- 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.
- 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.
- 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 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 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.
- 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 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 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 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.
- 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 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.
- 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 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.
- 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.
- AdaptiveSparsity implements algorithms for adaptive sparsity (Jeffrey's prior); 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.
- 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.
- 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 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 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 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 CMF package provides collective matrix factorization which finds joint low-rank representations for collections of matrices with shared row or column entities..
- 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 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..
- 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.
- 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.
- rlme implements rank-based estimation and prediction in random effects nested models.
- 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 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- penMSM estimates regularized multi-state models using L1 penalties.
- mlxR simulates of longitudinal data.
- 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.
- 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.
- graphicalVAR implements a graphical VAR for experience sampling data; it uses Rcpp and RcppArmadillo.
- seismicRoll computes fast rolling functions for seismology.
- glmgraph implements graph-constrained regularization for sparse generalized linear models; it uses Rcpp and RcppArmadillo.
- 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.
- 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.
- 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.
- brms fits Bayesian Regression Models via Stan with a focus on glm models.
- 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.
- 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
- 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.
- 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.
- 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.
- The creditr package prices credit default swaps using C code for the International Swaps and Derivatives Association (ISDA) CDS Standard Model.
- 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 DescTools package collects various tools to describe data.
- 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.
- 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.
- 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.
- frailtySurv simulates and fits general semiparametric shared frailty models.
- 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.
- 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.
- fourPNO fits a four-parameter Bayesiean IRT model; it uses Rcpp and RcppArmadillo.
- 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.
- 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.
- BEDMatrix supports matrices backed by binary PED / PLINK files without requiring to load them into memory.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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'.
- 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.
- 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.
- Countr estimates count process probabilities based on the Weibull distribution; it uses Rcpp and RcppArmadillo.
- 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.
- icd offers tools for working with ICD-9 and ICD-10 codes, and finding comorbidities.
- 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.
- protolite implements yet another serialization approach based on Protocol Buffers.
- RcppNumerical contains several libraries for numerical integration and optimization; 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.
- 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.
- SAMM estimates Gaussian linear mixed models; it uses Rcpp and RcppArmadillo.
- spduration fits split-population duration (cure) regression models; 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.
- 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).
- rcss offers numerical treatment of optimal convex switching problems in a finite time setting; it uses Rcpp and RcppArmadillo.
- qwraps2 contains 'quick wraps' helper functions for data summaries and formatted regression results; it uses Rcpp and RcppArmadillo.
- clusrank implements the Wilcoxon rank sum and signed sum tests for clustered data.
- flars computes functional lars models; it uses Rcpp and RcppEigen.
- dtwclust clusters times series with optimization for dynamic time warping.
- DiffusionRimp offers inference and analysis for diffusion processes; it uses Rcpp and RcppArmadillo.
- DLMtool simulates testing and implementation of data-limited fishery stock assessment.
- extraDistr computes d/p/q/r funtions for a number of distributions.
- ibm implements some (simple) individual based models for population dynamics models.
- jtGWAS computes standardized Jonckheere-Terpstra test statistics in genome-wide analysis.
- move visualizing and analyzing animal track data.
- perccal implements double boostrap regression confidence intervals; it uses Rcpp, RcppArmadillo and RcppEigen.
- sbrl provides scalable Bayesian list model algorithm.
- RPtests computes goodness-of-fit tests for high-dimensional models and can test for a variety of misspecifications.
- simstudy simulates data sets in order to explore modeling techniques or better understand data generating processes.
- MESS contains 'mixed esoteric statistical scripts'; it uses Rcpp and RcppArmadillo. synthACS adds synthetic microdata and spatial microsimulation modeling for American Community Survey (ACS) data.
- BTR trains and analyzes asynchronous Boolean Models from single-cell expression data.
- glmBfp implements the Bayesian paradigm for fractional polynomials in glm models; it uses Rcpp and RcppArmadillo.
- scoringRules adds scoring rules for parametric and simulated distribution forecasts.
- OpenImageR provides an image processing toolkit for preprocessing, filtering and image recognition; it uses Rcpp and RcppArmadillo.
- KernelKnn extends k-nearest neighbors algorithms via numerous kernel functions and distance metrics; it uses Rcpp and RcppArmadillo.
- Rfast implements a collection of fast (utility) functions for data analysis; it uses Rcpp and RcppArmadillo.
- MEGENA offers multiscale clustering of geometrical co-expression network data; it uses Rcpp and BH.
- triebeard adds radix trees, or 'tries', key-value data structures optimised for efficient lookups.
- rootWishart computes the distribution of the largest root for single and double Wishart settings; it uses BH and RcppEigen.
- milr estimates multiple-instance logistic regression under lasso penalty; it uses Rcpp and RcppArmadillo.
- sbfc offers a 'Selective Bayesian Forest Classifier' MCMC algorithm for feature selection and classification; it uses Rcpp and RcppArmadillo.
- SuperRanker adds tools for analysing the aggreement of two or more rankings of the same items.
- fasteraster processes rather images with vector recognition.
- yuima simulates and tests stochastic differential equations.
- IntegratedMRF implements integrated predictions using univariate and multivariate Random Forests.
- magick adds bindings to ImageMagickm the most comprehensive open-source image processing library available.
- RobustGaSP commputes robust parameter estimation and prediction of Gaussian stochastic process emulators; it uses Rcpp and RcppEigen.
- bigReg offers generalized linear models (GLM) for large data sets; it uses Rcpp and RcppArmadillo.
- GEEaSPU computes adaptive association tests for multiple phenotypes using generalized estimating equations (GEE); it uses Rcpp and RcppArmadillo.
- l0ara implements sparse generalized linear models with L0 approximation for feature selection; it uses Rcpp and RcppArmadillo.
- alakazam provides immunoglobulin (Ig) sequence lineage reconstruction, diversity profiling, and amino acid property analysis.
- MultiBD offers computationally efficient functions for direct likelihood-based inference for partially-observed multivariate birth-death processes; it uses Rcpp and RcppParallel.
- RcppGetconf interfaces libc to access system-level configuration values.
- AhoCorasickTrie implements fast searching for multiple keywords in multiple texts.
- bife estimates fixed effects binary choice models; it uses Rcpp and RcppArmadillo.
- NetRep computes permutation testing network module preservation across datasets; it uses Rcpp and RcppArmadillo.
- Cyclops provides cyclic coordinate descent for logistic, poisson and survival analysis; it uses Rcpp and RcppEigen.
- inca implements integer calibration where specific functions are provided for rounding to integers for calibration problems; it uses Rcpp and RcppArmadillo.
- oXim computes oxycline index from matrix echograms using median-filter and 2D-convolution based algorithms.
- acebayes sets up optimal bayesian experimental design using the ACE algorithm; it uses Rcpp and RcppArmadillo.
- ICAOD finds optimal designs via an imperialist competitive algorithm for optimal designs; it uses Rcpp and RcppEigen.
- ph2bye calculates phase ii clinical trial design using Bayesian methods.
- dfpk computes Bayesian dose-finding design using pharmacokinetics(pk) for phase i clinical trials; it uses Rcpp and RcppEigen.
- rtk adds a rarefaction tool kit and allows normalization of very large abundance tables.
- ccdrAlgorithm learns sparse Gaussian Bayesian networks via sparse regularization and block-cyclic coordinate descent.
- btb estimates Kernel density 'beyond the border' dedicated to urban geography.
- discretecdAlgorithm uses coordinate-descent algorithm for discrete data to learn Bayesian networks; it uses Rcpp and RcppEigen.
- wordspace implements an interactive laboratory for research on distributional semantic models.
- microclass provides methods for taxonomic classification of Prokaryotes; it used Rcpp, RcppArmadillo, RcppEigen and RcppParallel.
- wand retrieves 'magic' attributes from files and directories.
- ctmcd estimates continuous-time markov chain parameters from discrete daya; it uses Rcpp and RcppArmadillo.
- fastcmh implements a fast Cochran-Mantel-Haenszel test with significant pattern mining to detect intervals in binary genotype data.
- ModelMetrics brings a collection of metrics for evaluating models written in C++.
- BuyseTest implements generalized pairwise comparisons to compare two groups of observations in randomized trials; it uses Rcpp and RcppArmadillo.
- GenomicTools collects tools for genomic data analysis, currently with the main focus on (e)QTL and MDR analysis; it uses Rcpp and RcppArmadillo.
- phybreak analyses outbreaks with sequence data to simulate outbreaks.
- GAS simulates, estimates and forecasts Generalized Autoregressive Score models; it uses Rcpp and RcppArmadillo.
- GAS simulates an inhomogeneous self-exciting process (IHSEP), or Hawkes process, with a given (time-varying) baseline intensity and an excitation function.
- catlearn offers formal modeling for psychology using independently-replicated data sets.
- kamila implements clustering mixed-type data, specifically combinations of continuous and nominal data.
- iprior runs linear regression with I-Priors; it uses Rcpp and RcppEigen.
- indelmiss provides insertion deletion analysis while accountning for possible missing data.
- JSM does semiparametric joint modeling of survival and longitudinal data; it uses Rcpp and RcppEigen.
- velox offers fast raster manipulation and extraction.
- MSGARCH estimates, simulates and forecasts Markov-Switching GARCH models; it uses Rcpp and RcppArmadillo.
- energy computes E-statistics (energy) tests and statistics for multivariate and univariate inference.
- IsoSpecR implements the IsoSpec algorithm for obtaining the most probable masses of a chemical compound.
- propr calculates proportionality between vectors of compositional data.
- ndjson implements a streaming JSON reader.
- MetaheuristicFPA implementation a flower pollination algorithm in R; it uses Rcpp and RcppArmadillo.
- BayesBD carries out Bayesian analysis of image boundaries for binary (Bernoulli) and continuous (Gaussian) images; it uses Rcpp and RcppArmadillo.
- factorstochvol adds a Markov chain Monte Carlo (MCMC) sampler for estimation of latent factor stochastic volatility models; it uses Rcpp and RcppArmadillo.
- RNifti provides very fast access to images stored in the NIfTI-1 file format.
- TreeBUGS offers hierarchical multinomial processing tree (MPT) modeling; it uses Rcpp and RcppArmadillo.
- ClusterR implements Gaussian mixture models, K-means, mini-batch-Kmeans and K-medoids clustering; it uses Rcpp and RcppArmadillo.
- lowmemtkmeans performs the trimmed k-means clustering algorithm with lower memory use; it uses Rcpp and RcppArmadillo.
- IAPWS95 adds functions for thermodynamic water and steam properties based on the IAPWS Formulation 1995.
- htmltidy cleans up or pretty prints gnarly HTML and XHTML.
- SnakeCharmR integrates R and and Python code to make function calls, assign and retrieve variables, etc. from R.
- JOUSBoost implements under/oversampling for probability estimation to be used with machine learning methods.
- anytime converts input in 'any' form into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats.
- bayesAB adds fast Bayesian methods that allow the user to analyze A/B test data in a Bayesian framework.
- spectral offers common methods of spectral data analysis such as Fourier and Hilbert transforms.
- StepwiseTest implements a multiple testing method to control generalized family-wise error rate; it uses Rcpp and RcppArmadillo.
- RSSL provides semi-supervised learning for classification; it uses Rcpp and RcppArmadillo.
- qrencoder computes quick response codes (QR codes) used to authenticate transactions.
- rFTRLProximal adds an efficient implementation of "Follow The (Proximally) Regularized Leader" online learning algorithm;it uses Rcpp and RcppArmadillo.
- smooth provides forecasting using smoothing functions; it uses Rcpp and RcppArmadillo.
- htdp provides bindings to horizontal time dependent positioning via htdp.
- recexcavAAR offers a toolset for 3-d reconstruction and analysis of excavations.
