CRAN usage

The following CRAN packages use Rcpp:
  • RQuantLib, an R interface to QuantLib quantitative finance libraries
  • RInside, a set of C++ classes that make it easy to embed R in your C++ applications
  • RProtoBuf, an interface from R to the Google ProtoBuf library
  • mvabund, a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology.
  • sdcTable, a package for statistical disclosure control for tabular data.
  • bifactorial, a package for global and multiple inference for given bi- and tri-factorial clinical trial designs.
  • RcppExamples, a example package illustrating use of Rcpp and providing concrete examples.
  • RcppArmadillo, an interface from R to the Armadillo C++ linear algebra library using Rcpp.
  • minqa which provides derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.
  • termstrc offers a wide range of functions for term structure estimation based on static and dynamic coupon bond and yield data.
  • phylobase implements a base S4 class for comparison of phylogenetic structures and data.
  • RSNNS wraps the Stuttgart Neural Network Simulator (SNNS), a library containing many standard implementations of neural networks, and brings these to R.
  • parser implements a detailed source code parser based on the R parser and grammar with a different representation of the parsed expressions. (This package is now archived as the functionality has largely been integreated into R itself.)
  • RcppGSL which provides an interface from R to the GNU GSL vector and matrix types.
  • orQA can be used to assess repeatability, accuracy and cross-platform agreement of titration microarray data.
  • RcppDE provides differential evolution optimization (just like (DEoptim which it is based) and serves as a small case study in porting from plain C to the combination of C++ and Rcpp.
  • RcppBDT provides (parts of) Boost Date.Time by using Rcpp modules to easily expose the Boost functionality to R.
  • unmarked uses Rcpp and RcppArmadillo to provide code to fit hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling.
  • The simFrame package provides an object-oriented general framework for statistical simulations.
  • The rgam package also uses Rcpp and RcppArmadillo to provide an outlier-robust fit for Generalized Additive (gam) Models.
  • The spacodiR package implements an interface to SPACoDi which is primarily designed to characterise the structure and phylogenetic diversity of communities using abundance or presence-absence data of species among community plots.
  • The VIM package provides visualization for missing values.
  • The SBSA package uses RcppArmadillo to provides functions for simplified Bayesian sensitivity analysis.
  • GUTS contains functions for the fast calculation of the likelihood of a stochastic survival model.
  • The wordcloud package uses Rcpp to accelerate rendering word clouds from text.
  • The cda pakages uses Rcpp modules and RcppArmadillo to model coupled dipole approximations: Given a set of ellipsoidal nanoparticles, it calculates the polarizability tensor for the dipoles associated with each particle, and solves the coupled-dipole equations by direct inversion of the interaction matrix.
  • The planar pakages uses Rcpp modules and RcppArmadillo to solves the electromagnetic problem of reflection and transmission at a multilayer planar interface. Also computes the decay rates for a dipolar emitter near a multilayer structure.
  • The maxent package provides tools for text classification using multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm package.
  • fdaMixed offers functional data analysis in a mixed-model framework via a likelihood-based analysis; it uses Rcpp and RcppArmadillo.
  • KernSmoothIRT fits nonparametric item and option characteristic curves using kernel smoothing, and allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools.
  • The rugarch package can estimate a variety of univariate GARCH models including ARFIMA, in-mean effects, use of external regressors and various other GARCH flavours using both Rcpp and RcppArmadillo.
  • bcp provides an implementation of an approximation to the product partition model for the normal errors change point problem using Markov Chain Monte Carlo, and also extends the methodology to independent multivariate series with an assumed common change point structure.
  • RVowpalWabbit provides an interface to the Vowpal Wabbit fast on-line learner by John Langford et al.
  • The rococo package provides a robust gamma rank correlation coefficient along with a permutation-based rank correlation test both of which are explicitly designed for dealing with noisy numerical data.
  • The LaF package provides methods to efficiently access data from large ascii files, including subsetting and block-wise access.
  • The Rclusterpp package provides flexible native clustering routines that can be linked against in downstream packages, and uses Rcpp and RcppEigen.
  • The bfa package provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models; it uses Rcpp and RcppArmadillo.
  • RSofia provides an R interface to the sofia-ml suite of fast incremental algorithms for machine learning suitable for training models for classification or ranking.
  • The fastGHQuad package implements functions for fast (and numerically stable) Gauss-Hermite quadrature.
  • The SpatialTools package provides tools for spatial analysis with an emphasis on kriging using Rcpp and RcppArmadillo.
  • RcppSMC implements several Sequential Monte Carlo / Particle Filter models using the SMC template library by Adam Johansen.
  • The psgp package provides projected spatial gaussian process methods for sparse spatial kriging; it uses Rcpp and RcppArmadillo.
  • The WideLm package uses Rcpp as well the NVidia CUDA API (>= 4.1) to simultaneously estimate a large number of 'tall and skinny' models from the same dataset.
  • The forecast package provides methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling; it uses Rcpp and RcppArmadillo.
  • The openair package provides tools to analyse, interpret and understand air pollution data, typically from hourly time series and both monitoring data and dispersion model output can be analysed.
  • The Rmixmod package implements high-performance model-based cluster analysis for mixture modelling.
  • The sdcMicro package contains statistical disclosure control methods for the generation of public- and scientific-use files and can be used for the generation of anonymized (micro)data, i.e. for the generation of public- and scientific-use files.
  • The Rmalchains package implements an algorithm family for continuous optimization called memetic algorithms with local search chains (MA-LS-Chains); memetic algorithms are hybridizations of genetic algorithms with local search methods.
  • The growcurves package provides Bayesian semiparametric growth curve models that additionally include multiple membership random effects, using both Rcpp and RcppArmadillo.
  • The apcluster package implements Frey's and Dueck's Affinity Propagation clustering algorithm in R, and also provides an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation.
  • The survSNP package provides power and sample size calculations for SNP association studies with right censored time to event outcomes.
  • The robustHD package provides robust methods for high-dimensional data, in particular linear model selection techniques based on least angle regression and sparse regression; it uses RcppArmadillo.
  • The sparseLTSEigen package implements an RcppEigen-based back-end for sparse least trimmed squares regression with an L1 penalty; it uses RcppEigen.
  • The waffect package simulates phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations.
  • The zic package implements Bayesian inference for zero-inflated count models using MCMC written in C++; the package uses Rcpp and RcppArmadillo.
  • The rcppbugs package provides an R bindings to the CppBugs C++ library for MCMC and aims to make writing mcmc models as painless as possible by incorporating features from both WinBugs and PyMC. It uses both Rcpp and RcppArmadillo.
  • The mirt package implements multidimensional item response theory for the analysis of dichotomous and polychotomous response data using latent trait models under the Item Response Theory paradigm.
  • The mets package helps with the analysis of multivariate event times by implementing various statistical models for multivariate event history data, including multivariate cumulative incidence models, and bivariate random effects probit models (liability models).
  • The bfp package implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms.
  • The gof package implements model-checking techniques for generalized linear models and linear structural equation models based on cumulative residuals; it uses Rcpp and RcppArmadillo.
  • The RcppOctave package provides a bidirectional interface to GNU Octave, allowing R to call Octave functions and script files.
  • The blockcluster package provides co-clustering for Binary, contingency and continuous utility functions to visualize the results.
  • The RcppCNPy package uses Carl Rogers to read / write files created by / for Numeric Python (aka "numpy").
  • The MVB package fits log-linear models for multivariate Bernoulli distributions with mixed effect models and LASSO.
  • The surveillance package provides statistical methods for modeling and change-point detection in time series of counts, proportions and categorical data for temporal and spatio-temporal modeling and monitoring of epidemic phenomena.
  • The fugeR package provides "FUzzy GEnetic" machine learning for prediction models.
  • classify provides classification accuracy under IRT models.
  • The ccaPP package implements robust canonical correlation analysis via projection pursuit; it uses Rcpp and RcppArmadillo.
  • trustOptim provides a trust region algorithm for nonlinear minimization with methods that are designed to be efficient when the Hessian is sparse; it uses Rcpp and RcppEigen.
  • The clusteval package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.
  • oem implements orthogonolizing expectations maximisation to fit penalized regression; it uses Rcpp and RcppArmadillo.
  • The quadrupen package fits classical sparse regression models with efficient active set algorithms by solving quadratic problems and also provides a few methods for model selection purpose (cross-validation, stability selection); it uses Rcpp and RcppArmadillo.
  • The pbdBASE package implements methods and classes for distributed data types using MPI, and the pbdDMAT provides distributed linear algebra computations; both are part of a set of packages for Programming with Big Data.
  • The robustgam package implements robust estimation for generalized additive models by implementing the fast and stable algorithm in Wong, Yao and Lee (2012).
  • The sparseHessianFD package computes the sparse Hessian using ACM TOMS Algorithm 636; it uses Rcpp and RcppEigen.
