and scale
RobLoxBioC Infinitesimally robust estimators for preprocessing omics data
RobRex Optimally robust influence curves for regression and scale
robust Robust Library
RobustAFT Truncated Maximum Likelihood fit and Robust Accelerated Failure Time regression for Gaussian and log-Weibull case
robustbase Basic Robust Statistics
robustfa An Object Oriented Framework for Robust Factor Analysis
robustgam Robust Estimation for Generalized Additive Models
robustHD Robust methods for high-dimensional data
robustlmm Robust Linear Mixed Effects Models
robustloggamma Robust estimation of the generalized log gamma model
RobustRankAggreg Methods for robust rank aggregation
robustreg Robust Regression Functions
robustX eXperimental Functionality for Robust Statistics
rocc ROC based classification
rockchalk Regression Estimation and Presentation
rococo RObust rank COrrelation COefficient and test
rocplus ROC, Precision-Recall, Convex Hull and other plots
ROCR Visualizing the performance of scoring classifiers
ROCwoGS Non-parametric estimation of ROC curves without Gold Standard Test
RODBC ODBC Database Access
RODM R interface to Oracle Data Mining
ROI R Optimization Infrastructure
ROI.plugin.glpk ROI-plugin GLPK
ROI.plugin.quadprog ROI-plugin quadprog
ROI.plugin.symphony ROI-plugin symphony
rolasized Solarized colours in R
R.oo R object-oriented programming with or without references
Rook Rook – a web server interface for R
rootSolve Nonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations
ropensnp Interface to OpenSNP API methods
ROptEst Optimally robust estimation
ROptEstOld Optimally robust estimation – old version
ROptRegTS Optimally robust estimation for regression-type models
ror Robust Ordinal Regression MCDA library
ROracle OCI based Oracle database interface for R
ROSE ROSE: Random Over-Sampling Examples
roxygen Literate Programming in R
roxygen2 In-source documentation for R
roxyPackage Utilities to automate package builds
royston Royston’s H Test: Multivariate Normality Test
rpanel Simple interactive controls for R using the tcltk library
rpart Recursive Partitioning
rpart.plot Plot rpart models. An enhanced version of plot.rpart
rpartScore Classification trees for ordinal responses
RPCLR RPCLR (Random-Penalized Conditional Logistic Regression)
rpf Response Probability Functions
rphast R interface to PHAST software for comparative genomics
rPlant R interface to the iPlant Discovery Environment
rplos Interface to PLoS Journals search and altmetrics API’s
rplotengine R as a plotting engine
RPMG Graphical User Interface (GUI) for interactive R analysis sessions
RPMM Recursively Partitioned Mixture Model
Rpoppler PDF tools based on Poppler
rportfolios Random portfolio generation
RPostgreSQL R interface to the PostgreSQL database system
RPPanalyzer Reads, annotates, and normalizes reverse phase protein array data
RProtoBuf R Interface to the Protocol Buffers API
rpsychi Statistics for psychiatric research
rpubchem rpubchem – Interface to the PubChem Collection
rpud R functions for computation on GPU
RPyGeo ArcGIS Geoprocessing in R via Python
rPython Package allowing R to call Python
RQDA R-based Qualitative Data Analysis
Rquake Seismic Hypocenter Determination
RQuantLib R interface to the QuantLib library
Rramas Matrix population models
rrBLUP Ridge regression and other kernels for genomic selection
rrBlupMethod6 Re-parametrization of RR-BLUP to allow for a fixed residual variance
rrcov Scalable Robust Estimators with High Breakdown Point
rrcovHD Robust multivariate Methods for High Dimensional Data
rrcovNA Scalable Robust Estimators with High Breakdown Point for Incomplete Data
rrdf rrdf – support for the Resource Description Framework
rrdflibs rrdflibs – package with Jena and Apache HTTP libraries for use with rrdf
rredis Redis client for R
RRF Regularized Random Forest
rriskBayes Predefined Bayes models fitted with Markov chain Monte Carlo (MCMC) (related to the ‘rrisk’ project)
rriskDistributions Fitting distributions to given data or known quantiles
rrlda Robust Regularized Linear Discriminant Analysis