- Barycenter computers Wasserstein Barycenters; it uses Rcpp and RcppArmadillo.
- dfphase1 plots phase I control charts with emphasis on distribution-free methods.
- combiter provides iterators for combinations, permutations, and subsets.
- bio3d offers utilities to process, organize and explore protein structure, sequence and dynamics data.
- sBIC computes a singular BIC for multiple models.
- smam implements statistical modeling of animal movements.
- meteoland estimates weather variables at any position of a landscape.
- graphql parses GraphQL and exports the resulting AST in JSON.
- gamreg computes robust and sparse regression via gamma-divergence with L1, elastic net and ridge; it uses Rcpp and RcppArmadillo.
- sharpeRratio offers an efficient moment-free estimator of the Sharpe ratio, or signal-to-noise ratio, for heavy-tailed data.
- bmlm estimates multi-level models via stan; it uses Rcpp and RcppEigen.
- GauPro fits Gaussian process models; it uses Rcpp and RcppArmadillo.
- QuantTools adds enhanced quantitative (financial) modeling functions.
- MAINT.Data implements methodologies for modelling interval data by Normal and Skew-Normal distributions; it uses Rcpp and RcppEigen.
- unsystation computes a second-order stationarity test for time series based on unsystematic sub-samples; it uses Rcpp and RcppArmadillo.
- jwutil adds various tools for data manipulation and testing; it uses Rcpp and RcppArmadillo.
- moveWindSpeed estimates wind speeds from bird trajectories using maximum likelihood.
- validatejsonr validates JSON input against JSON Schema Draft v4.
- RI2by2 offers randomization inference for treatment effects on binary outcomes.
- rpms fits a linear model to survey data in nodes obtained by recursive partitioning the data; it uses Rcpp and RcppArmadillo.
- MultivariateRandomForest models and predicts multivariate cases using Random Forests.
- lexRankr summarizes text via the LexRank algorithm.
- sf supports the 'Simple Features' standard for encoding geospatial data.
- raptr adds a representative and adequate prioritization toolkit for biodiversity; it uses Rcpp and RcppEigen.
- BCSub provides a Bayesian semiparametric factor analysis model for gene expression subtype identification.
- MatrixLDA fits penalized matrix-normal models for linear discriminant analysis with matrix-valued predictors; it uses Rcpp and RcppArmadillo.
- diagis creates a diagnostic plot and multivariate summary statistics from importance sampling; it uses Rcpp and RcppArmadillo.
- rtext offers R6 data objects support for text and data.
- bayesImageS implemebts Bayesian methods for image segmentation using a Potts model; it uses Rcpp and RcppArmadillo.
- tesseract offers R bindings to the open source optical-character recognition engines.
- s2 connects R to Google's s2 library for geometry on the sphere.
- ManifoldOptim adds an interface to ROPTLIB for Riemannian Manifold Optimization; it uses Rcpp and RcppArmadillo.
- xyz offers the 'xyz' algorithm for fast interaction search in high-dimensional data to find strong interactions in almost linear time.
- bsearchtools exposes C++ binary search functions (std::lower_bound, std::upper_bound) plus other convenience functions.
- diffrprojects provides data structures and methods for measuring, coding, and analysing text within text corpora.
- nprobust implements robust inference for local polynomial regression and kernel density estimation; it uses Rcpp and RcppArmadillo.
- rucrdtw adds R bindings to the UCR suite for ultrafast subsequence search for best match under dynamic time warping and euclidean distance.
- varband implements variable banding for modeling local dependence and estimating precision matrices; it uses Rcpp and RcppArmadillo.
- pirate provides the generated effect modifier (GEM) method; it uses Rcpp and RcppArmadillo.
- flockimplements process synchronization using file locks.
- vdiffr adds visual regression testing and graphical diffing as an extension to the 'testthat' package.
- medfate simulates Mediterranean forest dynamics using cohort-based description of vegetation.
- EMbC implements expectation-maximization binary clustering for annotation of data; it uses Rcpp and RcppArmadillo.
- gcKrig provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas; it uses Rcpp and RcppArmadillo.
- gdpc computes the generalized dynamic principal components of Peña and Yohai; it uses Rcpp and RcppArmadillo.
- forecastSNSTS forecasts stationary and non-stationary time-series.
- eDMAperforms dynamic model averaging with grid search as in Dangl and Halling; it uses Rcpp and RcppArmadillo.
- ffstrean implements a adaptive forgetting factor scheme to estimates mean and variance to detect multiple changepoints in streaming data.
- lclGWAS offers efficient estimation of a discrete-time multivariate frailty model for grouped survival data.
- queuecomputer adds an efficient method for simulating queues with arbitrary arrival and service times; it uses Rcpp and RcppArmadillo.
- ibmcraftr offers a toolkit to develop individual-based models in infectious disease.
- ABCoptim implements Artificial Bee Colony (ABC) optimization.
- bcROCsurface provides bias-corrected methods for estimating the ROC surface; it uses Rcpp and RcppArmadillo.
- gwfaperforms geographically-weighted fractal analysis (gwfa) to calculate the local fractal dimension of a set of points.
- NestedCategBayesImpute fits the nested Dirichlet process mixture of products of multinomial distributions (NDPMPM).
- benchr provides infrastructure to accurately measure and compare the execution time of R expressions.
- valr implements genome interval arithmetic in R to read and manipulate genome intervals and signals.
- ggforce accelerates ggplot2 via new stats and geoms.
- Rdtq implements density tracking by quadrature (DTQ) for stochastic differential equations (SDEs).
- strat provides the stratification index by Zhou (2012); it uses Rcpp and RcppArmadillo.
- robets computes robust exponential smoothing forecasts as an alternative to
`ets()`

. - SpaCCr offers genomic region detection via spatial convex clustering; it uses Rcpp and RcppArmadillo.
- SmartSVA introduces a fast and efficient surrogate variable analysis (SVA) algorithm; it uses Rcpp and RcppEigen.
- rIsing fits an Ising model to a binary dataset using L1 regularized logistic regression and extended BIC; it uses Rcpp and RcppEigen.
- DEploid deconvolute mixed genomes with unknown proportions using a modified Li and Stephens algorithm with Markov chain Monte Carlo (MCMC).
- diffusr implementation network diffusion algorithms such as insulated heat propagation or Markov random walks; it uses Rcpp and RcppEigen.
- RSQLite embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package.
- esaddle fits the Extended Empirical Saddlepoint (EES) density; it uses Rcpp and RcppArmadillo.
- GWmodel introduces geographically-weighted models for suitably localised calibration; it uses Rcpp and RcppArmadillo.
- ramcmc implements robust adaptive Metropolis sampling as in Vihola (2012); it uses Rcpp and RcppArmadillo.
- cstab selects number of cluster via normalized clustering instability.
- robustlmm fits robust linear mixed effects models; it uses Rcpp and RcppEigen.
- imagine provides an imaging engine to apply image filters to data matrices.
- optimization offers a flexible multi-purpose optimizer with numerous input specifications.
- phangorn estimates phylogenetic trees and networks using maximum likelihood, maximum parsimony, distance methods and Hadamard conjugation.
- GLMaSPU implements an adaptive test on high-dimensional parameters in generalized linear models; it uses Rcpp and RcppArmadillo.
- rrr implements reduced rank regressions along with diagnostics and graphics.
- eulerr draws area-proportional Euler diagrams which generalize Venn diagrams; it uses Rcpp and RcppArmadillo.
- bindrcpp provides an easy way to fill an environment with active bindings that call a C++ function.
- divest converts images from the DICOM format into the NIfTI-1 format.
- cubature offers adaptive multivariate integration over hypercubes; it uses Rcpp and RcppArmadillo.
- GDINA implements the generalized DINA models for cognitive diagnostic analyses; it uses Rcpp and RcppArmadillo.
- valuer prices variable annuity life insurance contracts by means of Monte Carlo methods; it uses Rcpp and RcppEigen.
- LBSPR simulates expected equilibrium length composition using the length-based spawning potential ratio.
- BTYDplus provides methods to describe and predict customers' purchase behavior in a non-contractual setting.
- factorcpt identifies change-points in common and idiosyncratic components via factor modelling; it uses Rcpp and RcppArmadillo.
- striprtf extracts plain text from RTF (Rich Text Format) files.
- acc processes accelerometer data from uni-axial and tri-axial devices; it uses Rcpp and RcppArmadillo.
- acrt robustly tests affine hypotheses on regression coefficients in models with autocorrelated errors; it uses Rcpp and RcppEigen.
- ICtest estimates and tests the number of interesting components in linear dimension reduction; it uses Rcpp and RcppArmadillo.
- qualpalr generates qualitative color palettes that are maximally distinct; it uses Rcpp, RcppArmadillo and RcppParallel.
- pgee.mixed performs simultaneous estimation and variable selection for correlated bivariate mixed outcomes; it uses Rcpp and RcppArmadillo.
- PLMIX fits finite mixtures of Plackett-Luce models for partial top rankings/orderings within a Bayesian framework.
- SpaTimeClus implements model-based clustering of spatio-temporal data via mixture models; it uses Rcpp and RcppArmadillo.
- mixlink fits 'mixture link', an extension to glms where the outcome distribution is a finite mixture of densities; it uses Rcpp and RcppGSL.
- ReIns contains functions from the book 'Reinsurance: Actuarial and Statistical Aspects'.
- rlas reads and write 'las' and 'laz' binary files containing LiDAR data.
- ETAS fits the space-time 'Epidemic Type Aftershock Sequence' (ETAS) model to earthquake catalogs using a stochastic declustering approach.
- joineRML jointly models multivariate longitudinal data and time-to-event outcomes; it uses Rcpp and RcppArmadillo.
- attrCUSUM implements tools for design of attribute variable sampling intervals; it uses Rcpp and RcppArmadillo.
- dynamichazard fits dynamic hazard models with binary outcomes; it uses Rcpp and RcppArmadillo.
- ludic provides probabilistic record linkage with direct identifiers; it uses Rcpp and RcppArmadillo.
- lidR adds airborne LiDAR data manipulation and visualization.
- BAMBI fits and simulates mixtures of univariate and bivariate angular distributions; it uses Rcpp and RcppArmadillo.
- semver offers tools and functions for parsing, rendering and operating on semantic version strings.
- testforDEP provides dependence tests for two variables.
- textTinyR offers text processing for small and big data files; it uses Rcpp, RcppArmadillo and BH.
- xslt extends the xml2 package by transforming XML documents via XSL stylesheets.
- fst offers fast serialization serialization of data.frame objects.
- robCompositions implements robust estimation for compositional data.
- microseq adds basic functions for microbial sequence data analysis.
- mrfDepth computes depth measures in multivariate, regression and functional settings; it uses Rcpp and RcppEigen.
- baitmet automates quantification of metabolites.
- kdevine computes multivariate kernel density estimation with Vine copulas.
- ziphsmm fits zero-inflated Poisson hidden (semi-)Markov models; it uses Rcpp and RcppArmadillo.
- pdSpecEst offers positive-definite wavelet-based multivariate spectral analysis; it uses Rcpp and RcppArmadillo.
- multinet implements functions for the creation/generation and analysis of multilayer social networks.
- TLMoments calculate empirical trimmend L-moments of arbitrary order and trimming, and converts them to distribution parameters.
- padr transforms datetime data into a format ready for analysis.
- MADPop analyses population differences using Major Histocompatibility Complex (MHC) genotypes of samples having a variable number of alleles.
- grattan supplies a series of functions focused on costing and evaluating Australian tax policy.
- Rlabkey exchanges data with a LabKey server.
- RLumModel solves ODEs to simulate luminescense signal in the mineral quartz; it uses Rcpp and RcppArmadillo.