  • The gMWT package provides generalized Mann-Whitney type tests based on probabilistic indices; it uses Rcpp and RcppArmadillo.
  • The Kmisc package contains a collection of miscellaneous functions to improve the R coding experience
  • The ngspatial package provides tools for analyzing spatial data, especially non-Gaussian areal data; it use Rcpp and RcppArmadillo.
  • The surveillance package implements tools for temporal and spatio-temporal modeling and monitoring of epidemic phenomena.
  • The GeneticTools package contains a collection of routines for the analysis of expression and genotype data, it uses Rcpp and RcppArmadillo.
  • RcppClassicExamples regroups examples from the deprecated initial API now provided by RcppClassic.
  • The ConConPiWiFun package implements continuous convex piecewise linear functions which are useful for large class of optimization problems.
  • The RcppRoll package supplies fast functions for rolling over vectors and matrices, and provides utility functions 'rollit' and 'rollit_raw' as an interface for generating C++ backed rolling functions; it uses Rcpp and RcppArmadillo.
  • rforensicbatwing calculates forensic trace-suspect match probabilities using a modified version of Ian Wilson's BATWING program.
  • The RcppXts package facilitates access to the C API functions of xts from Rcpp.
  • The stochvol package implements efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via MCMC.
  • The marked provides a framework for handling data and analysis for mark-recapture.
  • The PReMiuN package implements Dirichlet pricess Bayesian clustering also known as profile regression.
  • The ALKr package provides several algorithms for generating age-length keys for fish population from incomplete data.
  • The ecp package computes hierarchical change point analysis through the use of the energy statistic for multiple change point analysis of multivariate data.
  • The rexpokit packages implements wrappers for EXPOKIT, a Fortran library for matrix exponentiation.
  • The Amelia package for missing data imputation now uses Rcpp and RcppArmadillo. exponentiation.
  • The HLMdiag package provides a suite of diagnostic tools for hierarchical (multilevel) linear models; it uses Rcpp and RcppArmadillo.
  • The stream package implements a framework for data stream modeling and data mining tasks such as classification and clustering..
  • httpuv provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R.
  • cladoRcpp implements various cladogenesis-related calculations in C++ which are slow in pure R.
  • The Delaporte package implements probability mass, distribution, and quantile functions as well as a random number generator for the Delaporte distribution.
  • FastPCS implements the FastPCS algorithm for computing the FastPCS outlying index; it uses Rcpp and RcppEigen.
  • rmgarch implements multivariate GARCH models using Rcpp and RcppArmadillo.
  • The FBFsearch package implements an algorithm for searching the space of Gaussian directed acyclic graphical models through moment fractional Bayes factors (and uses Rcpp and RcppArmadillo).
  • The dclong.spt package provides sequential permutation tests in R and C++, using Rcpp and RcppArmadillo.
  • The sequences package illustrate OO programming and package development using biological sequences (DNA and RNA) as a working example.
  • The MPTinR packages analyzes Multinomial Processing Tree Models.
  • The msgl package implements high-dimensional multiclass classification using the sparse group lasso; it uses Rcpp and RcppArmadillo.
  • The sirt package provides supplementary item-response theory functionality; it uses Rcpp and RcppArmadillo.
  • The GSE package implements robust estimation of multivariate location and scatter in the presence of missing data, it use Rcpp and RcppArmadillo.
  • The diversitree package provides a number of comparative phylogenetic methods, mostly focusing on analysing diversification and character evolution.
  • The miscF package contains various functions for random number generation, density estimation, classification, curve fitting, and spatial data analysis; it uses Rcpp and RcppArmadillo.
  • The clogitL1 package fits exact conditional logistic regression with lasso and elastic net penalties.
  • The tbart packages implements the Teitz and Bart p-median algorithm.
  • The climdex.pcic packages contains routines for the computation of climate indices provided by the Pacific Climate Impact Consortium.
  • The coneproj packages provides routines for cone projection and quadratic programming, as well as routines to do estimation and inference for constrained parametric regression and shape-restricted regression problems; it uses Rcpp and RcppArmadillo.
  • FastRCS implements the FastRCS algorithm for computing the FastRCS outlying index; it uses Rcpp and RcppEigen.
  • The inarmix package fits mixtures models for longitudinal data and is appropriate when the data are counts and when the correlation structure is assumed to be AR(1).
  • The accelerometry package implements functions to process uniaxial minute-to-minute accelerometer data.
  • prospectr implements miscellaneous functions for processing and sample selection of visible and near infrared diffuse reflectance spectra; it uses Rcpp and RcppArmadillo.
  • The CDM package provides functions for cognitive diagnosis modeling as well as multidimensional item response modeling.
  • The Funclustering package proposes a model-based clustering algorithm for multivariate functional data. It uses Rcpp and RcppEigen.
  • Rankcluster implements a model-based clustering algorithm for ranking.
  • The rotations package provides tools for working with rotation data; it uses Rcpp and RcppArmadillo.
  • The lme4 package implements S4 based classes and functions to fit linear mixed-effects models; it uses Rcpp and RcppEigen.
  • The NetSim package allows to combine and simulate a variety of micro-models of social networks.
  • The AdaptiveSparsity package implements algorithms for adaptive sparsity (Jeffrey's prior) used in supervised learning; it uses Rcpp and RcppArmadillo.
  • The RcppZiggurat package provides several Ziggurat implementations of the fast N(0,1) RNG due to Marsaglia and Tsang (as well as the correction by Leong et al).
  • The GxM package implements maximum likelihood estimation for gene-by-measured environment interaction in behavior genetic designs.
  • disclapmix provides inference for mixtures of discrete Laplace distributions via the EM algorithm.
  • The PedCNV package implements association analysis for CNV data; it uses Rcpp and RcppArmadillo..
  • The lm.br package provides exact significance tests for a changepoint in linear or multivariate linear regression.
  • The bcpa package estimates behavioral change point analysis of animal movement.
  • The hsphase package implements phasing and imputation of half-sib families using SNP data; it uses Rcpp and RcppArmadillo..
  • The hypervolume package implements high-dimensional kernel density estimation and geometry.
  • dils provides data-informed link strength and combines multiple-relationship networks into a single weighted network by imputing (fill-in) missing network links.
  • The ClustVarLV package provides functions to cluster sets of variable around latent variables.
  • The ndl package implements naive discriminant learning and classification models..
  • The strum package provides latent variable and structural equation models for pedigree data; it uses Rcpp and RcppArmadillo.
  • protViz offers quality checks, visualizations and analysis of mass spectrometry data.
  • The Ruchardet package helps to detect character encodings.
  • The snplist package offers a set of functions to create SQL table from gne and SNP information.
  • The CARBayes implements Bayesian hierarchical spatial areal unit models in which the spatial correlation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution.
  • roxygen2 implements a Doxygen-like documentation system for Rd files, NAMESPACE and DESCRIPTION.
  • The sglOptim package provides a solver for sparse group lasso generic optimization, using Rcpp and RcppArmadillo.
  • geoCount implements analysis and modeling for geostatistical count data, it uses Rcpp and RcppArmadillo.
  • VideoComparison takes the vectors of motion for two video to quantify similarity.
  • The kmc package provides a Kaplan-Meier estimator with constraints for right-censored data via a recursive algorithm.
  • The pROC package can visualize, smooth and compare receiver operator characteristic (ROC) curves.
  • The XBRL package for the extraction of data from Extensible Business Reporting Language (XBRL) used by the SEC's Edgar system.
  • The wsrf package offers a parallel implementation of the Weighted Subspace Random Forest algorithm.
  • The hawkes package implements a Hawkes process simulation and calibration toolkit. It uses RcppArmadillo and Rcpp.
  • The IsingSampler package provides sampling methods and distribution functions for the Ising model.
  • The TAQMNGR implements tools for tick-by-tick (equity) transaction data.
  • The dplyr package provides a fast and consistent tool for working with data frame like objects, both in memory and out of memory.
  • IBHM implements the Incrementally Built Heterogeneous Model (IBHM) designed for solving real number approximation problems in a highly automated fashion.
  • The HUM package extimates the HUM ("hypervolume under the manifold") value to estimate feature ability to discriminate class labels, and visualizes the ROC curve for two or three class labels.
  • Rvcg provides an interface to the Visualization and Computer Graphics Library (VCGLIB) API. It uses Rcpp and RcppEigen.
  • The GMCM package implements fast estimation of Gaussian Mixture Copula Models (GMCM) for unsupervised clustering and meta-analysis; it uses Rcpp and RcppArmadillo.
  • GPvam provides Maximum Likelihood estimation of Multiple Membership Mixed Models used in Value-Added Modeling via an EM algorithm; it uses Rcpp and RcppArmadillo.
  • mice implements Multivariate Imputation by Chained Equations (mice) with built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds).
  • The propagate package implements propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation.