R.rsp Dynamic generation of scientific reports
rrules Generic rule engine for R
RSA Response surface analysis
RSADBE Data related to the book “R Statistical Application Development by Example”
rsae Robust Small Area Estimation
RSAGA SAGA Geoprocessing and Terrain Analysis in R
RSAP SAP Netweaver RFC connector for R
RSclient Client for Rserve
rscproxy statconn: provides portable C-style interface to R (StatConnector)
RSDA RSDA – R to Symbolic Data Analysis
RSearchYJ RSearchYJ
RSeed borenstein analysis
rseedcalc Estimating the proportion of genetically modified stacked seeds in seedlots via multinomial group testing
RSEIS Seismic Time Series Analysis Tools
rsem Robust Structural Equation Modeling with Missing Data and Auxiliary Variables
Rserve Binary R server
rSFA Slow Feature Analysis in R
rsgcc Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data
RSGHB Functions for Hierarchical Bayesian Estimation: A Flexible Approach
RSiena Siena – Simulation Investigation for Empirical Network Analysis
RSiteCatalyst Adobe (Omniture) Reporting API
RSKC Robust sparse K-means
rsm Response-surface analysis
RSNNS Neural Networks in R using the Stuttgart Neural Network Simulator (SNNS)
RSofia Port of sofia-ml ( to R
Rsolnp General Non-linear Optimization
rspa Adapt numerical records to fit (in)equality restrictions with the Successive Projection Algorithm
rspear Calculate SPEARpesticide in R (
rsprng R interface to SPRNG (Scalable Parallel Random Number Generators)
RSQLite SQLite interface for R
RSQLite.extfuns Math and String Extension Functions for RSQLite
Rssa A collection of methods for singular spectrum analysis
rstiefel Random orthonormal matrix generation on the Stiefel manifold
rstream Streams of random numbers
Rsundials Suite of Nonlinear Differential Algebraic Equations Solvers in R
RSurvey Analysis of Spatially Distributed Data
RSvgDevice An R SVG graphics device
RSVGTipsDevice An R SVG graphics device with dynamic tips and hyperlinks
Rsymphony Symphony in R
rSymPy R interface to SymPy computer algebra system
rtape Manage and manipulate large collections of R objects stored as tape-like files
RTConnect Tools for analyzing sales report files of iTunes Connect
RTDAmeritrade RTDAmeritrade
RTextTools Automatic Text Classification via Supervised Learning
rtf Rich Text Format (RTF) Output
rtfbs R Transcription Factor Binding Site identification tool
rtiff A tiff reader for R
RTisean R interface to Tisean algorithms
RTOMO Visualization for seismic tomography
rtop Interpolation of data with variable spatial support
RTriangle Triangle – A 2D Quality Mesh Generator and Delaunay Triangulator
rts Raster time series analysis
Rttf2pt1 Package for ttf2pt1 program
rugarch Univariate GARCH models
RUnit R Unit test framework
Runiversal Runiversal – Package for converting R objects to Java variables and XML
runjags Interface utilities for MCMC models in Just Another Gibbs Sampler (JAGS) using parallel and distributed computing methods
Runuran R interface to the UNU.RAN random variate generators
RunuranGUI A GUI for the UNU.RAN random variate generators
R.utils Various programming utilities
rv Simulation-based random variable objects
RVAideMemoire Diverse basic statistical and graphical functions
Rvelslant Downhole Seismic Analysis in R
rvertnet Search VertNet database from R
rvgtest Tools for Analyzing Non-Uniform Pseudo-Random Variate Generators
rvHPDT Calling haplotype-based and variant-based pedigree disequilibrium test for rare variants in pedigrees
RVideoPoker Play Video Poker with R
Rvmmin Variable metric nonlinear function minimization with bounds constraints
RVowpalWabbit R interface to the Vowpal Wabbit
RVtests Rare Variant Tests
Rwave Time-Frequency analysis of 1-D signals
RWeather R wrapper around the Yahoo! Weather, Google Weather and NOAA APIs
RWeka R/Weka interface
RWekajars R/Weka interface jars
RWiener Wiener process distribution functions
RWinEdt R Interface to WinEdt
Rwinsteps Running Winsteps in R
rwm R Workspace Management
rworldmap Mapping global data, vector and raster
rworldxtra Country boundaries at high resolution
rwt Rice Wavelet Toolbox wrapper