- SpecsVerification is a collection of routines with an emphasis on comparitive verification of ensemble forecast; it uses Rcpp and RcppArmadillo.
- wicket implements tools to process 'well-known text' (WKT) spatial data.
- hBayesDM fits an array of decision-making tasks in a hierarchical Bayesian framework; it uses Rcpp and RcppEigen.
- beyondWhittle implements Bayesian spectral inference for stationary timeseries.
- skm solves the selective k-means; it uses Rcpp, RcppParallel and RcppArmadillo.
- nse offers multiple ways to calculate numerical standard error (NSE) of univariate time series.
- classifierplots ; it uses Rcpp and RcppArmadillo.
- fastJT computes efficient Jonckheere-Terpstra test statistics for robust machine learning and genome-wide association studies.
- penalized fits high-dimensional penalized (lasso, fused lasso, ridge) regresion models; it uses Rcpp and RcppArmadillo.
- alphabetr implements algorithms for high-throughput sequencing of antigen-specific T cells.
- gbp adds basic infrastructure and several algorithms for 1d-4d bin packing problem; it uses Rcpp and RcppArmadillo.
- MAVE implements several methods for dimension reduction; it uses Rcpp and RcppArmadillo.
- reads 'untidy' Excel files into R; it uses Rcpp and RcppArmadillo.
- palm fits point process models using the Palm likelihood.
- iBST fits bagging survival trees on a mixture of populations.
- PhylogeneticEM implements an automatic shift detection method for trait evolution models; it uses Rcpp and RcppArmadillo.
- KoulMde fits via Koul's minimum distance estimation in linear regression and autoregression model by coordinate descent algorithm.
- prophet provides an automated forecasting procedure for time series based on an additive model with non-linear trends.
- cleanEHR offers a toolset for the Critical Care Health Informatics Collaborative datset.
- grove computes functional denoising and functional ANOVA through wavelet-domain Markov groves; it uses Rcpp and RcppArmadillo.
- odbc connect to ODBC-compatible databases using the DBI interface.
- BayesianTools implements general-purpose MCMC and SMC samplers and tools for Bayesian statistics.
- RcppHMM collects functions to evaluate sequences, decode hidden states and estimate parameters from a discrete-time Hidden Markov Models.
- mousetrap offers functions for importing, preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
- ipft implements algorithms and utility functions for indoor positioning using fingerprinting techniques.
- pacotest tests for partial copulas and the simplifying assumption in vine copulas.
- opusminer provides an R interface to the OPUS Miner algorithm and implementation.
- dlib connects R to the DLib toolkit for machine learning and computer vision algorithms.
- stdvectors creates and manipulates C++ std::vector objects from R.
- sppmix models spatial Poisson processes where the intensity surface is analogous to a finite additive mixture; it uses Rcpp and RcppArmadillo.
- filesstrings offers file and string utilities on top of base R and 'stringr'.
- optiSel implements a framework for the optimization of breeding programs via optimum contribution selection; it uses Rcpp and RcppArmadillo.
- planor generates factorial designs, including fractional designs, orthogonal block designs, and more; it uses Rcpp and RcppArmadillo.
- ggraph implements the grammar of graphics for graphs and networks.
- dynsbm offers a dynamic stochastic block model for the evolution of nodes through time; it uses Rcpp and RcppArmadillo.
- mixR performs maximum likelihood estimation for finite mixture models.
- interflex performs diagnostic tests of multiplicative interaction models; it uses Rcpp and RcppArmadillo.
- tm provides a framework for text-mining applications with R.
- DiffNet detects statistically significant changes in complex biological networks; it uses Rcpp and RcppEigen.
- observer manipulates Microsoft Word and PowerPoint Documents.
- pinbasic offers fast and stable esitimation of the probability of informed trading.
- rdist calculates pairwise distance using a common framework; it uses Rcpp and RcppArmadillo.
- FSelectorRcpp implements the 'FSelector' entropy-based feature selection algorithm; it uses Rcpp and RcppArmadillo.
- cpr implements control polygon reduction and control net reduction for parsimonious B-spline regressions; it uses Rcpp and RcppArmadillo.
- FRK offers fixed-rank kriging for spatial/spatio-temporal modelling and prediction.
- riskRegression provides risk regression models for survival analysis with competing risks; it uses Rcpp and RcppArmadillo.
- BNSL implements Bayesian network structure learning.
- gsynth provides a generalized synthetic control method: causal inference with interactive fixed-effect models; it uses Rcpp and RcppArmadillo.
- iNextPD adds interpolation and extrapolation for phylogenetic diversity.
- mrgsolve simulates from ODE-based population pk/pd and systems pharmacology models; it uses Rcpp, BH and RcppArmadillo.
- POUMM implements a phylogenetic Ornstein-Uhlenbeck mixed model; it uses Rcpp and RcppArmadillo.
- reticulate provides a bi-directional interface between R and Python.
- gee4 estimates generalized estimating equations; it uses Rcpp and RcppArmadillo.
- kohonen offers supervised and unsupervised self-organising maps (SOMs).
- CNull implements fast algorithms for frequency-preserving Null models in ecology.
- graphkernels adds a fast C++ implementation of various graph kernels.
- treespace explores the distribution of phylogenetic trees.
- supc computes via the Self-Updating Process Clustering algorithm.
- Rvoterdistance calculates the distance between voter and multiple polling locations.
- bayesDP augments data with historical controls using the Bayesian discoint prior; it uses Rcpp and RcppArmadillo.
- CVR performs canonical variate regression (CVR) for two sets of covariates and a univariate response; it uses Rcpp and RcppArmadillo.
- frailtyEM fits shared frailty models with a semi-parametric baseline hazard with the EM algorithm.
- sbart implements sequential Bayesian additive regressive trees for imputation.
- multdyn estimates multivariate graphical model for multidimensional time series with time-varying effective connectivity; it uses Rcpp and RcppArmadillo.
- secure fits sparse factor regression using sequential estimation; it uses Rcpp and RcppArmadillo.
- varbvs adds fast algorithms for fitting Bayesian variable selection models and computing Bayes factors.
- icenReg offers regression models for interval censored data; it uses Rcpp and RcppEigen.
- joinXL performs join queries on Excel files; its use of Rcpp is spurious.
- mafs implements meta-forecasting; ; its use of Rcpp is spurious.
- OpenMx provides extended structural equation modelling; it uses Rcpp and RcppEigen.
- RmixmodCombi combines mixture components for clustering; its use of Rcpp is spurious.
- BatchMap creates high density linkage maps in outcrossing species; it uses Rcpp and RcppArmadillo.
- flexsurv estimate flexible parametric survival and multi-state models for time-to-event data.
- geojsonR processes GeoJSON objects per RFC 7945 via the 'json11' library; it uses Rcpp and RcppArmadillo.
- CircularDDM computes circular drift-diffusion models; it uses Rcpp and RcppArmadillo.
- SMMA provides soft maximin estimation for large scale array-tensor models; it uses Rcpp and RcppArmadillo.
- GenomicMating implements an efficient breeding by genomic mating algorithm; it uses Rcpp and RcppArmadillo.
- MCMCprecision calculates precision of discrete parameters in transdimensional MCMC; it uses Rcpp, RcppArmadillo and RcppEigen.
- ctsem adds continuous-time structural equation modeling.
- treatSens analysises sensitivity for causal inference by investigating unmeasured confounding; it uses Rcpp, RcppEigen and BH.
- BART fits Bayesian Additive Regression Trees for flexible nonparametric modeling.
- imputeTS imputes missing values in univariate time series.
- vennplot calculates and plots Venn diagrams in two and three dimensions.
- GRADAG uses genetic algorithms to learn sparse acyclic directed graphs; it uses Rcpp and RcppArmadillo.
- imp4p analyse missing value mechanisms and imputes data for bottom-up MS-based proteomics.
- phantom does gene set Pareto heterogeneity analysis of time-course gene expression data; it uses Rcpp and RcppArmadillo.
- PRIMME adds an interface to the PRIME eigenvalue and SVD library.
- bigKRLS offers optimised regularized least squares; it uses Rcpp and RcppArmadillo.
- mnis gives easy downloading capabilities for the members' name information service operated by the UK parliament.
- ompr models and solves mixed integer linear programs.
- icosa computes global triangular and penta-hexagonal grids based on tessellated icosahedra.
- cna provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA).
- RcppQuantuccia links R with Quantuccia, the headers-only subset of QuantLib.
- Rsampletrees offers MCMC sampling of gene genealogies conditional on genetic data.
- kernelboot calculates smoothed bootstrap and random generation from kernel densities.
- HardyWeinberg adds statistical tests and graphics for Hardy-Weinberg equilibria.
- autothresholdr provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users.
- GGIR is a tool to process and analyse data collected with wearable raw acceleration sensors.
- idem offers inference in randomized controlled trials with death and missingness; it uses Rcpp and RcppEigen.
- trackdem can obtain population density and body size structure from video material or image sequences; it uses Rcpp and RcppArmadillo.
- partialCI analysis partially cointegrated time series.
- philentropy computes 46 optimized distance and similarity measures for comparing probability functions.
- cctools implements the continuous convolution trick in nonparametric estimation; it uses Rcpp and RcppArmadillo.
- purrrlyr contains tools from the intersection of purrr and dplyr.
- Peptides calculates indices and theoretical physiochemical properties of protein sequences.
- DataGraph exports either '.dtable' or '.dtbin' files that can be read by DataGraph, a graphing and analysis application for macOS.
- kmcudaR implements "Yinyang K-Means" using CUDA and OPneMP 4.0.
- anMC efficiently computes orthant probabilities of high-dimensional Gaussian vector; it uses Rcpp and RcppArmadillo.
- miRNAss performs genome-wide discovery of pre-miRNAs with few labeled examples using machine learning methods.
- gastempt fits gastric emptying time series from MRI or scintigraphic measurements; it uses Rcpp and RcppEigen.
- olsrr adds tools for teaching and learning ordinary least squares regression.
- LAM contains procedures for latent variable modelling with a particular focus on multilevel data.
- fastTextR interfaces the 'fastText' library for text classification and word vector learning.
- breathteststan adds Stan-based fits to gastric emptying curves.
- mbgraphic offers measure-based exploratory data analysis.
- LocalControl generates high-quality comparative effectiveness evidence via nonparametric approaches to address biases and confounding.
- poisbinom provides the p/d/q/r functions for the Poisson-Binomial distribution.
- hommel implements methods for closed testing with Simes inequality, in particular Hommel's method.
- GeneralizedUmatrix computes credible visualization for two-dimensional projections of data; it uses Rcpp and RcppArmadillo.
- osmdata download and imports OpenStreetMap ('OSM') data as 'sf' or 'sp' objects.
- castor offers efficient comparative phylogenetics on large trees.
- stepR allows fitting of step-functions to univariate serial data where neither the number of jumps nor their positions is known.
- PhenotypeSimulator allows for the flexible simulation of phenotypes under different models.
- brlrmr estimates bias reduction with missing binary response.
- coga computes convolutions of the Gamma distribution.
- rtdists provides response time distributions (density/PDF, distribution function/CDF, quantile function, and random generation).
- piton wraps the 'Parsing Expression Grammar Template Library' for generating parsing expression grammars.
- rust uses the generalized ratio-of-uniforms method to simulate from univariate and multivariate distributions; it uses Rcpp and RcppArmadillo.
- nandb offers number and brightness image analysis.
- bikedata downloads and aggregates data from public hire bicycle systems.
- libstableR computes fast and accurate evaluations, random draws and estimation for the skew stable distribution.
- rangeBuilder implements occurrence filtering, geometric + taxonomic standardization and generation of species range polygons.
- Emcdf computes and visualizes the empirical joint distribution of multivariate data.