  • The Morpho package provides a toolset for Geometric Morphometrics and mesh processing includingmesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement. It uses Rcpp and RcppArmadillo.
  • The CIDnetworks package implements generative models for networks with conditionally independent dyadic structure.
  • The CorReg package provides code for linear regression based on linear structure between covariates using sequential linear regression based on a recursive structural equation model which permits use of highly correlated datasets. It uses Rcpp and RcppEigen.
  • glcm computes textures from grey-level co-occurrence matrices (GLCMs) in R, it uses Rcpp and RcppArmadillo.
  • The FastHCS package computes the FastHCS outlyingness index for finding outliers in high dimensional data-sets. It uses Rcpp and RcppEigen.
  • The miceadds package provides additional imputation methods, particularly for mice. It uses Rcpp and RcppArmadillo.
  • The clere package implements an empirical Bayes approach for simultaneous variable clustering and regressions; it uses Rcpp and RcppEigen.
  • The scrypt package implements Colin Percival's scrypt function for a password-based key derivation function which makes it costly to perform large-scale custom hardware attacks by requiring large amounts of memory.
  • The plyr package provides tools for splitting, applying and combining data.
  • The fastM package implements a fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators; it uses Rcpp and RcppArmadillo.
  • The pcalg package provides methods for graphical models and causal inference, it uses Rcpp and RcppArmadillo.
  • MTS implements an all-purpose toolkit for analyzing multivariate time series (MTS) and estimating multivariate volatility models.
  • The FDRreg package provides tools for false discovery rate regressions; it uses Rcpp and RcppArmadillo.
  • resemble implements regression and similarity evaluation for memory-based learning in spectral chemometrics; it uses Rcpp and RcppArmadillo.
  • The mcIRT package provides functions to estimate two popular IRT-models: The Nominal Response Model and the Logit Model; it uses Rcpp and RcppArmadillo.
  • dendextendRcpp offers faster manipulation of dendrogram objects in R.
  • The BIPOD package implements BIPOD (Bayesian Inference for Partially Observed diffusions), ie Bayesian parameter estimation for (partially observed) two-dimensional diffusions; it uses Rcpp and RcppArmadillo.
  • The dbmss package implements distance-based measures of spatial structures.
  • The synlink package provides a framework for synthetic likelihood inference for models where the likelihood is unavailable or intractable.
  • The BalancedSampling package implements balanced and spatially balanced samples in multi-dimensional spaces with prescribed inclusion probabilities.
  • The SocialNetworks package generates social networks based on distance.
  • The lsgl package implements linear multiple output fits via a sparse group lasso; it uses Rcpp and RcppArmadillo.
  • The CMF package provides collective matrix factorization which finds joint low-rank representations for collections of matrices with shared row or column entities..
  • The iterpc package provides an efficient iterator for permutations and combinations.
  • The EWGoF package implements Goodness-of-Fit tests for the expenential and two-parameter Weibull distributions..
  • The EWGoF package implements Goodness-of-Fit tests for the expenential and two-parameter Weibull distributions..
  • The TFMPvalue package provides efficient and accurate P-value computation for positive weight matrices.
  • The Rsomoclu package provides a cluster-oriented implementation of self-organizing maps which relies on MPI and can also deploy CUDA.
  • fwsim simulations populations under the Fisher-Wright model with a one-step neutral mutation process.
  • FisHiCal implements iterative FISH-based calibration of Hi-C data for chromosomal spatial analysis; it uses Rcpp and RcppArmadillo.
  • The flip package provides multivariate permutation tests; it uses Rcpp and RcppArmadillo.
  • The openxlsx package allows the writing, styling and editing of xlsx worksheets.
  • The reshape2 package implements flexible restructuring and aggregating of data.
  • polywog provides routines for bootstrapped basis regression with oracle model selection, a flexible functional form estimation via basis regression with model selection via the adaptive LASSO or SCAD.
  • diveRsity is a package which allows the calculation of both genetic diversity partition statistics, genetic differentiation statistics and locus informativeness for ancestry assignment.
  • stosim implements stochastic simulator for reliability modeling of repairable systems: A toolkit for reliability availability and maintainability (ram) modeling of industrial process systems.
  • The slfm package providestools to find coherent patterns in microarray data using Bayesian sparse latent factor models; it uses Rcpp and RcppArmadillo..
  • The TED package implements turbulence time series event detection and classification; it uses Rcpp and RcppArmadillo.
  • RcppRedis connect R to the Redis key/value store by using the hiredis C library.
  • The CDS package provides tools for pricing Credit Default Swaps.
  • The ripa package includes various functions for image processing and analysis.
  • miscset provides a set of miscellaneous R tools to work with data types and formats.
  • The QRM package provides code to examine quantitative risk management concepts.
  • The DNAprofiles package implements methods for forensic DNA profiling.
  • Rtsne provides t-distributed stochastic neighbor embedding.
  • The FLSSS package solves fixed size subset sum solution problems via a recursive compression algorithm.
  • The randomUniformForest implements forests of unpruned and randomized binary trees for classification and regression.
  • The Mosterior package implements a general framework for estimating a median of subset posterior measures (M-posterior). It uses Rcpp and RcppArmadillo.
  • The SpatialEpi package provides cluster detection and disease mapping methods for spatial epidemiology; it uses Rcpp and RcppArmadillo.
  • The mvnfast package implements fast multivariate normal random draws using OpenMP, Rcpp and RcppArmadillo and based on the parallel RNG generator by van den Berg.
  • The RSNPset package implements efficient score statistics in genome-wide SNP set analysis with complex traits; it uses RcppEigen.
  • spBayesSurv provides spatial copula modelling to Bayesian survival analysis; it uses Rcpp and RcppArmadillo.
  • The qVarSel implements variable selection for clustering and classification.
  • ESGtoolkit provides a Monte Carlo simulation toolkit for the simulation of financial assets and interest rates models involved in an Economic Scenario Generator (ESG).
  • The mmand package implements tools for mathematical morphology operation such as erosion and dilation; it uses Rcpp and RcppArmadillo.
  • PerMallows implements permutations and mallows distributions for the Mallows, Generalized Mallows and Weighted Mallows model.
  • revealedPrefs computes (direct and indirect) revealed preferences, fast non-parametric tests of rationality axioms (WARP, SARP, GARP) and detection of axiom-consistent subpopulations; it uses Rcpp and RcppArmadillo.
  • spaMM provides spatial mixed models including spatial GLMMs.
  • The icensmis package models study design and data analysis in the presence of error-prone diagnostic tests and self-reported outcomes.
  • The BIFIEsurvey package provides tools for survey statistics in educational assessment; it uses Rcpp and RcppArmadillo.
  • rpf implements item factor analysis fitting, diagnostics, and analysis. It uses RcppEigen.
  • dslice implements a dynamic slicing method designed for dependency detection between a categorical variable and a continuous variable.
  • eive provides a compact genetic algorithm search to reduce errors-in-variables bias in linear regression.
  • icamix implements estimation of ICA mixture models using Rcpp and RcppArmadillo.
  • The SOD package provides multidimensional scaling via Self-Organising-Deltoids by gradually reducing the dimensionality of an initial space.
  • CompGLM contains a function (with an interface similar to glm) to fit a Conway-Maxwell-Poisson GLM.
  • rkvo provides functionality to read files containing observations which consist of arbitrary key/value pairs.
  • plotSEMMa graphs nonlinear latent variable interaction in SEMM models using LISREL output.
  • The metafolioa package provides tools for simulating salmon population conservation through portfolio optimization; it uses Rcpp and RcppArmadillo.
  • btf implements Bayesian Trend Filtering using Rcpp and RcppEigen.
  • HDPenReg provides high-dimensional penalized regression.
  • The bayou package provides tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods; it uses Rcpp and RcppArmadillo.
  • ReorderCluster implements tools for leaf reordering of dendograms that preserve the hierarchical clustering result while attempting to group instances from the same class.
  • rpg provides another interface for R to PostgreSQL.
  • The pryr package provides tools to compute on the R languages and to pry back some covers of R.
  • mwaved offers multichannel wavelet deconvolution with additive long memory noise.
  • rPref implements preferences in R to retrieve maxima for given strict partial orders.
  • treeclim addresses the numerical calibration of proxy-climate relationships via bootstrapped response and correlation functions, seasonal correlations and evaluation of reconstruction skills for use in dendroclimatology and dendroecology; it uses Rcpp and RcppArmadillo.
  • rplexos reads and analysises PLEXOS solutions from R.
  • growfunctions supplies estimation Bayesian non-parametric dependent models for time-indexed functional data via either of Gaussian process (GP) or intrinsic Gaussian Markov random field (iGMRF) prior formulations; it uses Rcpp and RcppArmadillo.
  • CARBayesST models Poisson log-linear models with spatio-temporal random effects.
  • RcppMLPACK provides R integration for the MLPACK machine learning library; it uses Rcpp and RcppArmadillo.