RxCEcolInf R x C Ecological Inference With Optional Incorporation of Survey Information
RXKCD Get XKCD comic from R
RXMCDA An XMCDA parser for R
RXshrink Maximum Likelihood Shrinkage via Generalized Ridge or Least Angle Regression
Ryacas R interface to the yacas computer algebra system
rysgran Grain size analysis, textural classifications and distribution of unconsolidated sediments
Rz GUI Tool for Data Management like SPSS or Stata
rzmq R binding for zmq (
s20x Stats 20x
s4vd Biclustering via sparse singular value decomposition incorporating stability selection
sac Semiparametric Analysis of Changepoint
sae Small Area Estimation
saemix Stochastic Approximation Expectation Maximization (SAEM) algorithm
SAFD Statistical Analysis of Fuzzy Data
safeBinaryRegression Safe Binary Regression
SAM Sparse Additive Modelling
SamplerCompare A framework for comparing the performance of MCMC samplers
sampleSelection Sample Selection Models
samplesize Sample size calculation for various t-Tests and Wilcoxon-Test
SampleSizeMeans Sample size calculations for normal means
SampleSizeProportions Calculating sample size requirements when estimating the difference between two binomial proportions
sampling Survey Sampling
samplingbook Survey Sampling Procedures
samplingEstimates Sampling Estimates
SamplingStrata Optimal stratification of sampling frames for multipurpose sampling surveys
samplingVarEst Sampling Variance Estimation
sampSurf Sampling Surface Simulation for Areal Sampling Methods
samr SAM: Significance Analysis of Microarrays
SAMURAI Sensitivity Analysis of a Meta-analysis with Unpublished but Registered Analytical Investigations
sandwich Robust Covariance Matrix Estimators
sanon Stratified Analysis with Nonparametric covariable adjustment
sapa Spectral Analysis for Physical Applications
SAPP Statistical Analysis of Point Processes
sas7bdat SAS Database Reader (experimental)
SAScii Import ASCII files directly into R using only a SAS input script
SASmixed Data sets from “SAS System for Mixed Models”
SASPECT Significant AnalysiS of PEptide CounTs
SASxport Read and Write SAS XPORT Files
SAVE Bayesian emulation, calibration and validation of computer models
saves Fast load variables
saws Small-Sample Adjustments for Wald tests Using Sandwich Estimators
sBF Smooth Backfitting
sbgcop Semiparametric Bayesian Gaussian copula estimation and imputation
SBSA Simplified Bayesian Sensitivity Analysis
sca Simple Component Analysis
scagnostics Compute scagnostics – scatterplot diagnostics
scaleboot Approximately Unbiased P-values via Multiscale Bootstrap
scales Scale functions for graphics
scam Shape constrained additive models
scape Statistical Catch-at-Age Plotting Environment
scapeMCMC MCMC Diagnostic Plots
scar Shape-Constrained Additive Regression: a Maximum Likelihood Approach
scaRabee Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models
scatterplot3d 3D Scatter Plot
SCEPtER Stellar CharactEristics Pisa Estimation gRid
SCEPtERextras Additional grids for SCEPtER
SCGLR Supervised Component Generalized Linear Regression (SCGLR)
schoolmath Functions and datasets for math used in school
schoRsch Tools for analyzing factorial experiments
schwartz97 A package on the Schwartz two-factor commodity model
scidb An R interface to SciDB
SciencePo A Tool for Analyzing Political Behaviour
scio Sparse Column-wise Inverse Operator
sciplot Scientific Graphing Functions for Factorial Designs
SciViews SciViews GUI API – Main package
SCMA Single-Case Meta-Analysis
scoring Proper scoring rules
ScottKnott The ScottKnott Clustering Algorithm
scout Implements the Scout method for Covariance-Regularized Regression
SCperf Supply Chain Perform
scrapeR Tools for Scraping Data from HTML and XML Documents
ScreenClean Screen and clean variable selection procedures
scrime Analysis of High-Dimensional Categorical Data such as SNP Data
scriptests Transcript-based unit tests that are easy to create and maintain
SCRT Single-Case Randomization Tests
scuba Scuba diving calculations and decompression models
SCVA Single-Case Visual Analysis