- cld2 interfaces Google's Compact Language Detector 2.
- parallelDist calculates distance matrices for continuous, binary, and multi-dimensional input matrices; it uses Rcpp and RcppArmadillo.
- themetagenomics explores thematic structure and predicted functionality of 16s rRNA Amplicon Data.
- clampSeg implements the non-parametric JUmp Local dEconvolution Segmentation filter JULES to idealise patch clamp recordings.
- cld3 interfaces Google's Compact Language Detector 3.
- robustBLME robustly fits linear mixed effects models through weighted ML and ABC; it uses Rcpp and RcppArmadillo.
- GPGame solves complex game problems using Gaussian processes.
- RcppMsgPack includes the msgpack-c C/C++ headers for efficient binary serialization.
- meshimp simplifies surface triangular meshes with associated distributed data; it uses Rcpp and RcppEigen.
- DPWeibull estimates Dirichlet process Weibull mixture model for survival data.
- genepop offers population genetic data analysis using 'Genepop'.
- walker performs fully bayesian linear regression where regression coefficients vary over "time"; it uses Rcpp, RcppEigen and BH.
- catSurv provides methods of computerized adaptive testing for survey researchers; it uses Rcpp, RcppArmadillo and RcppGSL.
- interp does bivariate data interpolation on regular and irregular grids, either linear or using splines; it uses Rcpp and RcppEigen.
- ECFsup tests the equality of several covariance functions of functional data; it uses Rcpp and RcppArmadillo.
- momentuHMM offers maximum likelihood analysis of animal movement behavior using multivariate hidden Markov models; it uses Rcpp and RcppArmadillo.
- womblR models spatiotemporal boundary detection for areal unit data; it uses Rcpp and RcppArmadillo.
- diceR performs cluster analysis using an ensemble clustering framework.
- POMaSPU evaluates an association between an ordinal response and multiple phenotypes; it uses Rcpp and RcppArmadillo.
- SFS implements the Similarity-First Search combinatorial algorithm (SFS); it uses Rcpp and RcppArmadillo.
- JumpTest focuses on jump detection via a fast simulation model for stochastic volatility model; it uses Rcpp and RcppEigen.
- rrpack implements multivariate regression methodologies with a focus on reduced-rank regression (RRR); it uses Rcpp and RcppArmadillo.
- aphid uses hidden Markov models and profile HMMs for biological sequence analysis.
- bssm implements efficient methods for Bayesian inference of state space modesl; it uses Rcpp, BH and RcppArmadillo.
- later adds utilities for delaying function execution until after the R execution stack has emptied.
- SeqKat detects kategis, a localized hyermutation.
- cytometree computes automated cytomety gating; it uses Rcpp and RcppArmadillo.
- tidygenomics adds tidy verbs for dealing with genomic data frames.
- goldi does gene ontology label discernment and identification; it uses Rcpp and RcppArmadillo.
- hyper2 offers a suite of routines for the hyperdirichlet distribution.
- sparsio adds I/O operations with sparse matrices via the fast 'SVMlight' reader and writer.
- BradleyTerryScalable fits the Bradley-Terry model to large and sparse networks of data ; it uses Rcpp and RcppArmadillo.
- rxylib provides access to the 'xylib' C library for to import xy data from powder diffraction, spectroscopy and other experimental methods.
- survHE contains a suite of functions for survival analysis in health economics. ; it uses Rcpp and RcppArmadillo.
- abcrf Performs approximate Bayesian computation model choice and parameter inference via random forests; it uses Rcpp and RcppArmadillo.
- adeba does univariate and multivariate non-parametric kernel density estimation with adaptive bandwidth using a Bayesian approach.
- FastSF offers fast structural filtering with a L0 penalty; it uses Rcpp and RcppArmadillo.
- grf adds generalized random forests for estimation and inference.
- IncDTW implements incremental calculation of the DTW (Dynamic Time Warping) distance of two vectors.
- landscapeR simulates categorical maps on actual geographical realms.
- msde implements an MCMC sampler for the posterior distribution of arbitrary time-homogeneous multivariate SDE models.
- SobolSequence provides Sobol sequence with better two-dimensional projections.
- SuperGauss offer 'super fast' likelihood inference for stationary Gaussian times series; it uses Rcpp and RcppEigen.
- teachingApps contains apps and gadgets for teaching data analysis and statistics concepts.
- tidygraph offers a tidy API for graph manipulation.
- RcppTN generate random deviates from and calculate moments of a Truncated Normal distribution using the algorithm of Robert (1995).
- datastructures implements advanced data structures such as hashmaps, heaps, or queues; it uses Rcpp and BH.
- fastLink implements a Fellegi-Sunter probabilistic record linkage model; it uses Rcpp, RcppEigen and RcppArmadillo.
- LowWAFOMNX implements the Low Walsh Figure of Merit (WAFOM) sequence based on Niederreiter-Xing sequence.
- WGCNA performs weighted correlation network analysis on high-dimensional data.
- SubTite chooses subgroup specific optimal doses in a phase I dose finding clinical trial; it uses Rcpp and RcppArmadillo.
- RBesT adds Bayesian evidence synthesis tools; it uses Rcpp and RcppEigen.
- ClusVis offers Gaussian-based visualization of clustering achieved by mixture model on any type of data; it uses Rcpp and RcppArmadillo.
- LowWAFOMSobol implements a Low Walsh Figure of Merit (WAFOM) sequence based on Sobol sequence.
- RPresto implements a DBI-compliant interface to Presto, an open-source distributed SQL engine.
- swmmr interfaces the Storm Water Management Model of the US EPA.
- bayeslm offers efficient sampling for Gaussian linear regression with arbitrary priors; it uses Rcpp and RcppArmadillo.
- revdbayes provides functions for the Bayesian analysis of extreme value model; it uses Rcpp and RcppArmadillo.
- DrImpute imputes dropout events in single-cell RNA-sequencing data; it uses Rcpp and RcppArmadillo.
- vennLasso provides variable selection and estimation routines for models stratified by binary factors; it uses Rcpp and RcppEigen.
- APML0 fits linear and Cox models via an augmented penalized minimization method; it uses Rcpp and RcppEigen.
- bsplinePsd implements a Metropolis-within-Gibbs MCMC sampler for Bayesian nonparametric spectral density estimation.
- coda.base adds a basic set of functions for compositional data analysis; it uses Rcpp and RcppArmadillo.
- social quantifies and visualizes social autocorrelation.
- BiDAG implements a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs).
- ProjectionBasedClustering clusters via projections based on the generalized U*-matrix visualization of a topographic map.
- tidyselect is a backend for selecting functions of the so-called 'tidyverse'.
- curstatCI computes the (smoothed) ml estimator and pointwise bootstrap CIs for the distribution function under current status data.
- iRF iteratively grows feature weighted random forests and finds high-order feature interactions in a stable fashion.
- dHSIC implements the d-variable Hilbert Schmidt independence criterion and several hypothesis tests based on it.
- optiSolve solves linear, quadratic, and rational programs with linear, quadratic, and rational constraints.
- ordinalForest runs ordinal regression with high and low dimensional data.
- GreedyEPL summarises collection of partitions into single optimal partition under expected posterior loss; it uses Rcpp and RcppArmadillo.
- RcppXPtrUtils provides helper functions to compile C++ functions and retrieve an 'XPtr' to be passed to other C++ components.
- VARtests implements the wild bootstrap tests for autocorrelation in VAR models; it uses Rcpp and RcppArmadillo.
- dggridR computes discrete global grids for spatial analysis.
- ICRanks constructs simultaneous confidence intervals for ranks.
- BCEE implements the Bayesian causal effect estimation algorithm; it uses Rcpp and RcppArmadillo.
- SpaDES.tools provides GIS/map utilities and additional modeling tools for cellular automata and agent based models in 'SpaDES'.
- knor offers a non-uniform memory access ('NUMA') optimized, parallel k-means routine.
- GrpString converts series of event names to strings, finding common patterns, discovering featured patterns and more.
- elo calculates Elo ratings and rankings of any two-team-per-matchup system, evaluates matchups, rating updates, and win probabilities.
- esreg simultaneously models quantile estimate and expected shortfall; it uses Rcpp and RcppArmadillo.
- fuser enables high-dimensional penalized 'lasso' regression across heterogeneous subgroups; it uses Rcpp and RcppEigen.
- odpc compute the one-sided dynamic principal components useful for forecasting; it uses Rcpp and RcppArmadillo.
- skpr generates and evaluates D, I, A, Alias, E, T, and G optimal designs; it uses Rcpp and RcppArmadillo.
- rrecsys generates rating predictions and lists of recommended items from recommendation datasets.
- DatabionicSwarm implementing interacting agent populations which may exhibit self-organization and swarm intelligence.
- STARTdesign calibrates the design parameters for single-to-double arm transition design for phase II clinical trials.
- PKPDmisc offers a toolbox for data management common to pharmacokinetic and pharmacokinetic modeling and simulation.
- Seurat provides tools for quality control, analysis, and exploration of single cell RNA sequencing data; it uses Rcpp and RcppEigen.
- StepSignalMargiLike provides function to estimate multiple change points using marginal likelihood method
- Eagle implements multiple-locus association mapping on a genome-wide scale; it uses Rcpp and RcppEigen.
- sptemExp fits constrained spatiotemporal mixed models for exposure estimation.
- GBJ offers the Generalized Berk-Jones test for set-based inference in genetic association studies; it uses Rcpp and BH.
- rDotNet implements a low-level interface to '.NET' along the lines of the R C .call interface.
- rvinecopulib interfaces a high performance C++ version of 'VineCopula'; it uses Rcpp, RcppEigen and BH.
- BNPMIXcluster adds a Bayesian nonparametric approach for clustering; it uses Rcpp and RcppArmadillo.
- anomalyDetectionimplements augmented network log anomaly detection procedures; it uses Rcpp and RcppArmadillo.
- bigstatsr provides file-backed big matrices via memory-mapping; it uses Rcpp, BH and RcppArmadillo.
- udpipe adds tokenization, parts-of-speech tagging, lemmatization and dependency parsing with the 'UDPipe' 'NLP' toolkit.
- RGeode provides a hybrid Bayesian method for geometric density estimation.
- VeryLargeIntegers adds a multi-precission library to store and manage arbitrarily big integers without loss of precision.
- BosonSampling implements Boson sampling; it uses Rcpp and RcppArmadillo.
- re2r provides an interface to the primarily deterministic finite automaton based regular expression engine RE2 from Google.
- FDRSeg estimates step functions via multiscale inference with controlled false discovery rate (FDR).
- scanstatistics detects anomalous space-time clusters using the scan statistics methodology; it uses Rcpp and RcppArmadillo.
- cOde generated C code for 'deSolve', 'bvpSolve' and 'Sundials'; it uses Rcpp and RcppArmadillo.
- mclustcomp implements measures to compare clusters; it uses Rcpp and RcppArmadillo.
- xtensor adds headers for the 'xtensor' C++ library for numerical analysis with multi-dimensional array expressions.
- fastrtext interfaces the 'fastText' library to learn text representations and text classifiers.
- lime adds 'Local Interpretable Model-Agnostic Explanations' for black-box models; it uses Rcpp and RcppEigen.
- EAinference estimates augmentation methods for statistical inference on high-dimensional data; it uses Rcpp and RcppArmadillo.
- vegclust performs fuzzy clustering of vegetation data.
- JMbayes jointly models longitudinal and time-to-event data under a Bayesian approach; it uses Rcpp and RcppArmadillo.
- binaryGP fit and predict a Gaussian process model with (time-series) binary response; it uses Rcpp and RcppArmadillo.
- cartography covers cartographic representations such as proportional symbols, chroropleth, typology, flows or discontinuities maps.