  • RLRsim provides exact (restricted) likelihood ratio tests for mixed and additive models which test the presence of variance components/nonparametric terms for models fit with the nlme, lme4, gamm4, mgcv and SemiPar.
  • tvd implements total variance denoising, a regularized denoising method which effectively removes noise from piecewise constant signals whilst preserving edges
  • DStree implements recursive partitioning for discrete-time survival and bagged trees.
  • DepthProc models data depth; it uses Rcpp and RcppArmadillo.
  • survAccuracyMeasures estimates accuracy measures for risk prediction markers from survival datamodels data depth; it uses Rcpp and RcppArmadillo.
  • mkde provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions.
  • StereoMorph provides functions for the collection of 3D points and curves using a stereo camera setup.
  • remote implements functions for empirical orthogonal teleconnection analysis.
  • SelvarMix implements regularization for variable selection in model-based clusterning and discriminant analysis using Rcpp and RcppArmadillo.
  • Crossover provides different crossover designs from combinatorial or search algorithms; it uses Rcpp and RcppArmadillo.
  • NPBayesImpute implements routines for multiple imputation of missing at random, with or without structural zero, using non-parametric Bayesian modeling.
  • cgAUG compute the AUC-type measure of Obuchowski.
  • bvarsv offers a bayesian analysis of vector autoregressive models with stochastic volatility and time-varying parameters.
  • lbfgs implements both a limited-memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) as well as a Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization routine.
  • The PP package estimates Person Parameter models.
  • iBATCGH implements integrative Bayesian analysis of transcriptomic and CGH data; it uses Rcpp and RcppArmadillo.
  • nabor wraps libnabo, a fast K Nearest Neighbour library for low dimensions; it uses Rcpp and RcppEigen.
  • DNAtools analyses forensic genetic DNA data by comparing all pairs of profiles in a DNA database.
  • The GUILDS package implements sampling formulas for the unified neutral model of biodiversity and biogeography, with or without guild structure.
  • JAGUAR provides joint analysis of genotype and group-specific variability for gene expression data.
  • copCAR fits three types of regression modesl for areal data; it uses Rcpp and RcppArmadillo.
  • recosystem implements a recommender system via matrix factorization based on the libmf library.
  • GENLIB takes genealogical data frame and calculates different demographic variables.
  • NHMM implements Bayesian NMMM modeling for multiple time series.
  • MAT simulates multidimensional adaptive testing; it uses Rcpp and RcppArmadillo.
  • PoweR computes power and level tables for hypothesis tests; it uses Rcpp and RcppArmadillo.
  • snipEM provides snipping methods for robust estimation and clusterng; it use Rcpp and RcppArmadilo.
  • StMoSim plots qq-norm plots with several gaussian simulations.
  • segmag contains functions to determine event boundares in event segmentaton experiments.
  • rtkpp provides bindings to the STK++ "Statistical ToolKit" library.
  • segmag contains functions to determine event boundares in event segmentaton experiments.
  • scrm simulates the evolution of biological sequences.
  • DetMCD computes a robust and deterministic esimate of location and scatter; it uses Rcpp and RcppEigen.
  • FDGcopulas computes multivariate dependence with FDG Copulas.
  • BayesFactor offers computation of Bayes factors for common designs.
  • fICA implements classical, reloaded and adaptive FastICA algorithms using Rcpp and RcppArmadillo.
  • pander provides an interface to pandoc and markdown report creation.
  • robustreg computes robust linear regression functions using Huber and Bisquare psi functions; it uses Rcpp and RcppArmadillo.
  • RealVAMS fits a multivariate value-added model (VAM) with normally distributed test scores and a binary outcome indicator; it uses Rcpp and RcppArmadillo.
  • myTAI provides a framework to perform phylotranscriptomics analyses for Evolutionary Developmental Biology research.
  • tagcloud computes tag and word clouds.
  • dfmta implements phase I/II adaptive dose-finding design for mta; it uses Rcpp and RcppArmadillo.
  • lpme implements two local polynomial estimators for the errors-in-variables problem; it uses Rcpp and RcppArmadillo.
  • dfcomb implements phase I/II adaptive dose-finding design for combination studies.
  • DetR offers a suite of deterministic and robust algorithms for linear regression; it uses Rcpp and RcppEigen.
  • mp implementation multidimensional projection techniques using Rcpp and RcppArmadillo.
  • RcppAnnoy provides bindings for the Annoy library for approximate nearest neighbours.
  • simPop simulates synthetic populations for survey data considering auxiliary information.
  • quantspec implements methods to determine, smooth and plot quantile (ie Laplace or copula) periodograms for univariate time series.
  • matchingMarkets implements a structural estimator to correct for the sample selection bias from observed outcomes in matching markets; it uses Rcpp and RcppArmadillo.
  • jiebaR provides Chinese text segmentation, keyword extraction and text tagging via the included cppjieba library.
  • iccbeta computes multilevel model intraclass correlation for slope heterogeneity; it uses Rcpp and RcppArmadillo.
  • cqrReg estimate quantile regression and composite quantile regression with adaptive lasso penalty; it uses Rcpp and RcppArmadillo.
  • GCPM analyzes default risk of credit risk models.
  • pedometrics contains functions to employ many tools and techniques used in the field of pedometrics.
  • ASPBay offers Bayesian inference on causal genetic variants; it uses Rcpp and RcppArmadillo.
  • rncl implements an interface to the Nexus Class library for phylogenetic tree file formats.
  • algstat provides functionality for algebraic statistics.
  • textreg performs n-gram Text Regression, ie a concise comparative summarization function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.
  • V8 provides the V8 embedded JavaScript engine by Google.
  • urltools implements vectorised tools for URL handling and parsing.
  • timma offers target inhibition interaction using minimization and maximation averaging; it uses Rcpp and RcppArmadillo.
  • OneArmPhaseTwoStudy -- implements the planning, monitoring and evaluation of oncological phase -- two studies. --
  • RcppDL implements deep learning methods with many layers (deep learning), including dA (Denoising Autoencoder), SdA (Stacked Denoising Autoencoder), RBM (Restricted Boltzmann machine) and DBN (Deep Belief Nets).
  • GPareto implements Gaussian process regression models for Pareto fron estimation and optimization.
  • ddalpha computes depth-based classification and calculation of data depth.
  • FeatureHashing provides a method to transform features to vector using murmurHash.
  • reconstructr aids in reconstructing (web-data) sessions and provinding various metrics.
  • onlinePCA implements online principal components analysis; it uses Rcpp and RcppArmadillo.
  • strataG analyses population genetic haplotypic and genotypic data.
  • NAM implements nested association mapping for biparental and random populations.
  • ISOpureR conmputes the deconvolution of mixed tumor profiles; it uses Rcpp and RcppEigen.
  • ISOpureR conmputes the deconvolution of mixed tumor profiles; it uses Rcpp and RcppEigen.
  • penMSM estimates regularized multi-state models using L1 penalties.
  • mlxR simulates of longitudinal data.
  • lfl provides functions for linguistic fuzzy logic.
  • mirtCAT implements computerized adaptive testing with with multidimensional item response theory; it uses Rcpp and RcppArmadillo.
  • SpatPCA provides regularized principle components analysis for spatial data; it uses Rcpp and RcppArmadillo.
  • icd9 calculates comorbidities, and performs fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9-CM (clinical modification) codes.
  • partialAR fits time series models which consist of a sum of a permanent and a transient component.
  • RcppStreams brings access to the Streamulus library for stream event processing.
  • poisDoubleSamp computes confidence intervals with Poisson double sampling.
  • SVMMatch Causal Effect Estimation and Diagnostics with Support Vector Machines; uses Rcpp and RcppArmadillo.
  • Rlibeemd provides ensemble empirical mode decomposition (EEMD) and its conplete variant (CEEMDAN).
  • cccp implements optimization for cone constraind convex problems via cvxopt; it uses Rcpp and RcppArmadillo.
  • gaselect uses a genetic algorithm for variable selection in high-dimensions; it uses Rcpp and RcppArmadillo.
  • lsbclust implements least-squares bilinear clustering for three-way data.
  • readstata13 adds functions to read and write Stata 13 files.
  • tmg provides truncated multivariate Gaussian sampling using Hamiltonian Monte Carlo; it uses Rcpp and RcppEigen.
  • mbbefd computes Maxwell Bolzano Bose Einstein Fermi Dirac distribution and exposure curves.
  • Rborist implements an extensible and prallelizable Random Forests for scalable decision tree training and prediction; it uses Rcpp and RcppArmadillo.
  • FRESA.CAD implements Feature Selection Algorithms for Computer Aided Diagnosis; it uses Rcpp and RcppArmadillo.
  • FunChisq provides Chi-square tests for non-parametric functional dependencies.
  • rivr computes steady and unsteady open-channel flow and hydraulics.