sda Shrinkage Discriminant Analysis and CAT Score Variable Selection
SDaA Sampling: Design and Analysis
SDBP Calculate the third-order accurate Unbiased P-values via Speedy double bootstrap method
sdcMicro Statistical Disclosure Control methods for the production of public- and scientific-use files
sdcMicroGUI Graphical user interface for package sdcMicro
sdcTable Methods for SDC (statistical disclosure control) in tabular data
SDD Serial Dependence Diagrams
SDDA Stepwise Diagonal Discriminant Analysis
sddpack Semidiscrete Decomposition
sde Simulation and Inference for Stochastic Differential Equations
sdef Synthesizing List of Differentially Expressed Features
SDisc Integrated methodology for the identification of homogeneous subtypes in data
SDMTools Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
sdnet Soft Discretization-based Bayesian Network Inference
sdprisk Measures of Risk for the Compound Poisson Risk Process with Diffusion
sdtoolkit Scenario Discovery Tools to Support Robust Decision Making
seacarb seawater carbonate chemistry with R
SearchTrees Spatial Search Trees
seas Seasonal analysis and graphics, especially for climatology
season Seasonal analysis of health data
SECP Statistical Estimation of Cluster Parameters (SECP)
secr Spatially explicit capture-recapture
seeg Statistics for Environmental Sciences, Engineering, and Geography
seem Simulation of Ecological and Environmental Models
SEER2R reading and writing SEER*STAT data files
SEERaBomb SEER Setup and Use with A-Bomb Data
seewave Sound analysis and synthesis
seg A set of tools for residential segregation research
segmented Segmented relationships in regression models with breakpoints/changepoints estimation
Segmentor3IsBack A Fast Segmentation Algorithm
SE.IGE Standard errors of estimated genetic parametes
Sejong KoNLP static dictionaries and Sejong project resources
SEL Semiparametric elicitation
selectiongain Expected gain from multi-stage selection and its optimization
selectMeta Estimation of weight functions in meta analysis
selectr Translate CSS Selectors to XPath Expressions
SeleMix Selective Editing via Mixture models
sem Structural Equation Models
semdiag Structural equation modeling diagnostics
semGOF Goodness-of-fit indexes for structural equation models
SEMID Identifiability of linear structural equation models
SemiMarkov Multi-States Semi-Markov Models
SemiPar Semiparametic Regression
SemiParBIVProbit Semiparametric Bivariate Probit Modelling
SemiParSampleSel Semiparametric Sample Selection Modelling with Continuous Response
semisupKernelPCA Kernel PCA projection, and semi-supervised variant
SEMModComp Model Comparisons for SEM
semPlot Path diagrams and visual analysis of various SEM packages’ output
semPLS Structural Equation Modeling Using Partial Least Squares
semTools Useful tools for structural equation modeling
sendmailR send email using R
sendplot Tool for sending interactive plots with tool-tip content
sensitivity Sensitivity Analysis
SensitivityCaseControl Sensitivity Analysis for Case-Control Studies
sensitivityPStrat Principal Stratification Sensitivity Analysis Functions
SensoMineR Sensory data analysis with R
sensR Thurstonian models for sensory discrimination
SenSrivastava Datasets from Sen & Srivastava
separationplot Separation Plots
seq2R Simple method to detect compositional changes in genomic sequences
seqCBS CN Profiling using Sequencing and CBS
SeqGrapheR Simple GUI for graph based visualization of cluster of DNA sequence reads
seqinr Biological Sequences Retrieval and Analysis
seqMeta Efficient meta analysis for the SKAT test
seqminer Efficiently Read Sequencing Data (VCF format, METAL format) into R
seqmon Sequential Monitoring of Clinical Trials
seqPERM Generates a permutation matrix based upon a sequence
seqRFLP Simulation and visualization of restriction enzyme cutting pattern from DNA sequences
sequences Generic and biological sequences
Sequential Exact Sequential Analysis for Poisson Data
seriation Infrastructure for seriation
SesIndexCreatoR Computation and visualization of socioeconomic indices and categories distributions