- dng provides density, distribution function, quantile function and random generation for the split-t distribution.
- orthoDr uses an orthogonality constrained optimization algorithm to solve dimension reduction problems;it uses Rcpp and RcppArmadillo.
- Rdimtools provides a collection of linear and nonlinear dimension reduction techniques; it uses Rcpp and RcppArmadillo.
- augSIMEX implements the augmented Simulation-Extrapolation (SIMEX) algorithm.
- spiderbarparses and tests robots exclusion protocol files and rules.
- DPP performs inference of parameters of Normal distributions from a mixture of Normals.
- dodgr computes distances on dual-weighted directed graphs using priority-queue shortest paths.
- hetGP performs Gaussian process regression with heteroskedastic noise.
- qGaussian provides d/p/q/r functions for the q-gaussian distribution with parameters mu and sig.
- repfdr estimates Bayes and local Bayes false discovery rates for replicability analysis.
- Rlinsolve iteratively solves systems of (sparse) linear equations; it uses Rcpp and RcppArmadillo.
- fRLR fits set of repeated linear regressions faster.
- transport solves optimal transport problems.
- incgraphprovides efficient and incremental graphlet counting for network optimization; it uses Rcpp and BH.
- corpustools focuses on tokenized text formats for text analysis.
- rENA offers epistemic network analysis; it uses Rcpp, RcppArmadillo, RcppParallel and RcppEigen.
- RMariaDB implements a 'DBI'-compliant interface to 'MariaDB' and 'MySQL' databases.
- RxODE facilitates simulating from ODE-based models; it uses Rcpp and RcppArmadillo.
- RmecabKo interfaces the Eunjeon Project for part-of-speech tagging of Korean text.
- HistDAWass performs histogram-valued data analysis; it uses Rcpp and RcppArmadillo.
- rerf implements Random Forester by Tomita; it uses Rcpp, RcppArmadillo and RcppZiggurat.
- kvh reads and writes files in key-value-hierarchy format.
- miic provides multivariate information induction causation.
- onemap constructs of genetic maps in experimental crosses: Full-Sib, RILs, F2 and Backcrosses.
- SNPknock generates knockoff variables from discrete Markov chains and hidden Markov models.
- meaRtools offers core algorithms for micro-electro array (MEA) analysis.
- geoops adds tools for 'GeoJSON' objects topology calculations and manipulations.
- ANN2 implements an artificial neural networks for anomaly detection; it uses Rcpp and RcppArmadillo.
- regnet uses network-based regularization for generalized linear models; it uses Rcpp and RcppArmadillo.
- SILGGM offers inference for large-scale Gaussian graphical models in gene networks.
- CovTools collects geometric and inferential tools for analysis of covariance structures; it uses Rcpp and RcppArmadillo.
- fdadensity adds functional data analysis for density functions by transformation to a hilbert space.
- RZigZag implements the Zig-Zag algorithm with subsampling and control variates; it uses Rcpp and RcppEigen.
- GreedySBTM performs clustering on the nodes of an undirected binary dynamic network; it uses Rcpp and RcppArmadillo.
- HHG implenents the Heller-Heller-Gorfine ('HHG') tests for multivariate k-sample homogeneity and independence.
- rarhsmm fits Gaussian hidden (semi-)Markov models; it uses Rcpp and RcppArmadillo.
- hogsvdR implements higher-order generalized singular value decomposition; it uses Rcpp and RcppArmadillo.
- securitytxt identifies and parses web security policies files.
- tvR provides tools for denoising noisy signal and images via Total Variation Regularization; it uses Rcpp and RcppArmadillo.
- detrendr permits detrending of images; it uses Rcpp and RcppParallel.
- FarmTest performs robust multiple testing for means in the presence of known and unknown latent factors; it uses Rcpp and RcppArmadillo.
- pense computes robust penalized elastic net S and MM estimator for linear regression; it uses Rcpp and RcppArmadillo.
- basad does Bayesian variable selection with shrinking and diffusing priors; it uses Rcpp and RcppEigen.
- RcppAlgos adds tools for combinatorics and computational mathematics.
- PieceExpIntensity fits a Bayesian model to find changepoints based on rates and count data; it uses Rcpp and RcppArmadillo.
- episode estimates with penalisation in systems of ordinary differential equations; it uses Rcpp and RcppArmadillo.
- dynfrail fits semiparametric dynamic frailty models with the EM algorithm; it uses Rcpp and RcppArmadillo.
- lubridate makes dealing with dates a little easier.
- ape contains a variety of phylogenetics functions.
- n1qn1 ports the 'n1qn1' modules for unconstrained BFGS optimization from SciLab; it uses Rcpp and RcppArmadillo.
- ADMM solve optimization problems based on Alternating Direction Method of Multipliers (ADMM); it uses Rcpp and RcppArmadillo.
- DatAssim provides data assamiliation using Kalman filter incorporating previous results; it uses Rcpp and RcppArmadillo.
- equateMultiple equates multiple forms using Item Response Theory (IRT); it uses Rcpp and RcppArmadillo.
- Mega2R accesses and processes a 'Mega2' genetic database.
- mobsim does spatial simulation and scale-dependent analysis of biodiversity changes.
- readobj contains a fast reader for 'Wavefron' OBJ 3D scene files.
- StepReg performs 'forward' and 'stepwise' variable selection; it uses Rcpp and RcppEigen.
- lslx fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL); it uses Rcpp and RcppEigen.
- spatialwarnings compute early-warnings signals (EWS) of ecosystem degradation on raster data sets.; it uses Rcpp and RcppArmadillo.
- vmd ports and extends code by Dragomiretskiy and Zosso for conducting Variational Mode Decomposition (VMD).
- dvmisc does faster computation of common statistics and miscellaneous functions.
- PCMRS implements the partial credit model with response styles (PCMRS); it uses Rcpp and RcppArmadillo.
- changepointsHD does change-point estimation for expensive and high-dimensional models; it uses Rcpp and RcppArmadillo.
- ClinicalTrialSummary estimates summary measures for clinical trials.
- prioritizr undertakes conservation prioritization using integer programming techniques; it uses Rcpp, RcppArmadillo and BH.
- UniIsoRegression performs unimodal and isotonic l1, l2, and linf regression.
- GeDS computes geometrically designed splines for regressions.
- nlmixr fits and compares nonlinear mixed-effects models in differential equations; it uses Rcpp, RcppArmadillo, RcppEigen, and BH.
- bigtime estimates large VAR models with lasso penalties; it uses Rcpp, RcppArmadillo, and RcppEigen.
- predkmeans implements predictive k-means clustering using a mixture of experts model; it uses Rcpp and RcppArmadillo.
- SELF provides the Structural Equation Embedded Likelihood Framework criteria to learn causal structure.
- sentometrics does textual sentiment time series agggreation and prediction; it uses Rcpp and RcppArmadillo.
- imbalance offers preprocessing algorithms for imbalanced datasets; it uses Rcpp and RcppArmadillo.
- ipumsr reads 'IPUMS' extract files for census, survey and geographic data; it uses Rcpp and RcppArmadillo.
- fDMA; it uses Rcpp and RcppArmadillo.
- lwgeom; it uses Rcpp and RcppArmadillo.
- ordinalClust performs ordinal data classification, clustering and co-clustering; it uses Rcpp and RcppArmadillo.
- YPInterimTesting provides monitoring boundaries for interim testing using the adaptively weighted log-rank test.
- CVXR offers an object-oriented modeling language for disciplined convex programming (DCP); it uses Rcpp and RcppEigen.
- strider implements a strided iterator and range; it uses Rcpp and BH.
- biofiles interfaces and parses GenBank/GenPept flat files.
- trialr showcases Bayesian clinical trial design implemented in RStan and R; it uses Rcpp, RcppEigen and BH.
- covTestR implements testing functions for covariance matrices; it uses Rcpp and RcppArmadillo.
- JMcmprsk; it uses Rcpp and RcppArmadillo.
- RClickhouse provides a DBI interface to the 'Yandex Clickhouse' database.
- TexExamRandomizer personalizes and randomizes exams written in 'LaTeX'.
- outbreaker2 implements Bayesian reconstruction of disease outbreaks.
- UniDOE provides procedures for uniform design of experiments.
- Numero adds a statistical framework to define subgroups in complex datasets.
- hesim offers functions for developing and analyzing the output of health-economic simulation models; it uses Rcpp and RcppArmadillo.
- HMMEsolver implements a fast solver for Henderson Mixed Model Equations; it uses Rcpp and RcppArmadillo.
- RPostgres provides a DBI-compliant interface to PostgreSQL.
- recurse computes revisitation metrics for trajectory data.
- TukeyRegion determines Tukey regions: polytopes in the Euclidean space; it uses Rcpp and BH.
- NetworkDistance computes distance measures for networks; it uses Rcpp and RcppArmadillo.
- filling offers matrix completion, imputation, and inpainting methods; it uses Rcpp and RcppArmadillo.
- support computes support points of a possibly non-uniform distribution; it uses Rcpp, RcppArmadillo and BH.
- mmapcharr memory-maps character matrices as if they were simple R(cpp) matrices; it uses Rcpp and BH.
- Umatrix visualizes structures in high-dimensional data via emergement self-organizing maps.
- PUlasso offers high-dimensional variable selection with presence-only data; it uses Rcpp and BH.
- pccc implements the pediatric complex chronic conditions (CCC) classification.
- rbacon does age-depth modelling via Bayesian statistics to reconstruct accumulation histories for deposits.
- BClustLonG provides a Dirichlet process mixture model for clustering longitudinal gene expression data; it uses Rcpp and RcppArmadillo.
- humanleague generates high-entropy integer synthetic populations using quasirandom sampling.
- mizer offers multi-species size spectrum modelling.
- implements quantile regression forests using the fast random forest package 'ranger'.
- afCEC provides active function cross-entropy clustering; it uses Rcpp and RcppArmadillo.
- PPforest implements projection pursuit forest algorithm for supervised classification; it uses Rcpp and RcppArmadillo.
- BVSNLP adds Bayesian variable selection in high-dimensional settings; it uses Rcpp, RcppArmadillo and RcppEigen.
- JuniperKernel implements 'Jupyter' messaging protocol via 'Xeus'.
- kexpmv computes matrix exponentials using Krylov subspace routines.
- reda implements recurrent event analysis; it uses Rcpp and RcppArmadillo.
- ijtiff imports TIFF files saved from 'ImageJ' and writes TIFF files than can be read by 'ImageJ'.
- tmbstan provides MCMC sampling from 'TMB' model objects via 'stan'; it uses Rcpp, RcppEigen and BH.
- tibbletime makes 'tibble' types time-aware with subsetting and aggregating functionality.
- ensembleEN constructs ensembles of regularized linear model estimates; it uses Rcpp and RcppArmadillo.
- refinr clusters and merges similar values within a character vector.
- metacoder provides tools for parsing, manipulating, and graphing taxonomic abundance data.
- ICcalib calibrates and fits Cox proportional hazard models with intermittent observations; it uses Rcpp and RcppArmadillo.
- netrankr implements methods for centrality related analyses of networks; it uses Rcpp and RcppArmadillo.
- googlePolylines encodes 'sf' objects and coordinates using the 'Google' polyline algorithm ; it uses Rcpp and BH.
- KSgeneral computing p-values of the K-S test for (dis)continuous Null distribution.
- AnaCoDa analyses codon data under stationarity using a Bayesian framework.
- REddyProc post-processes (half-)hourly eddy-covariance measurements.
- tsibble adds 'tidy' temporal data frames and tools.
- RcppCWB adds bindings for the 'Corpus Workbench'.
- popkin estimates kinship and FST under arbitrary population structure ; it uses Rcpp and RcppEigen.