  • stocks implements functions to compute maximum draw-down, Sharpe ratio, Sterling ratio, and other commonly-sed performance metrics.
  • RcppAPT interfaces the APT Package Management system on Debian-based systems.
  • multicool computes permutations of multisets in cool-lex order to generate integer partitions.
  • emIRT computes Expectation Maximization (EM) algorithms for estimating item response theory models.
  • haven imports data files from SPSS, Stata and SAS via the ReadStat C library.
  • Gmisc provides descriptive statistics, transition plots, and more.
  • MRIaggr provides management, display, and processing of medical imaging data; it uses Rcpp and RcppArmadillo.
  • graphicalVAR implements a graphical VAR for experience sampling data; it uses Rcpp and RcppArmadillo.
  • graphicalVAR computes fast rolling functions for seismology.
  • glmgraph implements graph-constrained regularization for sparse generalized linear models; it uses Rcpp and RcppArmadillo.
  • Coxnet implements a regularized Cox model with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalties; it uses Rcpp and RcppEigen.
  • graphicalVAR computes fast rolling functions for seismology.
  • staTools provides statistical tools for social network analysis.
  • psd produces adaptive power spectral density estimates through iterative refinement of the optimal number of sine-tapers at each frequency; it uses Rcpp and RcppArmadillo.
  • RoughSets helps analyse data through rough set and fuzzy rough set theories.
  • systemicrisk provides a toolbox for systemic risk based on liabilities matrices via a Gibbs sampler.
  • VarSelLCM implements variable selection for model-based clustering using the integrated complete-data likelihood of a latent class model; it uses Rcpp and RcppArmadillo.
  • Luminescence offers a collection of functions for Luminescence data analysis.
  • MixAll implements algorithms and models for parametric mixture models with missing data.
  • chopthin provides the chopthin resampler (which keeps a bound on the ratio between the largest and the smallest weights after resampling) for particle filters and sequential monte carlo methods.
  • gdm contains functions to fit, plot and summarize Generalized Dissimilarity Models.
  • gdm contains functions to fit, plot and summarize Generalized Dissimilarity Models.
  • PAFit computes nonparametric estimation of preferential attachment and node fitness in temporal complex networks.
  • relSim implements a relative simulator: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved.
  • quanteda delivers a fast and flexible toolset for managing, processing and quantitative analysis of textual data in R; it uses Rcpp and RcppArmadillo.
  • readr reads tabular or flat text files.
  • readxl reads xls or xlsw files from a popular spreadsheet application.
  • blockmodels estimates latent or stochastic block model estimation via a V-EM algorithm; it uses Rcpp and RcppArmadillo.
  • xml2 works with XML files using the libxml2 library.
  • lifecontingencies offers financial and actuarial mathematics for life contingencies
  • h5 interfaces the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format.
  • RcppTOML parses configuration files in "Tom's Obvious Markup Language" (TOML).
  • SLOPE provides efficient procedures for sorted L1-penalized estimation.
  • markovchain implements functions and S4 methods for easy handling of discrete time Markov chains.
  • mixedMem provides tools for discrete multivariate mixed membership models; it uses Rcpp and RcppArmadillo.
  • rankdist implements distance based probability models for ranking data where supported distance metrics include Kendall distance and Weighted Kendall distance.
  • SEERaBomb creates SEER (Surveillance, Epidemiology, and End Result) and A-bomb data binaries from ASCII sources.
  • fbroc offers a fast boostrap for ROC curves and derived performance metrics.
  • sgd implements Stochastic Gradient Desc ent for large scale inference; it uses Rcpp and RcppArmadillo.
  • PPtreeViz provides tools for exploring projection pursuit classification trees; it uses Rcpp and RcppArmadillo.
  • odeintr wraps the Boost odeint library to provide ODE solvers on demand.
  • matchingR implements the Gale-Shapley algorithm for stable matching.
  • FSInteract computes Fast Searches for Interactions in large-scale data using the method of random intersection trees by Shah and Meinshausen.
  • redist implements Markov Chain Monte Carlo methods for redistricting simulations; it uses Rcpp and RcppArmadillo.
  • lamW provides both real-valued branches of the Lambert-W function.
  • ClustMMDD implements variable selection for clustering of multinomial models for discrete data.
  • forestFloor visualizes Random Forests with feature contributions to form appropriate visualization of high dimensional mapping curvature of random forests.
  • Rphylopars implements phylogenetic comparative tools for missing data and within-species variation; it uses Rcpp and RcppArmadillo.
  • nonlinearTseries analyses nonlinear time series via generalized correlation dimension, information dimension, largest Lyapunov exponent, sample entropy and recurrence quantification analysis (RQA).
  • RcppFaddeeva computes various error functions of arbitrary complex arguments.
  • EditImputeCont provides an integrated editing and imputation method for continuous microdata under linear constraints.
  • scales maps graphical scales data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.
  • bayesm supports Bayesian inference for marketing and micro-econometrics; it uses Rcpp and RcppArmadillo.
  • BaBooN offers Bayesian bootstrap predictive mean matching for multiple and single imputation for discrete data; it uses Rcpp and RcppArmadillo computes various error functions of arbitrary complex arguments.
  • kdecopula implements kernel smoothing for bivariate copula densities; it uses Rcpp and RcppArmadillo.
  • TESS provides diversification rate estimation and fast simulation of reconstructed phylogenetic trees.
  • missDeaths analysis disease recurrence with missing at risk information using population mortality.
  • sbmSDP uses semidefinite programming to fit block models of equal block sizes; it uses Rcpp and RcppArmadillo.
  • kergp implements Gaussian Processes with customized covariance kernels.
  • primes tests whether a number is prime using Wilson's algorithm.
  • flam implements the fused lasso additive model which fits piecewise constant models with data-adaptive knots.
  • hts analyses and forecasts hierarchical and grouped time series
  • gkmSVM imports the Gapped-Kmer Support Vector Machine into R.
  • autovarCore automatically finds optimal Vector Autoregressive Models and networks.
  • iptools manipulates, validates and resolves IP addresses.
  • raster provides geographic data analysis and modeling of gridded spatial data.
  • AHR estimates and tests average Hazard ratios; it uses Rcpp and RcppArmadillo.
  • neuroim reads, writes, and processes brain imaging data.
  • signalHsmm predicts presence of signal peptides in eukaryotic protein using hidden semi-Markov models.
  • markophylo fits Markov chain models for phylogenetic trees; it uses Rcpp and RcppArmadillo.
  • coala provides a framework for coalescent simulation for biological sequences; it uses Rcpp and RcppArmadillo.
  • FCNN4R implements fast commpressed neural networks.
  • spsann optimizes sample configurations using spatial simulated annealing.
  • dbscan provides a fast implementation of the DBSCAN density-based cluster algorithm.
  • webreadr reads formatted access log files from several common web servers.
  • pcIRT estimates the multidimensional polytomous Rasch modeland the Continous Rating Scale model.
  • rstan interfaces the Stan package for Bayesian inference from R.
  • sparsereg provides sparse Bayesian models for regression, subgroup analysis and panel data; it uses Rcpp and RcppArmadillo.
  • satellite supplies various functions for handling and manipulating remote sensing data.
  • FastGP offers to efficiently use Gaussian processes; it uses with Rcpp and RcppEigen.
  • saturnin implements Bayesian inference of graphical model structures using spanning trees; it uses Rcpp and RcppEigen.
  • SparseFactorAnalysis provides scaling Count and Binary Data with Sparse Factor Analysis, it uses Rcpp and RcppArmadillo.
  • BayesComm estimates multivariate binary probit regression models analysing ecological communities; it uses Rcpp and RcppArmadillo.
  • EstHer estimates heritability in high-dimensional sparse linear mixed models; it uses Rcpp and RcppArmadillo.
  • rgeolocate provides geolocation information for IP addresses.
  • packcircles arranges non-overlapping circles in a rectangle.
  • rstpm2 implements the Stats function stpm2 (for flexible link-based survival models); it uses Rcpp and RcppArmadillo.
  • stm estimates structural topic models; it uses Rcpp and RcppArmadillo.
  • ranger implements a fast Random Forest classifyer particularly suited for high-dimensional data.
  • D3M computes the two sample test with Wasserstein metric motivated from detection of differential DNA-methylation sites based on underlying distributions.
  • StatMethRank contains functions and datasets to support "Statistical Methods for Ranking Data" by Mayer Alvo and Philip L.H. Yu(2014).
  • EPGLM computes Gaussian approximationa of Bayesian binary probit/logit regression models; it uses Rcpp and RcppArmadillo.
  • optmatch implements functions for optimal matching: distance based bipartite matching to reduce covariate imbalance between treatment and control groups in observational studies.
  • mcmcse computes Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings; it uses Rcpp and RcppArmadillo.
  • yakmoR provides a wrapper for the yakmo K-Means library.
  • olctools provides utilities for validating, encoding and decoding entries that follow the 'Open Location Codes' standard.