session Functions for interacting with, saving and restoring R sessions
sessionTools Tools for saving, restoring and teleporting R sessions
SetMethods SetMethods: A Package Companion to “Set-Theoretic Methods for the Social Sciences”
setRNG Set (Normal) Random Number Generator and Seed
sets Sets, Generalized Sets, Customizable Sets and Intervals
setwidth Set the value of options(“width”) on terminal emulators
severity Mayo’s Post-data Severity Evaluation
sExtinct Calculates the historic date of extinction given a series of sighting events
sfa Stochastic Frontier Analysis
sfsmisc Utilities from Seminar fuer Statistik ETH Zurich
sft Functions for Systems Factorial Technology Analysis of Data
SGCS Spatial Graph based Clustering Summaries for spatial point patterns
sgeostat An Object-oriented Framework for Geostatistical Modeling in S+
SGL Fit a GLM (or cox model) with a combination of lasso and group lasso regularization
sgof Multiple hypotheses testing
SGP An R Package for the Calculation and Visualization of Student Growth Percentiles & Percentile Growth Trajectories
sGPCA Sparse Generalized Principal Component Analysis
SGPdata Exemplar data sets for SGP analyses
sgr Sample Generation by Replacement
shape Functions for plotting graphical shapes, colors
shapefiles Read and Write ESRI Shapefiles
shapes Statistical shape analysis
SharpeR Statistical significance of Sharpe ratio
sharx Models and Data Sets for the Study of Species-Area Relationships
shiny Web Application Framework for R
SHIP SHrinkage covariance Incorporating Prior knowledge
shotGroups Analyze shot group data
shrink Global, Parameterwise, and Joint Shrinkage of Regression Coefficients
siar Stable Isotope Analysis in R
sideChannelAttack Side Channel Attack
sidier SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
sifds Swedish inflation forecast data set
sig Print function signatures
sigclust Statistical Significance of Clustering
SightabilityModel Wildlife Sightability Modeling
signal Signal processing
signalextraction Real-Time Signal Extraction (Direct Filter Approach)
SigWinR SigWin-detector implementation in R
SII Calculate ANSI S3.5-1997 Speech Intelligibility Index
simba A Collection of functions for similarity analysis of vegetation data
simboot Simultaneous inference for diversity indices
SimComp Simultaneous Comparisons for Multiple Endpoints
SimCorMultRes Simulates Correlated Multinomial Responses
simctest Safe implementation of Monte Carlo tests
simecol Simulation of ecological (and other) dynamic systems
simex SIMEX- and MCSIMEX-Algorithm for measurement error models
simexaft simexaft
simFrame Simulation framework
SimHap A comprehensive modeling framework for epidemiological outcomes and a simulation-based approach to haplotypic analysis of population-based data
Simile Interact with Simile models
SIMMS Subnetwork Integration for Multi-Modal Signatures
simMSM Simulation of event histories based on nonlinear hazard rate functions and potentially nonlinear covariate effects
simPH Tools for simulating and plotting quantities of interest estimated from Cox Proportional Hazards models
simpleboot Simple Bootstrap Routines
SimpleTable Bayesian Inference and Sensitivity Analysis for Causal Effects from 2 x 2 and 2 x 2 x K Tables in the Presence of Unmeasured Confounding
simPopulation Simulation of synthetic populations for surveys based on sample data
Simpsons Detecting Simpson’s Paradox
simsem SIMulated Structural Equation Modeling
simSummary Simulation summary
SimultAnR Correspondence and Simultaneous Analysis
SIN A SINful Approach to Selection of Gaussian Graphical Markov Models
sinartra A simple web app framework for R, based on sinatra
sirad Functions for calculating daily solar radiation and evapotranspiration
sirt Supplementary Item Response Theory Models
SIS Sure Independence Screening
sisus SISUS: Stable Isotope Sourcing using Sampling
sitools Format a number to a string with SI prefix
SixSigma Six Sigma Tools for Quality and Process Improvement
SiZer SiZer: Significant Zero Crossings
sjdbc JDBC Driver Interface
SKAT SNP-set (Sequence) Kernel Association Test