- chunkR reads external data tables in chunks.
- FarmSelect implements factor-adjusted robust model selection; it uses Rcpp and RcppArmadillo.
- npsf Provides a variety of tools for nonparametric and parametric efficiency measurement.
- binnednp implements nonparametric estimation for interval-grouped data.
- junctions analyses the breakdown of genomic ancestry blocks in hybrid lineages.
- Bioi performs single linkage clustering and connected component analyses are often performed on biological images.
- FENmlm estimates multiple fixed-effects maximum likelihood models with possibly non-linear parameters.
- fs offers cross-platform file system operations based on 'libuv'.
- gkmSVM adds gapped-Kmer support vector machine functionality.
- icr computes and plot Krippendorff's inter-coder reliability coefficient alpha.
- RTransProb analyses and forecasts credit migrations (transition) matrices; it uses Rcpp and RcppArmadillo.
- RcppGreedySetCover implementation of the greedy algorithm for the set cover problem; it uses Rcpp and BH.
- reproducible adds a set of tools that enhances reproducibility beyond package management.
- TSrepr offers different time series representation methods for more effective time-sries data mining.
- multinets analyses multilevel networks (as extends 'igraph').
- estimatr provides fast estimators for design-based inference; it uses Rcpp and RcppEigen.
- networkR does fast manipulation, handling, and analysis of large-scale networks from social data; it uses Rcpp and RcppArmadillo.
- rubias offers Bayesian inference from the conditial genetic stock indentification model.
- BeSS performs best subset selection in linear, logistic and CoxPH models; it uses Rcpp and RcppEigen.
- colorednoise simulates temporally autocorrelated population time series.
- DataVisualizations visualizes high-dimensional data; it uses Rcpp and RcppArmadillo.
- KRIG implements different methods for spatial statistics, particularly focused on kriging; it uses Rcpp and RcppArmadillo.
- cellWise adds tools for detecting cellwise outliers; it uses Rcpp and RcppArmadillo.
- essHist provides an optimal histogram in the sense of probability density estimation and feature detection.
- CENFA adds tools for climate- and ecological-niche factor analysis of spatial data.
- detectRUNS detects runs of homozygosity and of heterozygosity in diploid genomes.
- RaPKoD implements a random projection kernel outlier detector through random low-dimensional projections; it uses Rcpp and RcppArmadillo.
- Phase123 simulates and conducts 'Phase 123' trials; it uses Rcpp and RcppArmadillo.
- rosqp solves quadratic programs with optional equality and inequality constraints using the 'OSQP' library.
- amt manages and analyses animal movement data.
- specklestar obtains positional parameters for stellar systems from series of speckle images.
- idealstan fits Bayesian item-response theory ideal-point models with 'Stan'; it uses BH and RcppEigen.
- facilitation simulates a variety of spatial individual-based models of plant-plant interactions.
- NCutYX clusters omics data of multiple types with a multilayer network representation; it uses Rcpp and RcppEigen.
- SolveLS solves linear system of equations iteratively using a variety of methods; it uses Rcpp and RcppArmadillo.
- GPCMlasso detects differential item functioning (DIF) in generalized partial credit models (GPCM); it uses Rcpp and RcppArmadillo.
- micropan has functions for computation and visualizations of microbial pan-genomes; it uses Rcpp and BH.
- serrsBayes adds Bayesian modeling of Raman spectroscopy (SEERS); it uses Rcpp and RcppEigen.
- estudy2 implementation of most commonly used parametric and nonparametric test for event study methodology.
- forestControl compute approximate false positive rate control in selection freqeuncy for random forest.
- GpGp computes fast Gaussian processes using Vecchia's approximation.
- mfGARCH estimates mixed-frequency (MIDAS) GARCH models.
- projpred performs projection predictive feature selection for generalized linear model; it uses Rcpp and RcppArmadillo.
- geogrid turns geospatial polygons into regular or hexagonal grids; it uses Rcpp and RcppArmadillo.
- fingerPro quantifies the provenance of sediments in a catchment or study area; it uses Rcpp and RcppGSL.
- ncpen estimates the nonconvex penalized linear, logistic and Poisson regression models; it uses Rcpp and RcppArmadillo.
- wbsts detects number and locations of time-series change-points using the Wild Binary Segmentation and Locally Stationary Wavelet models.
- DGM fits dynamic graphical models to estimate directed dynamic networks in fMRI data; it uses Rcpp and RcppArmadillo.
- NlinTS provides non-linear time series forecasting and causality detection.
- dynamo implements methods to fit a three-dimensional dynamic array model; it uses Rcpp and RcppArmadillo.
- JuliaCall provides low- and high-level interfaces to Julia.
- segclust2d provides methods for segmentation/clustering of bivariate time-series; it uses Rcpp and RcppArmadillo.
- carSurv estimates correlation-adjusted regression survival (CARS) scores.
- particles implements a graph-based particle simulator based on d3-Force.
- bpnreg fits Bayesian multiple and fixed-effect models for circular data; it uses Rcpp, RcppArmadillo and BH.
- nmslibR wraps the 'Non-Metric Space Library' (NMSLIB); it uses Rcpp and RcppArmadillo.
- RobustCalibration implements full Bayesian analysis for calibrating mathematical models; it uses Rcpp and RcppEigen.
- linearQ adds a linear algorithm for simulating quantiles in multiscale change-point segmentation problems.
- belg calculates the Boltzmann entropy of a landscape gradient, it uses Rcpp and RcppArmadillo.
- kmer implements fast k-mer counting and clustering for biological sequence analysis.
- spp analyses ChIP-seq and other functional sequencing data; it uses Rcpp and BH.
- vlad contains functions to set up risk-adjusted quality control charts in health care; it uses Rcpp and RcppArmadillo.
- circglmbayes performs Bayesian analysis of circular outcome General Linear Models; it uses Rcpp, RcppArmadillo and BH.
- glm.deploy provides functions to inspect the predict function of fitted glm objects.
- hdme fits penalized regression with measurement error in high-dimension.
- decido provides constrained triangulation of polygons using the 'earcutt' library.
- TVsMiss uses regularization likelihood for variable selection.
- understandBPMN calculates understandibility metrics for Business Process Modelling Notation (BPMN).
- CaliCo calibrates computational code in a Bayesian framework; it uses Rcpp and RcppArmadillo.
- nngeo implments a k-nearest neighbor search for projected and non-project 'sf' spacial layers.
- BoltzMM provides probability computation, data generation and estimation for Boltzmann machines; it uses Rcpp, RcppArmadillo, and BH.
- miceFast offers fast imputation methods; it uses Rcpp and RcppArmadillo.
- PPRL adds a toolbox for deterministic, probabilistic and privacy-preserving record linkage techniques.
- cutpointr determines and evaluates optimal cutpoints in binary classification data.
- fasterize replaces the `raster::rasterize()` function with a faster alternative; it uses Rcpp and RcppArmadillo.
- nVennR provides the nVenn algorithm for pleasing and informative Venn diagrams.
- rare implements linear models with tree-based lasso-regularization for rare features; it uses Rcpp and RcppArmadillo.
- BSL implements Bayesian Synthetic Likelihood, an alternative to ABC; it uses Rcpp and RcppArmadillo.
- kde1d offers efficient univariate local polynomial kernel density estimation; it uses Rcpp, RcppEigen and BH.
- landsepi fits a spatio-temporal stochastic model to asses plant pathogen resistance.
- spGARCH estimates, simulates and visualizes spatial and spatiotemporanl GARCH models; it uses Rcpp and RcppEigen.
- RNOmni implements an omnibus test for genetic association analysis; it uses Rcpp and RcppEigen.
- EMMIXgene provides unsupervised selection and clustering of microarray data using mixture models; it uses Rcpp, RcppArmadillo and BH.
- ADMMsigma fits penalized precision matrix via alternating direction of multipliers algorithmn; it uses Rcpp and RcppArmadillo.
- autoFRK does automated fixed rank kriging; it uses Rcpp, RcppEigen and RcppParallel.
- BayesESS determines effective sample size in Bayesian models; it uses Rcpp, RcppArmadillo and RcppEigen.
- dcurver adds utility functions for Davidian curves; it uses Rcpp and RcppArmadillo.
- kdtools works with multidimensional data in R and C++; it uses Rcpp and BH.
- mosum implements MOSUM based statistical procedures for detecting multiple changes in the mean.
- pimeta offers prediction intervals for random-effect meta-analysis; it uses Rcpp and RcppEigen.
- MixAll clusters and classifies using model-based mixture models.
- gscounts implements design and analysis of group sequential designs with negative binomial outcomes.
- rres adds functions for studying realized genetic relatedness between people.
- WeMix computes weighted mixed-effects models using multilevel pseudo maximum likelihood.
- BreedingSchemeLanguage describes and simulates planned breding schemes.
- cbinom implements a continuous analog to the standard discrete binomial distribution.
- openCR offers open population capture-recapture modeling from animal populations subject to turnover.
- SimilaR implements a novel method to determine similarity for R source code based on program dependence ; it uses Rcpp and BH.
- WeibullR offers Weibull analysis for reliability engineering; it uses Rcpp and RcppArmadillo.
- promises provides abstractions for asynchronous programming in R using promises.
- RMCriteria solves most of multicriteria ranking problems using partial and total pre-order; it uses Rcpp and RcppEigen.
- pcadapt implements fast principal component analysis for outlier detection; it uses Rcpp and RcppArmadillo.
- iilasso efficiently fits linear / logistic regression models with independently interpretable lasso; it uses Rcpp and BH.
- meltt matches event data by location, time and type; it uses Rcpp and RcppArmadillo.
- geojsonsf converts GeoJSON object to simple features objects; it uses Rcpp and RcppArmadillo.
- ROI.plugin.qpoases adds a 'qpOASES' plugin to the ROI infrastructure for optimization.
- rpql offers regularized penalized quasi-likelihood for joint selection in GLMMs; it uses Rcpp and RcppArmadillo.
- EMVS implements expectation-maximization for fitting Bayesian spike-and-slab regularization paths; it uses Rcpp and RcppArmadillo.
- FRegSigCom uses signal processing methods for function-on-function regression with functional response; it uses Rcpp and RcppEigen.
- bigrquery interfaces the Google 'BigQuery' databases from R.
- logKDE computes log-transformed kernel density estimates for positive data.
- mdmb offers model-based treatment of missing data using maximum likelihood or Bayesian estimation; it uses Rcpp and RcppArmadillo.
- BLSM provides a Bayesian latent space model for complex network; it uses Rcpp and RcppEigen.
- timechange adds efficient routines for manipulating date-time ; it uses Rcpp and RcppArmadillo.
- mrbsizeR implements scale space multiresolution analysis of random signals.
- aricode computes standard clusteromh comparison measures efficiently.
- DtD estimates and simulates Merton's 'distance to default' model; it uses Rcpp and RcppArmadillo.
- intcensROC offers fast spline-based constrained estimation for AUC of interval censored survival data; it uses Rcpp and RcppEigen.
- microsamplingDesign finds optimal designs for non-compartmental pharmokinetic analysis; it uses Rcpp and RcppArmadillo.
- bioacoustics analyzes audio recordings to automatically extract animal vocalizations.
- GA provides a flexible general-purpose toolbox for genetic algorithm for stochastic optimisation; it uses Rcpp and RcppArmadillo.
- blorr has tools for developing and validating binary logistic regression models.
- dqrng implements several fast pseudo random number generators; it uses Rcpp and BH.
- groupedSurv efficiently estimate grouped survival models; it uses Rcpp, RcppEigen and BH.
- mgwrsar fits (mixed) geographycally weighted models with spatial autocorrelation; it uses Rcpp and RcppEigen.