  • GERGM estimates Generalized Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis Hastings with exponential down weighting; it uses Rcpp and RcppArmadillo.
  • JacobiEigen implements the classical Jacobi (1846) algorithm for the eigenvalues and eigenvectors of a real symmetric matrix, both in pure R and in C++.
  • The creditr prices credit default swaps using C code for the International Swaps and Derivatives Association (ISDA) CDS Standard Model.
  • walkr samples from the intersection of the complete solution space to Ax=b and the N-Simplex using two MCMC methods: hit-and-run and Dikin walk.
  • The mcemGLM estimates generalized linear mixed models via Monte Carlo EM; it uses Rcpp and RcppArmadillo.
  • Rblpapi connects R with the Bloomberg system (for which a working installation is required).
  • The RcppShark package interfaces R to the Shark C++ library for Machine Learning.
  • The DescTools package collects various tools to describe data.
  • The lasvmR package wraps the LASVM solver by Leon Bottou.
  • contoureR creates contour lines for a non-regular three-dimentsional series of points.
  • FastBandChol computes faster covariance matrix estimateby banding the Cholesky factor; it uses Rcpp and RcppArmadillo.
  • The mev package computes multivariate extreme value distributions; it uses Rcpp and RcppArmadillo.
  • lcopula provides estimation and random number generation for the Liouville copula.
  • imager implements fast processing of images in up to four dimensions based on CImg.
  • Langevin estimates drift and diffusion from time series for Langevin analysis; it uses Rcpp and RcppArmadillo.
  • SimReg performs Bayesian "Similarity Regression".
  • humainformat provides a parser for human names.
  • PanelCount computes randome effects and sample selection models for panel counting data; it uses Rcpp and RcppArmadillo.
  • BTLLasse models heterogeneity in paired comparison data; it uses Rcpp and RcppArmadillo.
  • glamlasso estimates with lasso penalization in large scale generalized linear array models; it uses Rcpp and RcppArmadillo.
  • mgm adds functions to estimate and sample from a mixed Graphical model
  • CoxPlus provides a high-performance estimator for proportional hazards model; it uses Rcpp and RcppArmadillo.
  • RStoolbox contains functions for remote sensing image processing and analysis.
  • datafsm estimating finite state machine models from data.
  • emil evaluates models without information leakage using resampling.
  • tidyr tidies data via the 'gather' and 'spread' functions.
  • gRain models probability propagation in graphical independence networks; it uses Rcpp, RcppArmadillo and RcppEigen.
  • treescape provides statistical exploration of distributions of phylogenetic trees.
  • immer implements some item response models for multiple ratings, it uses Rcpp and RcppArmadillo.
  • ClusterStability assesses stability of individual object or clusters in partitioning solutions.
  • cpgen computes parallized genomic prediction, it uses Rcpp and RcppEigen.
  • ChannelAttribution offers a Markov model for online multi-channel attribution problems using Rcpp and RcppArmadillo.
  • RNiftyReg implements image registration using the NiftyReg library; it uses Rcpp and RcppEigen.
  • TDA provides statistical tools for topological data analysis, persistent homology and density clustering.
  • cord computes community estimates in G-models via the Cord metric, it uses Rcpp and RcppArmadillo.
  • Rip46 contains utilities for converting IP4 and IP6 addresses.
  • cord offers a moving-window add-on for the plyr package.
  • cycleRtools has tools for analysing cycling data.
  • tnam provides temporal network autocorrelation models.
  • polyfreqs implements a Gibbs sampler for Bayesian population genomics in autopolyploids.
  • bWGR provides bagging whole-genome regression using a Gibbs sampler.
  • tmlenet estimates targeted maximum likelihood models for network data.
  • frailtySurv simulates and fits general semiparametric shared frailty models.
  • iLaplace computed improved Laplace approximations for integrals of unimodal functions; it uses Rcpp and RcppArmadillo.
  • purrr provides functional programming tools.
  • FIACH supplies useful functions for fRMI processing and retrospective noice control; it uses Rcpp and RcppArmadillo.
  • gaston focusses on genetic data manipulation, linear mixed models, and association testing.
  • gmum.r interfaces two SVM libraries and also provides Growing Neural Gas and other models; it uses Rcpp and RcppArmadillo.
  • prodlim implements nonparametric estimators for censored event history analysis.
  • starma identifies, estimates and diagnoses STARMA processes; it uses Rcpp and RcppArmadillo.
  • LANDD models network dynamics detection using liquid association.
  • TauStar computes the t* Statistic of Bergsma and Dassios (2014); it uses Rcpp and RcppArmadillo.
  • DiffusionRgqd provides inference and analysis for generalized quadratic diffusions; it uses Rcpp and RcppArmadillo.
  • EloChoice computes preference ratings for visual stimuli based on elo ratings; it uses Rcpp and RcppArmadillo.
  • fourPNO fits a four-parameter Bayesiean IRT model; it uses Rcpp and RcppArmadillo.
  • rwirelesscom provides helper functions for operating systems, particularly for Windows.
  • rags2ridges computes ridge estimations of precision matrices from high-dimensional data; it uses Rcpp and RcppArmadillo.
  • jmotif offers a set of tools for time series classification based on time series symbolic discretization and vector space models.
  • bigmemory manages massive matrices with share memory and memory-mapped files.
  • hit offers hierarchical inference testing linear models with correlated covariates.
  • bigtabulate extends 'bigmemory' with 'table', 'tapply', and 'split' support for 'big.matrix' objects.
  • gdtools adds utilities for graphical rendering.
  • ddR implements distributed data structures in R to simplify distributed computing.
  • moveHMM tracks animal movement using hidden Markov models; it uses Rcpp and RcppArmadillo.
  • batman convert categorical representations of logicals to actual logicals.
  • phylosignal explores the phylogenetic signal in continuous traits; it uses Rcpp and RcppArmadillo.
  • dina estimates the 'deterministic input, noisy and gate' (DINA) model via a Gibbs sampler; it use Rcpp and RcppArmadillo.
  • spatgraphs provides graph edhge computations for spatial point patterns.
  • Biocomb implements feature selection and classification with embedded validation procedures for biomedical data analysis.
  • lucr implements currency formatting and conversion.
  • textreuse detects text reuse and document similarity.
  • kmeans.ddR computes k-means for big data using the ddR API.
  • BEDMatrix supports matrices backed by binary PED / PLINK files without requiring to load them into memory.
  • gmwm offers the generalized method of wavelet moments to estimate time series models; it uses Rcpp and RcppArmadillo.
  • prclust implements penalized regression-based clustering methods.
  • tcR adds a platform for the advanced analysis of T cell receptor and immunoglobulin repertoires data.
  • kernDeepStackNet contains functions for estimation and model selection of kernel deep stacking networks.
  • synchronicity adds Boost mutex functionality.
  • steadyICA implements ICA and tests of independence via multivariate distance covariance.
  • simmer offers discreet event simulation.
  • fdasrvf has functions to support functional data analysis using the square root velocity framework.
  • gpuR provides GPU enabled functions for R objects without the need to know OpenCL.
  • rtkore integrates the STK++ "Statistical ToolKit" library.
  • smoof provides generators for single- and multi-objective test functions to benchmark (numerical) optimization algorithms.
  • clogitboost implements boosting for conditional logit models.
  • RcppCCTZ wraps the CCTZ timezone library from Google.
  • precrec calculate accurate precision-recall and ROC curves.
  • tsBSS provides estimates for the blind source separation of time series; it uses Rcpp and RcppArmadillo.
  • cIRT jointly models the accuracy of cognitive responses and item choices within a Bayesian hierarchical framework; it uses Rcpp and RcppArmadillo.
  • MRS implements the multi-resolution scanning algorithm for comparison across distributions; it uses Rcpp and RcppArmadillo.
  • BacArena offers a simulation modeling framework for cellular communities; it uses Rcpp, RcppArmadillo and RcppEigen.
  • mixpack adds tools to work with mixture components; it uses Rcpp and RcppArmadillo.
  • repolr fits linear models to repeated ordinal scores using GEE; it uses Rcpp and RcppArmadillo.
  • svglite implements a graphics device for scalable vector graphics.
  • rwfec simulates communications supporting forward error correction.
  • yCrypticRNAs calculates cryptic transcription analysis scores.
  • ADMMnet fits regularized linear and Cox models with selection of the number of non-zeros.
  • exif extracts EXIF metadata (ie camera make and model, ISO speed, the date-time the picture was taken) from JPEG images.
  • vita implements Variable Importance Testing Approaches (vita) using cross-validated random forest permutations.
  • jmcm estimates joint mean-covariance models for longtitudinal data; it uses Rcpp and RcppArmadillo.
  • mapview offers interactive viewing of spatial objects.
  • rmumps wraps the MUMPS library for sparse linear algebra.