skatMeta Efficient meta analysis for the SKAT test
SkewHyperbolic The Skew Hyperbolic Student t-Distribution
skewt The Skewed Student-t Distribution
skewtools Information Tools for analyze Skew-Elliptical distributions and related models
Skillings.Mack The Skillings-Mack test Statistic for block designs with missing observations
skmeans Spherical k-Means Clustering
slam Sparse Lightweight Arrays and Matrices
SLC Slope and level change
Sleuth2 Data sets from Ramsey and Schafer’s “Statistical Sleuth (2nd ed)”
Sleuth3 Data sets from Ramsey and Schafer’s “Statistical Sleuth (3rd ed)”
SLHD Maximin-Distance (Sliced) Latin Hypercube Designs
SlimPLS SlimPLS multivariate feature selection
sltl Time Series Decomposition using Loess and Harmonic Regression
sm Smoothing methods for nonparametric regression and density estimation
smaa Stochastic Multi-criteria Acceptability Analysis
smacof SMACOF for Multidimensional Scaling
smart Sparse Multivariate Analysis via Rank Transformation
SmarterPoland A set of tools developed by the Foundation
smatr (Standardised) Major Axis Estimation and Testing Routines
SMC Sequential Monte Carlo (SMC) Algorithm
smco A simple Monte Carlo optimizer using adaptive coordinate sampling
SMCP Smoothed minimax concave penalization (SMCP) method for genome-wide association studies
SMCRM Data Sets for Statistical Methods in Customer Relationship Management by Kumar and Petersen (2012)
smcure Fit Semiparametric Mixture Cure Models
smcUtils Utility functions for sequential Monte Carlo
smdata Data to accompany Smithson & Merkle, 2014
smdc Document Similarity
sme Smoothing-splines Mixed-effects Models
SMFI5 R functions and data from Chapter 5 of ‘Statistical Methods for Financial Engineering’
smfsb SMfSB 2e: Stochastic Modelling for Systems Biology, second edition
SMIR Companion to Statistical Modelling in R
smirnov Provides two taxonomic coefficients from E. S. Smirnov “Taxonomic analysis” (1969) book
SmithWilsonYieldCurve Smith-Wilson Yield Curve Construction
SMNCensReg Fitting univariate censored regression model under the scale mixture of normal distributions
SmoothHazard Fitting illness-death model for interval-censored data
smoothHR Smooth Hazard Ratio Curves taking a Reference Value
smoothie Two-dimensional Field Smoothing
smoothmest Smoothed M-estimators for 1-dimensional location
smoothSurv Survival Regression with Smoothed Error Distribution
smoothtail Smooth Estimation of GPD Shape Parameter
SMPracticals Practicals for use with Davison (2003) Statistical Models
SMR Studentized Midrange Distribution
sms Spatial Microsimulation
SMVar Structural Model for variances
sn The skew-normal and skew-t distributions
sna Tools for Social Network Analysis
snort Social Network-Analysis On Relational Tables
snow Simple Network of Workstations
Snowball Snowball Stemmers
SnowballC Snowball stemmers based on the C libstemmer UTF-8 library
snowfall Easier cluster computing (based on snow)
snowFT Fault Tolerant Simple Network of Workstations
snpEnrichment SNPs enrichment analysis
SNPmaxsel Maximally selected statistics for SNP data
SNPMClust A bivariate Gaussian genotype clustering and calling algorithm for Illumina microarrays
snp.plotter snp.plotter
SNPRelate Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
snpStatsWriter Flexible writing of snpStats objects to flat files
SNPtools Accessing, subsetting and plotting mouse SNPs
SNSequate Standard and Nonstandard Statistical Models and Methods for Test Equating
SOAR Memory management in R by delayed assignments
SoDA Functions and Examples for “Software for Data Analysis”
SODC Optimal Discriminant Clustering(ODC) and Sparse Optimal Discriminant Clustering(SODC)
softclassval Soft classification performance measures
softImpute matrix completion via iterative soft-thresholded svd
soilDB Soil Database Interface
SoilR Models of Soil Organic Matter Decomposition
soil.spec Soil spectral file conversion, data exploration and regression functions
soiltexture Functions for soil texture plot, classification and transformation
soilwater soilwater: Implements parametric formulas for soil water retention or conductivity curve