- cliqueMS annotates datafrom liquid chromatography and mass spectrometry experiments; it uses Rcpp, RcppArmadillo and BH.
- lvec offers out-of-memory vectors for several types; it uses Rcpp and BH.
- DstarM analyses two choice reaction data with the 'D*M' method; it uses Rcpp and RcppArmadillo.
- biwavelet conducts univariate and bivariate wavelet analyses.
- epiphy analyses plant disease epidemics over time and/or space.
- ldat works with large data sets which cannot fit in memory; it uses Rcpp and BH.
- irregulAR1 simulates and evaluates irregularly sampled stationary AR(1) processes; it uses Rcpp and RcppArmadillo.
- hdbinseg does change-point analysis of high-dimensional time series via binary segmentation; it uses Rcpp and RcppArmadillo.
- imagerExtra provides image processing functions based on 'imager'.
- comperank computes ranking and ratings based on competition results.
- heatwaveR detects heatwaves and cold-spells; it uses Rcpp and RcppArmadillo.
- Spbsampling draws spatially balanced samples.
- wdm implements weighted dependence measures and related symptotic tests for independence.
- MM4LMM performs inference of linear mixed models through the MM algorithm; it uses Rcpp and RcppEigen.
- reclin assist in performing probabilistic record linkage and deduplication.
- polysat offers tools for polyploid microsatellite analysis.
- implements measurement units for R vectors: progagation, conversion, derivation and simplification of errors.
- inplace provides in-places operators for R similar to the corresponding C++ operators.
- PQLseq does differential analysis of large-scale RNA sequencing data; it uses Rcpp and RcppArmadillo.
- pseudorank calculates pseudo-ranks efficiently.
- ratematrix estimates the evolutionary rate matrix using MCMC; it uses Rcpp and RcppArmadillo.
- CaseBasedReasoning seeks out 'similar' solutions to.
- jaccard calculates statistical significance of Jaccard/Tanimoto similarity coefficients for binary data.
- liger provides a lightweight iterative gene set enrichment toolkit; it uses Rcpp and RcppArmadillo.
- eseis implements a toolbox for environmental seismology.
- IntervalSurgeon manipulates integer-bounded intervals.
- Orcs contains 'omni-directional code snippets'.
- QTL.gCIMapping.GUI offers a GUI for QTL genome-wide composite interval mapping.
- RcppEigenAD computes first- and second-order partial derivatives ; it uses Rcpp, RcppEigen and BH.
- QTL.gCIMapping conducts multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect mixed linear model.
- exuber tests and dates periods of explosive dynamics in time series using recursive unit root tests.
- multistateutils provides functions for working with multi-state modelling.
- mixdir clusters high-dimensional categorical datasets.
- RcppMeCab wraps the 'MeCab' part-of-speech and morphological analyser; it uses Rcpp, RcppParallel and BH.
- DDPGPSurv performs MCMC inference for nonparametric Bayesian survival analysis; it uses Rcpp and RcppArmadillo.
- dynutils provides common functions for 'dynverse' packages for trajectory inference.
- glmmfields implements Bayesian spatial and spatialtemporal models; it uses Rcpp, RcppEigen and BH. "
- MuChPoint offers a nonparametric approach to estimate the location of block boundaries.
- umap uses uniform manifold approximation and project for dimension reduction.
- vsgoftest implements Vasicek and Song goodness-of-fit tests based on Kullback-Leibler divergence.
- mumm fits multiplicative mixed models via ML; it uses Rcpp and RcppEigen.
- ospq provides bindings to the OSQP solver for quadratic programs.
- L0Learn adds fast algorithms for best subset selection via L0 regularization; it uses Rcpp and RcppArmadillo.
- rollRegres does fast expanding and rolling linear regressions; it uses Rcpp and RcppArmadillo.
- princurve fits a principal curve in arbitrary dimension; it uses Rcpp and RcppArmadillo.
- CASMAP detects statistically significant combinations of SNPs in assocation mapping.
- elmNNRcpp trains and predicts using single hidden-layer feedforward neural networks; it uses Rcpp and RcppArmadillo.
- etm computes empirical transition matrices; it uses Rcpp and RcppArmadillo.
- gppm provides Gaussian process panel modeling for longitudinal panel data.
- lpirfs contains functions to estimate linear and nonlinear impulse responses; it uses Rcpp and RcppArmadillo.
- sundialr interfaces the 'SUNDIALS' ODE solvers.
- nmixgof provides residuals and overdispersion metrics to assess the goodness of fit of N-mixture models.
- puniform does meta-analysis correcting for publication bias.
- sarima adds functions, classes and methods for seasonal ARIMA time series models; it uses Rcpp and RcppArmadillo.
- updog implements empirical Bayes approaches to genotype polyploids; it uses Rcpp and RcppArmadillo.
- Rlda estimates a Bayesian LDA model for mixed-membership clustering; it uses Rcpp and RcppArmadillo.
- spCP implements a spatially varying change point model; it uses Rcpp and RcppArmadillo.
- xdcclarge estimates a (c)DCC-GARCH model in large dimensions; it uses Rcpp and RcppArmadillo.
- physiology estimates physiologic characteristics of infacts, children and adults.
- adpss provides functions for planning and conducting a clinical trial with adaptive sample size determination.
- CKLRT offers composite kernel machine regression based on likelihood ratio; it uses Rcpp and RcppEigen.
- TDAstats does topological data analysis via persistent homologies in a Veitoris-Rips complex.
- jmvconnect connect R to the Jamovi statistical spreadsheet; it uses Rcpp and BH.
- fpeek checks text files at a glance, similar to `head`, `tail`, `wc`, and `iconv`.
- RTransferEntropy measures information flow between time series.
- weibulltools contains methods for examining bench test or field data using Weibull analysis.
- demu implements the determinantal point process (DPP) based optimal design emulator; it uses Rcpp and RcppArmadillo.
- dexterMST computes conditional maximum likelihood calibration of multistage tests.
- bcf estimates binary treatments and continuous outcomes using Bayesian causal forests; it uses Rcpp and RcppArmadillo.
- bigreadr reads large text files by splitting them into smaller files.
- HDclust clusters high-dimensional data with Hidden Markov Models on variable blocks; it uses Rcpp and RcppProgress.
- hipread reads hierarchical fixed width files; it uses Rcpp and BH.
- gren does adaptive group-regularized logistic elastic net regression; it uses Rcpp and RcppArmadillo.
- circumplex analyses and visualises circular data; it uses Rcpp and RcppArmadillo.
- MultiFit computes in a multivariate multiscale frameworks for independence tests; it uses Rcpp and RcppArmadillo.
- robmixglm fits robusts generalized linear model using mixtures.
- alpaca fits GLM models with high-dimensional k-way fixed effects; it uses Rcpp and RcppArmadillo.
- lfl contains algorithms related to linguistic fuzzy logic.
- polyRAD computes genotype calling with uncertainty from sequencing data in polyploids and diploids.
- rmi provides mutual information estimators based on k-nearest neighbor estimates; it uses Rcpp and RcppArmadillo.
- BMSC implements constrained coefficient estimation and variable selection using Stan; it uses Rcpp, RcppEigen and BH.
- abn models multivariate data with Additive Bayesian Networks; it uses Rcpp and RcppArmadillo.
- fasterElasticNet fits Elastic Net, Lasso, and Ridge regression in a fast way; it uses Rcpp and RcppArmadillo.
- landscapemetrics calculates landscape metrics for categorical landscape patterns; it uses Rcpp and RcppArmadillo.
- SCPME estimates penalized precision matrix via ADMM; it uses Rcpp and RcppArmadillo.
- Rnmr1D processes proton nuclear magnetic resonance spectra.
- vapour offers lightweight access to the 'gdal' library.
- RWDataPlyr reads and handles data from 'RiverWare' simulations in a 'dplyr' pipeline.
- imptree creates classification trees with imprecise probabilities.
- NetworkInference infers latent diffusion networks.
- pGPx computes pseudo-realizations from the posterior of disitribution of a Gaussian Process; it uses Rcpp and RcppArmadillo.
- KeyboardSimulator simulates keyboard presses and mouse clicks with R code.
- sparseinv wraps 'SuiteSparse' routines executing the Takahashi equations.
- bgsmtr fits Bayesian group-sparse multi-task regression models using Gibbs sampling.
- ambient generates natural looking noise via the 'FastNoise' library.
- rayshader creates and visualizes hillshaded maps from elevation matrices.
- EstMix estimates tumor clones percentages for snp data and whole genome sequencing; it uses Rcpp and RcppArmadillo.
- runner contains (windowed, rolling, cumulative) windowed functions with varying windows size and options for missing values.
- SparseLPM models nonnegative entries in a rectangular adjacency matrix; it uses Rcpp and RcppArmadillo.
- strex provides extra string manipulation functions.
- ggdmc uses hierarchical Bayesian modelling to fit cognitive models; it uses Rcpp and RcppArmadillo.
- spatialrisk calculates concentration risk under the EU insurance regulation framework (Solvency II).
- sport does sequential pairwise online rating for multi-player challenges; it uses Rcpp and RcppArmadillo.
- ungroup estimates penalized composite link models from coarsely binned data; it uses Rcpp and RcppEigen.
- multivariance measures multivariate dependence using distance multivariance.
- BLPestimatoR performs demand estimation as described in Berry, Levinsohn and Pakes; it uses Rcpp and RcppArmadillo.
- farver implements vectorised colour comparison and comparison.
- VICmodel provides the variable infiltration capacity (VIC) model.
- conStruct models spatially continuous and discrete population strucure; it uses Rcpp, RcppEigen, and BH.
- bayesdfa implements Bayesian dynamic factor analysis with 'Stan'; it uses Rcpp, RcppEigen, and BH.
- metadynminer adds tools to read, analyze and visualize metadynmamics HILLS files.
- Ckmeans.1d.dp produces fast optimal univariate clustering and segmentation by dynamic programming.
- crfsuite wraps the 'CRFsuite' library for conditional random field models.
- MetaStan performs Bayesian meta-analysis via 'Stan'.
- colourvalues assigns colours to values, using a viridis or user-supplied palette; it uses Rcpp and BH.
- ggwordcloud implements a wordcloud geom for ggplot2 so that texts do not overlap.
- Opt5PL evaluates optimal designs for 3, 4 and 5 parameter logistic models.
- quantities integrates 'units' and 'error' for a complete quantity calculus.
- roptim performs general-purpose optimization in R using C++; it uses Rcpp and RcppArmadillo.
- oce supports the analysis of oceanographic data.
- texmex does extreme value modeling of threshold excesses, maxima and multivariate extremes.
- coxrt fits Cox regression based on retrospectively ascertained times-to-event; it uses Rcpp and RcppArmadillo.
- lolog estimates Latent Order Logistic (LOLOG) models for networks; it uses Rcpp and BH.
- Temporal performs likelihood-based estimation and inference on time-to-event data; it uses Rcpp and RcppEigen.
- BayesMallows implements a Bayesian version of the Mallows rank model; it uses Rcpp and RcppArmadillo.
- divDyn describes sampling and diversity dynamics of fossil occurence datasets.
- SMUT tests the mediation effect of multiple SNPs; it uses Rcpp and RcppEigen.
- AlphaSimR offers stochastic simulation of breeding programs; it uses Rcpp and RcppArmadillo.
- HARModel estimates, simulates and forecasts heterogenous autoregressive models; it uses Rcpp and RcppArmadillo.
- RcppNLoptExample shows how to access NLopt from C(++) code without linking.
- revealedPrefs computes direct and indirect revealed preferences; it uses Rcpp and RcppArmadillo.
- Immigrate performs iterative max-min entropy margin-maximization with interaction terms for feature selection.
- jsonify converts R objects to JSON using the rapidjson library.