  • CFC implements a cause-specific framework for competing-risk analysis; it uses Rcpp and RcppArmadillo.
  • seqHMM estimates Hidden Markov Models for life sequences and other multivariate categorical time series; it uses Rcpp and RcppArmadillo.
  • aSPU calculates adaptive sum of powered score tests; it uses Rcpp and RcppArmadillo.
  • HSAR provides a hierarchical spatial autoregressive model; it uses Rcpp and RcppArmadillo.
  • mediaK calculates mean distance association by k-nearest neighbor; it uses Rcpp and RcppEigen.
  • TransferEntropy estimates the transfer entropy between continuous time series.
  • NNLM offers fast and versatile non-negative matrix factorization; it uses Rcpp and RcppArmadillo.
  • phonics provides a collection of phonetic algorithms including Soundex, Metaphone, NYSIIS, Caverphone, and others.
  • textmineR adds functions for text mining and topic modeling; it uses Rcpp and RcppArmadillo.
  • rem calculate endogenous network effects in event sequences and fit relational event models.
  • forega offers as floating-point genetic algorithms with a statistical forecast-based inheritance operator.
  • AbsFilterGSEA implements improved false positive control of gene-permuting GSEA with absolute filtering; it uses Rcpp and RcppArmadillo.
  • gjam provides generalized joint attribute modeling with a combinations of continuous and discrete data with Gibbs sampling; it uses Rcpp and RcppArmadillo.
  • stlplus offers enhanced seasonal decomposition of time series by loess.
  • rvg implements a vector graphics device (svg, drawingml) for R.
  • ggrepel provides repulsive text and label geoms for 'ggplot2' which help to avoid overlapping text labels.
  • rstanarm runs Bayesian 'Applied Regression Modeling' code via 'rstan' as pre-compiled regression models; it uses Rcpp and RcppEigen.
  • text2vec sets up a fast and modern framework for text vectorization and learning word embeddings.
  • gsEasy adds gene set enrichment analysis in R by interfacing the rank/score permutation based GSEA test.
  • ontologySimilarity calculates semantic similarities between ontological terms or sets of ontological terms.
  • drgee implements doubly robust generalized estimating equations; it uses Rcpp and RcppArmadillo.
  • prototest adds inference procedures for testing for group-wide signal in clusters of variables; it uses Rcpp and RcppArmadillo.
  • stplanr offers sustainable transport planning tools; it uses Rcpp and RcppArmadillo.
  • blockseg implements two-dimensional changepoint detection; it uses Rcpp and RcppArmadillo.
  • ph2bayes computes Bayesian single-arm phase II designs for binary outcomes.
  • icRSF provides a modified Random Forest Survival algorithm for variable importance in high dimensions.
  • DiffusionRjgqd provides inference and analysis for jump generalized quadratic diffusion processes; it uses Rcpp and RcppArmadillo.
  • easyVeryfication implements ensemble forecast verification for large data sets.
  • scorer adds tools to quickly score models in data science and machine learning.
  • DDRTree projects data into a reduced dimensional space and construct a principal graph from the reduced dimension; it uses Rcpp and RcppEigen.
  • PACVB estimates variational Bayes approximation of Gibbs posteriors with hinge losses; it uses Rcpp and RcppArmadillo.
  • LambertW provides probabilistic models to analyze and gaussianize heavy-tailed, skewed data.
  • densityClust offers clustering by fast search and find of density peaks.
  • MixedDataImpute imputes missing data using nonparametric Bayesian Joint Models; it uses Rcpp and RcppArmadillo.
  • fractional displays numerical vector objects in their vulgar fractional form.
  • stpm provides stochastic models for the analysis of longitudinal data; it uses Rcpp and RcppArmadillo.
  • EBMAforecast implements ensemble methods for Bayesian model averaging forecasts.
  • VNM adds the V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design.
  • tweenr interpolates data for smooth transitions (suitable for animations).
  • ECctmc simulates from endpoint-conditioned continuous time Markov chains; it uses Rcpp and RcppArmadillo.
  • noncompliance models causal inference in the presence of treatment noncompliance under the binary instrumental variable model.
  • ACEt estimates age modification effects on genetic and environmental variance components in twin models; it uses Rcpp and RcppArmadillo.
  • arrApply offers a high-performance variant of apply() for a fixed set of functions; it uses Rcpp and RcppArmadillo.
  • biganalytics adds analytical utility functions for bigmemory matrices.
  • wrswoR implements weighted random sampling methods without replacement.
  • vcfR can work with Variant Call Format ('VCF') files, including 'GCF' and 'FASTA'.
  • GiRaF samples from Gibbs Random Fields, specificallt the homogeneous Poots model; it uses Rcpp, RcppArmadillo and BH.
  • pdftools extracts text and data from PDF documents (by relying on the poppler library).
  • crawl fits continuous-time correlated random walk models to animal movement data; it uses Rcpp and RcppArmadillo.
  • bnnSurvival estimates bagged k-nearest neighbors survival prediction probabilities.
  • fastAdaboost provides a fast implementation of Adaboost for (binary) classification.
  • RSpectra interfaces the Spectra library for large-scale eigenvalue and SVD problems; it use Rcpp and RcppEigen.
  • PWD performs time-series regression using power weighted densities (pwd).
  • deepboost adds deep boosting model training, evaluation, predicting and hyper parameter optimising using grid search and cross validation.
  • mateable provides tools to simulate, manage, visualize, and analyze spatially and temporally explicit datasets of mating potential.
  • biglasso extends the lasso to bigmemory matrices; it uses Rcpp and RcppArmadillo.
  • netcoh fits regression models with network cohesion effects; it uses Rcpp and RcppArmadillo.
  • treeplyr matches phylogenetic trees and trait data and allows simultaneous manipulation of the tree and data using 'dplyr'.
  • humarray simplifies the analysis and annotation of human microarray datasets.
  • rEDM offers empiricial dynamic modeling of timeseries via time delay embedding to perform state-space reconstruction and nonlinear forecasting.
  • genie implements a new, fast and outlier-resistant hierarchical clustering algorithm.
  • ProbitSpatial adds binomial spatial Probit models with spatial dependence, SAR and SEM; it uses Rcpp and RcppEigen.
  • glmmsr fits generalized linear mixed models via sequential reduction and other methods; it uses Rcpp and RcppEigen.
  • hunspell implements a spell checker and morphological analyzer library.
  • spray provides functionality for sparse arrays and multivariate polynomials.
  • Pijavski adds global univariate minimization of Lipschitz functions using Pijavski's method.
  • fdapace implements functional data analysis and empirical dynamics; it uses Rcpp and RcppEigen.
  • PenCoxFrail offers a regularization approach for Cox frailty models by penalization methods; it uses Rcpp and RcppArmadillo.
  • AlignStat compares alternative multiple sequence alignments (MSAs).
  • MatrixCorrelation computes and visualizes matrix correlation coefficients; it uses Rcpp and RcppArmadillo.
  • phylocurve adds phylogenetic comparative methods for high-dimensional traits; it uses Rcpp and RcppArmadillo.
  • MiSPU provides microbiome based sum of powered score (MiSPU) tests.
  • hyphenatr adds tools to hyphenate strings using the 'Hunspell' hyphenation library.
  • sitmo provides the parallel pseudo random number generator 'sitmo'.
  • htmltools adds tools for html generation and output.
  • tibble provides a simple 'tbl_df' data frame class (without requiring dplyr).
  • Countr estimates count process probabilities based on the Weibull distribution; it uses Rcpp and RcppArmadillo.
  • jqr is an R client for 'jq', a JSON Processor written in C.
  • futureheatwaves finds, characterizes, and explores heat waves in climate projectionsis.
  • mcga implements machine coded genetic algorithms for real-valued optimization problems.
  • PAC computes partition-assisted clustering using for more robust and accurate downstream clustering.
  • Gmedian estimates geometric median, k-median clustering and robust median PCA; it uses Rcpp and RcppArmadillo.
  • hkevp adds spatial extreme value analysis via a hierarchical model; it uses Rcpp and RcppArmadillo.
  • collUtils is an auxiliary package for 'CollapsABEL' and provides low-level functions to process PLINK files.
  • tokenizers convert natural language text into tokens proving a consistent interface and compatibility with Unicode.
  • mvcluster implements multi-view bi-clustering; it uses Rcpp and RcppArmadillo.
  • roll offers parallel functions for rolling statistics on times; it uses Rcpp, RcppArmadillo and RcppParallel.
  • snowboot adds Bootstrap sampling and snowball methods for network inference.
  • fromo computes fast robust moments for vectors and matrices.
  • regsem performs regularization on structural equation models via ridge and lasso penalties; it uses Rcpp and RcppArmadillo.
  • BWStest computes the 'Baumgartner-Weiss-Schindler' two-sample test of equal probability distributions.
  • hashmap implements an efficient hash table class for atomic vector types.
  • hierarchicalSets applies a set centric hierarchical clustering as a basis for a range of scalable visual representations.