solaR Solar Photovoltaic Systems
SOLOMON Parentage analysis
som Self-Organizing Map
soma General-purpose optimisation with the Self-Organising Migrating Algorithm
someKfwer Controlling the Generalized Familywise Error Rate
someMTP Some Multiple Testing Procedures
somplot Visualisation of hexagonal Kohonen maps
soobench Single Objective Optimization Benchmark Functions
SortableHTMLTables Turns a data frame into an HTML file containing a sortable table
sos Search contributed R packages, sort by package
sos4R An R client for the OGC Sensor Observation Service
source.gist Read R code from a GitHub Gist
sp classes and methods for spatial data
spa Implements The Sequential Predictions Algorithm
SPA3G SPA3G: R package for the method of Li and Cui (2012)
spaa SPecies Association Analysis
space Sparse PArtial Correlation Estimation
SPACECAP A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models
spaceExt Extension of SPACE
spacejam Sparse conditional graph estimation with joint additive models
spacetime classes and methods for spatio-temporal data
spacodiR Spatial and Phylogenetic Analysis of Community Diversity
spacom Spatially weighted context data for multilevel modelling
spam SPArse Matrix
sparcl Perform sparse hierarchical clustering and sparse k-means clustering
sparkTable Sparklines and graphical tables for tex and html
sparktex Generate LaTeX sparklines in R
sparr The sparr package: SPAtial Relative Risk
sparsediscrim Sparse Discriminant Analysis
SparseGrid Sparse grid integration in R
sparseHessianFD Interface to ACM TOMS Algorithm 636, for computing sparse Hessians
sparseLDA Sparse Discriminant Analysis
sparseLTSEigen RcppEigen back end for sparse least trimmed squares regression
SparseM Sparse Linear Algebra
sparsenet Fit sparse linear regression models via nonconvex optimization
SparseTSCGM Sparse time series chain graphical models
spartan Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
spatcounts Spatial count regression
spate Spatio-temporal modeling of large data using a spectral SPDE approach
spatgraphs Graphs for spatial point patterns
spatial Functions for Kriging and Point Pattern Analysis
spatialCovariance Computation of spatial covariance matrices for data on rectangles
SpatialEpi Performs various spatial epidemiological analyses
SpatialExtremes Modelling Spatial Extremes
spatialkernel Nonparameteric estimation of spatial segregation in a multivariate point process
SpatialNP Multivariate nonparametric methods based on spatial signs and ranks
SpatialPack Package for analysis of spatial data
spatialprobit Spatial Probit Models
spatialsegregation Segregation measures for multitype spatial point patterns R functions for working with spatial data
SpatialTools Tools for spatial data analysis
SpatialVx Spatial Forecast Verification
SpatioTemporal Spatio-Temporal Model Estimation
spatstat Spatial Point Pattern analysis, model-fitting, simulation, tests
spBayes Univariate and Multivariate Spatial-temporal Modeling
spc Statistical Process Control – Collection of Some Useful Functions
spcadjust Functions for calibrating control charts
spclust Selective phenotyping for experimental crosses
spcosa Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata
spcov Sparse Estimation of a Covariance Matrix
spd Semi Parametric Distribution
spdep Spatial dependence: weighting schemes, statistics and models
spe Stochastic Proximity Embedding
SPECIES Statistical package for species richness estimation
specificity Specificity of personality trait-outcome associations
spectralGP Approximate Gaussian processes using the Fourier basis
speedglm Fitting Linear and Generalized Linear Models to large data sets
speedRlibs Package containing the required libraries (jars) for speedR
speedRlibTF speedR’s table filter library
speff2trial Semiparametric efficient estimation for a two-sample treatment effect
SPEI Calculation of the Standardised Precipitation-Evapotranspiration Index
sperich Auxiliary functions to estimate centers of biodiversity
sperrorest Spatial Error Estimation and Variable Importance