- ppgmmga offers the projection pursuit algorithm via GMMs using GAs; it uses Rcpp and RcppArmadillo.
- touch implements software tools developed in the H-CUP and AHRQ projects.
- fclust implements fuzzy clustering, cluster validity indices and visualization; it uses Rcpp and RcppArmadillo.
- idefix generates efficient designs for discrete choice experiments; it uses Rcpp and RcppArmadillo.
- HRM tests main and interaction effects in high-dimensional repaeated measure factorial designs; it uses Rcpp and RcppArmadillo.
- KODAMA does un- and semi-supervised learning for feature extraction; it uses Rcpp and RcppArmadillo.
- JMI computes the Jackknife Mutual Information (JMI) between two vectors; it uses Rcpp and RcppArmadillo.
- lbfgsb3c provides a limited-memory BFGS minimiser with parameter bounds; it uses Rcpp and RcppArmadillo.
- stratEst implements the strategy frequency estimation method; it uses Rcpp and RcppArmadillo.
- DEploid deconvolutes mixed genomes with unknown proportions; it uses Rcpp and RcppArmadillo.
- SAMCpack computes Stochastic Approximation Monte Carlo MCMC; it uses Rcpp and RcppArmadillo.
- compboost implenents component-wise boosting; it uses Rcpp and RcppArmadillo.
- pgsc computes the generalized synthetic control estimator (Powell, 2017); it uses Rcpp and RcppArmadillo.
- RcppDist adds a header-only library with several distribution functions; it uses Rcpp and RcppArmadillo.
- sboost creates classifiers for binary outsomes using Adapative Boosting (AdaBoost).
- calculates the monthly and self-calibrating Palmer Drought Severity Index (PDSI and scPDSI).
- mapi implemnts Mapping Average Pairwise Information to expression spatial variation of spatial metrics.
- mudens computes density estimates for right-censored survival times.
- RcppEnsmallen connects R to the Ensmallen header-only optmization library; it uses Rcpp and RcppArmadillo.
- fabMix implements model-based clustering of multivariate continuous data; it uses Rcpp and RcppArmadillo.
- pbv compute probabilities of the bivariate Normal distribution; it uses Rcpp and RcppArmadillo.
- carfima fits continuous-time fractionally integrated ARMA processes; it uses Rcpp and RcppArmadillo.
- ggiraph creates interactive 'ggplot2' graphics via 'htmlwidgets'.
- lobstr visualizes data structures with trees.
- memnet efficiently implements network science tools.
- obliqueRSF computes oblique random survival forests; it uses Rcpp and RcppArmadillo.
- polylabelr wraps the 'polylabel' library to find approximate poles of inaccessibility of a polygon suitable for labeling.
- RiemBase estimates statistics including Fréchet mean and geometric median for manifold-valued data; it uses Rcpp and RcppArmadillo.
- ivtools contains tools for instrumental variable estimation.
- yardstick tools to quantify model fits to data such as confusion matrices, class probability summaries and metrics.
- ibs calculates B-splines with a given set and knots and order.
- interep; it uses Rcpp and RcppArmadillo.
- STARTS estimates the STARTS model by Kenny and Zautra; it uses Rcpp and RcppArmadillo.
- pvar calculates p-variation of finite sample data.
- BondValuation analyses fixed-coupon bonds valuation allowing for odd coupon periods a various days count conventions.
- GPM models Gaussian Processes in a general and efficient manner; it uses Rcpp and RcppArmadillo.
- mixggm models mixtures of Gaussian graphical models for model-based clustering; it uses Rcpp and RcppArmadillo.
- RCSF supports airborne LiDAR via Cloth Simulation Filter.
- rJST estimates the Joint Sentiment Topic model and its versed variety; it uses Rcpp, RcppArmadillo and RcppProgress. NLMR simulates neutral landscape models.
- OsteoBioR estimates temporal change of isotonic values of bone and teeth data; it uses Rcpp, RcppEigen and BH.
- BivRec implements bivariate alternating recurrent event data analysis.
- NPBayesImputeCat does non-parametric Bayesian multiple imputation for categorical missing at random.
- offers utility functions for handling, analysing and visualizing data from portable emissions measurement systems.
- BHSBVAR fits Structural Bayesian Vector Autoregressive Models; it uses Rcpp and RcppArmadillo.
- rcosmo handles and analysis spherical, HEALPix and cosmic microwave data.
- GenEst adds a command-line and Shiny-based Generalized Mortality Estimator for birds and bats at wind and solar facilities.
- spreadr simulates spreading activity in a network.
- supports analysis via unmanned aerial vehicle remote sensing tools.
- metacard implements a flexible approach to identify moderators in meta-analysis.
- changepoint.mv analyses multivariate timeseries for changepoints.
- ProFound add photometry tools for simple and advanced source extraction.
- HMB provides hierarchical model-based estimation; it uses Rcpp and RcppArmadillo.
- rCRM fits a two-parameter continual reassessment method model; it uses Rcpp and RcppEigen.
- compas does conformational manipulations of protein atomic structures; it uses Rcpp and RcppEigen.
- COMPoissonReg fits Conway-Maxwell Poisson (COM-Poisson) regression models.
- cglm fits conditional generalized linear models for clustered data; it uses Rcpp and RcppArmadillo.
- twosamples offers fast permutation-based two sample tests.
- emstreeR computes Euclidian minimum spanning trees; it uses Rcpp, RcppArmadillo, RcppMLPACK and BH.
- sommer solves structural multivariate-univariate linear mixed models; it uses Rcpp and RcppArmadillo.
- TreeSearch searches for phylogenetic trees that are optimal using a user-defined criterion.
- parglm estimates generalized linear models in parallel (without multithreaded LAPACK or BLAS); it uses Rcpp and RcppArmadillo.
- smurf implments sparse multi-type regularized feature modeling to fit glm models; it uses Rcpp and RcppArmadillo.
- transformr manipulates the shapes of polygons and paths.
- rsMove adds tools for the guided selection of satellite data and environmental predictors.
- minerva implements the 'minepy' maximal information-based nonparametric exploration statistics.
- mined approximates target distribution via minimum energy designs, deterministic sampling method; it uses Rcpp and RcppEigen.
- Buddle offers deep learning for statistical classification analysis; it uses Rcpp and RcppArmadillo.
- mirtjml does joint maximum likelihood estimation for high-dimensional item factor analysis; it uses Rcpp and RcppArmadillo.
- MTLR implements multi-task logistic regression for survival prediction; it uses Rcpp and RcppArmadillo.
- spatialwidget converts spatial data to JSON for use in htmlwidgets; it uses Rcpp and BH.
- CPAT computes statistical tests for structural change; it uses Rcpp and RcppArmadillo.
- riskParityPortfolio efficiently constructs risk-parity portfolios; it uses Rcpp and RcppEigen.
- BTM finds topics on in collections of short texts using 'biterm topic models'.
- mfbvar estimates mixed-frequency Bayesian VAR models; it uses Rcpp and RcppArmadillo.
- segMGarch detects multiple change-points in high-dimensional GARCH processes; it uses Rcpp and RcppArmadillo.
- blockForest offers a random forest variant using block-structure covariate data; it uses Rcpp and RcppEigen.
- lvmcomp provides stochastic EM algorithms for latent variable models; it uses Rcpp and RcppArmadillo.
- mvp does fast manipulation of symbolic multivariate polynomials.
- SuperpixelImageSegmentation implements image segmentations; it uses Rcpp and RcppArmadillo.
- mmsample implements multivariate matched sampling; it uses Rcpp and RcppArmadillo.
- proxyC computes proximity in large sparse matrices; it uses Rcpp, RcppArmadillo and RcppParallel.
- DriftBurstHypothesis calculates the tests statistic for the drift burst H0; it uses Rcpp and RcppArmadillo.
- FiRE finds rare entities: outliers to every sample in voluminous datasets.
- rstap estimates stap regression models using 'rstan'.
- ssMousetrack estimates previously compiled state-space models for mouse-tracking.
- RcppDynProg implements dynamic programming with example partition and fitting examples; it uses Rcpp and RcppArmadillo.
- EditImputeCont offers simutaneous edit-imputation for continuous microdata.
- BiProbitPartial estimates, summarizes and predicts bivariate probits with partial observability; it uses Rcpp and RcppArmadillo.
- curveDepth computes Tukey depth of curve and distance; it uses Rcpp and RcppArmadillo.
- FastGaSP implements fast and exact computation of Gaussian processes with Matern kernels; it uses Rcpp and RcppEigen.
- hergm fits exponential-family random graph models with local dependence.
- PPRL adds a toolbox for deterministic, probabilistic and privacy-preserving linkage techniques.
- ruimtehol wraps the StarSpace library for word, sentence, article, document, webpage, link, ... embeddings; it uses Rcpp and BH.
- cdcsis computes conditional distance correlation based feature screening and conditional independence inference.
- cPCG solves systems of linear equations via a preconditioned conjugate gradient algorithm; it uses Rcpp and RcppArmadillo.
- BMTME offers a Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis.
- apcf implements the adapted pair correct function for objects of finite size and irregular shape.
- netchain infers causal effects on collective outcomes under interference.
- Quartet compares phylogenic trees using quartet and bipartition measure.
- segmentr segments data using different algorithms to maximize likelihood of changepoints.
- WebGestaltR interfaces the WebGestalt.org service for analysis of over-representation, gene set enrichment and network topology.
- cmenet computes bi-level variable selection for conditional main effets; it uses Rcpp and RcppArmadillo.
- mapdeck offers interactive maps using 'Mapbox GL JS' and 'Deck.gl'.
- RcppHNSW implements approximate nearest neighbours via 'hnswlib'.
- ZVCV implements zero-variance control variates to reduce Monte Carlo estimator variance; it uses Rcpp and RcppArmadillo.
- qgraph implements graph plotting methods, psychometric data visualization and graphical model estimation.
- IMaGES adds Independent Multiple-sample Greedy Equivalence Search (IMaGES) causal inference algorithm; it uses Rcpp, RcppArmadillo and BH.
- surveysd estimates survey standard errors for cumulated estimates and their differences in complex panel designs.
- nonneg.cg minimizes a differentiable function subject to variables beging non-negative using a conjugate gradient method.
- GMMAT performs general linear mixed model assocation tests; it uses Rcpp and RcppArmadillo.
- lhs provides number of methods for creating and augmenting latin hypercube samples.
- simcdm simulates cognitive diagnostic model (CDM) data; it uses Rcpp and RcppArmadillo.
- readsdmx reads SDMX-XML data used in official statistics.
- bigMap offers unsupervised clustering for large structured data; it uses Rcpp, RcppArmadillo and BH. dosearch identifies causal effects via do-calculus and standard probability manipulations.
- SAR gives personalized recommendations based on user transactions and item descriptions; it uses Rcpp, RcppArmadillo and RcppParallel.
- hutilscpp provides utility functions with higher-performance than from base R.
- isoband generates contour (iso) lines and contour polygones (isobands) from regularly spaced grids containing elevation data.
- qs implements quick serialization of R objects to and from disk with 'zstd'-based compression.
- robFitConGraph robustly estimates scatter matrices subject to zero-constraints on its inverses.
- TestCor offers multiple testing procedures for correlation tests.
- CB2 adds CRISPR pooled screen analysis using a Beta-binomial test; it uses Rcpp and RcppArmadillo.
- expSBM implements an exponential stochastic block model for interaction length; it uses Rcpp and RcppArmadillo.
- Rfssa offers functional singular spectrum analysis for functional time series; it uses Rcpp and RcppArmadillo.
- rrum runs a Gibbs simapler for Bayesian estimation of Reduced Reparameterized Unified Model; it uses Rcpp and RcppArmadillo.
- Ropj reads data from 'Origin' files.

- 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