  • bootTimeInference computes robust performance hypothesis testing with the Sharpe ratio; it uses Rcpp and RcppArmadillo.
  • icd offers tools for working with ICD-9 and ICD-10 codes, and finding comorbidities.
  • geohash provides tools to encode latitude and longitide pairs into geohashes, decode those geohashes, and identify their neighbours.
  • LassoBacktracking efficiently models interactions in high-dimensions.
  • blackbox performs black box optimization and exploration of parameter space; it uses Rcpp and RcppEigen.
  • erah adds automated spectral deconvolution, alignment, and metabolite identification in GC/MS-based untargeted metabolomics.
  • DeLorean implements the DeLorean model to estimate pseudotimes for single cell expression data.
  • eggCounts adds hierarchical models for faecal egg count data to assess anthelmintic efficacy.
  • tensorBSS offers blind source separation methods for tensor-valued observations; it uses Rcpp and RcppArmadillo.
  • minimaxdesign models minimax design and minimax projection design using clustering and particle swarm optimization; it uses Rcpp and RcppArmadillo.
  • sourceR fits non-parametric Bayesian source attribution models; it uses Rcpp and RcppArmadillo.
  • brainGraph implements tools for graph-theoretic analyses of MRI data; it uses Rcpp and RcppEigen.
  • protolite implements yet another serialization approach based on Protocol Buffers.
  • RcppNumerical contains several libraries for numerical integration and optimization; it uses Rcpp and RcppEigen.
  • grpSLOPE computes group-sorted L1 penalized estimation for adaptive selection in high-dimensionsal models; it uses Rcpp and RcppEigen.
  • mlmc provides an R and C++ implementation of multi-level Monte Carlo with support for multi-core parallel sampling.
  • nmfgpu4r wraps a non-negative matrix factorization CUDA library.
  • NPflow adds Bayesian nonparametrics for automatic gating of flow-cytometry data; it uses Rcpp and RcppArmadillo.
  • plac estimates Cox models via semi-parametric methods for left-truncated data; it uses Rcpp and RcppEigen.
  • biwavelet conducts univariate and bivariate wavelet analyses.
  • recmap computes rectangular statistical cartograms using the RecMap MP2 heuristic.
  • surveybootstrap implements different tools for surveys with bootstraps; it uses Rcpp and RcppArmadillo.
  • BeviMed provides Bayesian evaluation of variant involvement in Mendelian disorders.
  • BigQuic computes big quadratic inverse covariance estimation to solve the L1 regularized Gaussian MLE inverse covariance matrix estimation problem.
  • beanz computes Bayesian analysis of heterogeneous treatment effect; it uses Rcpp and RcppEigen.
  • gapfill fills missing values in satellite data.
  • radiomics provides a radiomic image processing toolbox to extract first and second order statistics from images.
  • OjaNP offers multivariate methods based on the Oja median and related concepts.
  • imputeMulti implements imputation methods for multivariate data.
  • netdiffuseR adds empirical statistical analysis, visualization and simulation of network models of the diffusion of innovations; it uses Rcpp and RcppArmadillo.
  • rags2ridges does ridge estimation for VAR models; it uses Rcpp and RcppArmadillo.
  • pystr implements Python-style string methods.
  • SAMM estimates Gaussian linear mixed models; it uses Rcpp and RcppArmadillo.
  • spduration fits split-population duration (cure) regression models; it uses Rcpp and RcppArmadillo.
  • dnc implements dynamic networks clustering for community detection; it uses Rcpp and RcppArmadillo.
  • mcPAFit estimates node fitness from a single network snapshot by Markov Chain Monte Carlo.
  • SSL provides semi-supervised learning aiming for high accuracy with less annotating effort compared to supervised learning.
  • Ryacas interfaces the Yacas computer algebra system.
  • saeRobust adds methods to methods to fit robust alternatives to commonly used models used in small area estimation.
  • pvar calculates p-variation of sample data.
  • BigVAR estimates VAR and VARX models with structured Lasso penalties for multivariate time series; it uses Rcpp, RcppArmadillo and RcppEigen.
  • feather reads and writes feather files, a lightweight binary columnar data store designed for maximum speed.
  • wCorr computes Pearson, Spearman, polychoric, and polyserial correlation coefficients, in weighted or unweighted form; it uses Rcpp and RcppArmadillo.
  • SpatMCA provides regularized maximum covariance analysis; it uses Rcpp, RcppArmadillo and RcppParallel.
  • fourierin computes Fourier integrals of one and two variables using the FFT; it uses Rcpp and RcppArmadillo.
  • BAMMtools analyses and visualises macroevolutionary dynamics on phylogenetic trees (using BAMM).
  • elpatron facilitates cycling analysis from within R.
  • rflann provides a basic R interface to the FLANN C++ Library; it uses Rcpp and RcppArmadillo.

BioConductor usage

The following BioConductor packages use Rcpp:
  • pcaMethods provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA.
  • GRENITS uses Rcpp and RcppArmadillo to implement network inference models using Dynamic Bayesian Networks and Gibbbs Variable Selection.
  • mosaics provides functions for fitting MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data.
  • mzR provides a unified API to the common file formats and parsers available for mass spectrometry data.
  • Rdisop uses Rcpp and RcppClassic for the decomposition of isotopic patterns.
  • ddgraph distinguishes direct and indirect interact via Graphical Modeling
  • DESeq2 implements differential gene expression analysis based on the negative binomial distributions
  • flowType provides support for phenotyping flow cytometry assays
  • flowWorkspace imports flowJo Workspaces into BioConductor
  • GeneNetworkBuilder helps to build regulatory network from ChIP-chip/ChIP-seq and expression data
  • GOSemSim provides GO-terms semantic similarity measures
  • GOSim computes functional similarities between GO terms and gene products
  • metaSeq is for the meta-analysis of RNA-Seq count data in multiple studies
  • MSstats implements protein significance analysis in LC-MS, SRM and DIA for label-free or label-based proteomics experiments
  • pRoloc provides a unifying bioinformatics framework for spatial proteomics
  • Rchemcpp implements similarity measures for chemical compounds
  • Risa converts experimental metadata from ISA-tab into Bioconductor data structures
  • rTANDEM encapsulates X!Tandem in R
  • ABSSeq implements a new RNA-Seq analysis method based on absolute expression differences and generalized Poisson model
  • bamsignals extracts read count signals from bam files
  • birte offers Bayesian inference of regulatiry influence on expression
  • BrowserViz provides interactive R/browser graphics using websockets and JSON
  • BrowserVizDemo shows how to subclass BrowserViz
  • ChemmineOB implements an R interface to a subset of OpenBabel funcationality
  • ChemmineR provides a cheminformatics toolkit for R
  • chromDraw visualized linear and circular karyotypes
  • clipper offers gene set analysis exploiting pathway topology
  • CoGAPS computes coordinated gene activity in pattern sets
  • COMPASS implements combinatorial polyfunctionality analysis of single cells
  • cosmiq combines single masses into quantities
  • destiny creates diffusion maps
  • DMRcaller implements a differentially methylated regions caller
  • EDDA provides experimental design in differential abundance analysis
  • flowCore implements basic structures for flow cytometry data
  • flowMatch implements matching and meta-clustering for in flow cytometry
  • GenomicTuples offers representation and manipulation of genomic tuples
  • GOsummaries computes word cloud summaries of GOs enrichment analysis
  • IsoGeneGUI brings a graphical user interface to conduct a dose-response analysis of microarray data
  • kebabs provides kernel-based analysis of biological sequences
  • MAIT adds statistical analysis of metabolomic data
  • messina implements single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
  • MIMOSA computes mixture models for single-cell assays
  • msa computes multiple sequence alignment
  • MSnbas brings base functions and classes for MS-based proteomics
  • MSnID implements utilities for exploration and assessment of confidence of LC-MSn proteomics identifications
  • netbenchmark add benchmarking of several gene network inference methods
  • networkBMA offers regression-based network inference using Bayesian model averaging
  • OncoSimulR computes forward genetic simulation of cancer progresion with epistasis
  • PAA implements a protein array analyzer
  • Pbase manipulates and explores protein and proteomics data
  • podkat implements a position-dependent kernel association test
  • proteoQC provides proteomics data quality control
  • R3CPET analyses chromosome conformation capture and next-generation sequencing (3C-seq)
  • RCyjs display and manipulate graphs in Cytoscape.js
  • RMassBank offers a workflow to process tandem MS files and build MassBank records
  • RnaSeqSampleSize provides a sample size calculation method based on the negative binomial model
  • sapFinder is a package for variant peptides detection and visualization in shotgun proteomics
  • SIMAT implements a GC-SIM-MS data processing and alaysis tool
  • adds statistical assessment of cell state hierarchies from single-cell RNA-seq data

Last modified: Sun May 29 10:17:14 CDT 2016