spGoogle Interacting R with Google maps: Spatial visualization tool
spgrass6 Interface between GRASS 6+ geographical information system and R
spgwr Geographically weighted regression
sphereplot Spherical plotting
SphericalCubature Numerical integration over spheres and balls in n-dimensions; multivariate polar coordinates
SpherWave Spherical Wavelets and SW-based Spatially Adaptive Methods
sphet Estimation of spatial autoregressive models with and without heteroskedastic innovations
spi Compute SPI index
SPIAssay A genetic-based assay for the identification of cell lines
spider Species Identity and Evolution in R
spikeslab Prediction and variable selection using spike and slab regression
spikeSlabGAM Bayesian variable selection and model choice for generalized additive mixed models
SPIn Simulation-efficient Shortest Probability Intervals
splancs Spatial and Space-Time Point Pattern Analysis
splm Econometric Models for Spatial Panel Data
spls Sparse Partial Least Squares (SPLS) Regression and Classification
splus2R Supplemental S-PLUS functionality in R
splusTimeDate Times and Dates from S-PLUS
splusTimeSeries Time Series from S-PLUS
spMC Continuous Lag Spatial Markov Chains
SPMS Sub-Pathway Mining Software
sporm Semiparametric proportional odds rate model
SportsAnalytics Infrastructure for Sports Analytics
SPOT Sequential Parameter Optimization
sprint Simple Parallel R INTerface
sprsmdl Sparse modeling toolkit
SPSL Site Percolation on Square Lattice (SPSL)
spsmooth spsmooth: An Extension Package for ‘mgcv’
spsurvey Spatial Survey Design and Analysis
spt Sierpinski Pedal Triangle
spTimer Spatio-Temporal Bayesian Modelling Using R
spuRs Functions and Datasets for “Introduction to Scientific Programming and Simulation Using R”
sqldf Perform SQL Selects on R Data Frames
sqlshare API for access to SQLShare database
sqlutils Utilities for working with SQL files
SQN subset quantile normalization
SQUAREM Squared extrapolation methods for accelerating fixed-point iterations
squash Color-based plots for multivariate visualization
sra Selection Response Analysis
SRMA SRMA Analysis of Array-based Sequencing Data
sROC Nonparametric Smooth ROC Curves for Continuous Data
SRPM Shared Reproducibility Package Management
SRRS The Stepwise Response Refinement Screener (SRRS)
ssanv Sample Size Adjusted for Nonadherence or Variability of input parameters
SSDforR SSD for R to analyze single system data
ssfit Fitting of parametric models using summary statistics
ssize.fdr Sample Size Calculations for Microarray Experiments
ssmrob Robust estimation and inference in sample selection models
SSN Spatial Modeling on Stream Networks
sspir State Space Models in R
sss Tools for importing files in the triple-s .(Standard Survey Structure) format
SSsimple State space models
st Shrinkage t Statistic and CAT Score
stab data analysis of drug stability for shelf life estimation
stabledist Stable Distribution Functions
Stack Stylized concatenation of data.frames or ffdfs
stacomirtools stacomi ODBC connection class
stam Spatio-Temporal Analysis and Modelling
StAMPP Statistical Analysis of Mixed Ploidy Populations
StandardizeText Standardize Text
standGL Standardized Group Lasso
STAR Spike Train Analysis with R
stargazer LaTeX code and ASCII text for well-formatted regression and summary statistics tables
STARSEQ Secondary Trait Association analysis for Rare variants via SEQuence data
startupmsg Utilities for start-up messages
stashR A Set of Tools for Administering SHared Repositories
Stat2Data Datasets for Stat2
StatDA Statistical Analysis for Environmental Data
StatDataML implementation of the StatDataML proposal
StateTrace Bayesian Ordinal Analysis for State Trace Designs
StatMatch Statistical Matching
statmod Statistical Modeling
statnet Software tools for the Statistical Analysis of Network Data
statnet.common Common R Scripts and Utilities Used by the Statnet Project Software
SteinerNet Steiner Tree Approach for Graph Analysis
stellaR stellar evolution tracks and isochrones
Stem Spatio-temporal models in R
stepp Subpopulation Treatment Effect Pattern Plot (STEPP)