CRAN usage

The following CRAN packages use Rcpp:

• RQuantLib, an R interface to QuantLib quantitative finance libraries
• RInside, a set of C++ classes that make it easy to embed R in your C++ applications
• RProtoBuf, an interface from R to the Google ProtoBuf library
• mvabund, a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology.
• sdcTable, a package for statistical disclosure control for tabular data.
• 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.
• 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 VIM package provides visualization for missing values.
• 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.
• 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.
• 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.
• 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 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.
• Rmalschains implements a continuous optimization called memetic algorithms with local search chains (MA-LS-Chains).
• 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 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 implements statistical models for multivariate event history data.
• bfp implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms.
• blockcluster co-clusters Binary, contingency and continuous utility functions.
• RcppCNPy uses Carl Rogers 'cnpy' to read / write "numpy" files.
• 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.
• 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.
• tmg provides truncated multivariate Gaussian sampling using Hamiltonian Monte Carlo; it uses Rcpp and RcppEigen.
• oem implements orthogonolizing expectations maximisation to fit penalized regression; it uses Rcpp and RcppArmadillo.
• quadrupen fits classical sparse regression models with efficient active set algorithms by solving QPs; 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 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 jaatha package provides a fast parameter estimation method for evolutionary biology.
• 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.
• 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 MPTinR packages analyzes Multinomial Processing Tree Models.
• 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 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 accelerometry package implements functions to process uniaxial minute-to-minute accelerometer data.
• prospectr processes 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.
• 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).
• disclapmix provides inference for mixtures of discrete Laplace distributions via the EM algorithm.
• 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.
• The ClustVarLV package provides functions to cluster sets of variable around latent variables.
• The ndl package implements naive discriminant learning and classification models.
• protViz offers quality checks, visualizations and analysis of mass spectrometry data.
• 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.
• The kmc package provides a Kaplan-Meier estimator with constraints for right-censored data via a recursive algorithm.
• The pROC package can visualize, smooth and compare receiver operator characteristic (ROC) curves.
• The XBRL package for the extraction of data from Extensible Business Reporting Language (XBRL) used by the SEC's Edgar system.
• The wsrf package offers a parallel implementation of the Weighted Subspace Random Forest algorithm.
• The hawkes package implements a Hawkes process simulation and calibration toolkit. It uses RcppArmadillo and Rcpp.
• The IsingSampler package provides sampling methods and distribution functions for the Ising model.
• The TAQMNGR implements tools for tick-by-tick (equity) transaction data.
• The HUM package extimates the HUM ("hypervolume under the manifold") value to estimate feature ability to discriminate 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; 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.
• glcm computes textures from grey-level co-occurrence matrices (GLCMs) in R, it uses Rcpp and RcppArmadillo.
• The miceadds package provides additional imputation methods, particularly for mice. It uses Rcpp and RcppArmadillo.
• scrypt implements Colin Percival's scrypt function for a password-based key derivation function which makes it costly to perform large-scale custom hardware attacks by requiring large amounts of memory.
• The plyr package provides tools for splitting, applying and combining data.
• The fastM package implements a fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators; it uses Rcpp and RcppArmadillo.
• The pcalg package provides methods for graphical models and causal inference, it uses Rcpp and RcppArmadillo.
• MTS implements an all-purpose toolkit for analyzing multivariate time series (MTS) and estimating multivariate volatility models.
• resemble adds regression + 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 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.
• 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.
• stosim implements stochastic simulator for reliability modeling of repairable systems: A toolkit for reliability availability and maintainability (ram) modeling of industrial process systems.
• slfm finds 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.
• spBayesSurv provides spatial copula modelling to Bayesian survival analysis; it uses Rcpp and RcppArmadillo.
• The mmand package implements tools for mathematical morphology operation such as erosion and dilation; it uses Rcpp and RcppArmadillo.
• spaMM provides spatial mixed models including spatial GLMMs.
• The icensmis package models study design and data analysis in the presence of error-prone diagnostic tests and self-reported outcomes.
• The BIFIEsurvey package provides tools for survey statistics in educational assessment; it uses Rcpp and RcppArmadillo.
• rpf implements item factor analysis fitting, diagnostics, and analysis. It uses RcppEigen.
• dslice implements a dynamic slicing method designed for dependency detection between a categorical variable and a continuous variable.
• eive provides a compact genetic algorithm search to reduce errors-in-variables bias in linear regression.
• 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.
• The pryr package provides tools to compute on the R languages and to pry back some covers of R.
• rPref implements preferences in R to retrieve maxima for given strict partial orders.
• 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.
• 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.
• DepthProc models data depth; it uses Rcpp and RcppArmadillo.
• mkde computes and visualizes movement-based kernel density estimates 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.
• 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.
• 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.
• 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.
• 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.
• 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 scores and binary outcomes; 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 determines, smoothes and plots quantile (ie Laplace or copula) periodograms for univariate time series.
• matchingMarkets adds a structural estimator to correct for selection bias from observed outcomes; 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.
• rncl implements an interface to the Nexus Class library for phylogenetic tree file formats.
• 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.
• 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.
• NAM implements nested association mapping for biparental and random populations.
• ISOpureR computes the deconvolution of mixed tumor profiles; it uses Rcpp and RcppEigen.
• penMSM estimates regularized multi-state models using L1 penalties.
• 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.
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• RcppStreams brings access to the Streamulus library for stream event processing.
• poisDoubleSamp computes confidence intervals with Poisson double sampling.
• 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.
• 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.
• 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.
• 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.
• 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.
• blockmodels estimates latent or stochastic block model estimation via a V-EM algorithm; it uses Rcpp and RcppArmadillo.
• lifecontingencies offers financial and actuarial mathematics for life contingencies
• RcppTOML parses configuration files in "Tom's Obvious Markup Language" (TOML).
• SLOPE provides efficient procedures for sorted L1-penalized estimation.
• markovchain implements functions and S4 methods for easy handling of discrete time Markov chains.
• mixedMem provides tools for discrete multivariate mixed membership models; it uses Rcpp and RcppArmadillo.
• rankdist implements distance based probability models for ranking data where supported distance metrics include Kendall distance and Weighted Kendall distance.
• SEERaBomb creates SEER (Surveillance, Epidemiology, and End Result) and A-bomb data binaries from ASCII sources.
• fbroc offers a fast boostrap for ROC curves and derived performance metrics.
• sgd implements Stochastic Gradient Descent for large scale inference; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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).
• bayesm supports Bayesian inference for marketing and micro-econometrics; it uses Rcpp and RcppArmadillo.
• 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
• raster provides geographic data analysis and modeling of gridded spatial data.
• 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.
• 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.
• BayesComm estimates multivariate binary probit regression models analysing ecological communities; it uses Rcpp and RcppArmadillo.
• 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 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.
• olctools provides utilities for validating, encoding and decoding entries that follow the 'Open Location Codes' standard.
• JacobiEigen implements the Jacobi (1846) algorithm for eigenvalues and eigenvectors of a real symmetric matrix in pure R and in C++.
• 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.
• 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.
• 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.
• 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.
• cord computes community estimates in G-models via the Cord metric, it uses Rcpp and RcppArmadillo.
• cord offers a moving-window add-on for the plyr package.
• cycleRtools has tools for analysing cycling data.
• bWGR provides bagging whole-genome regression using a Gibbs sampler.
• frailtySurv simulates and fits general semiparametric shared frailty models.
• 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.
• EloChoice computes preference ratings for visual stimuli based on elo ratings; it uses Rcpp and RcppArmadillo.
• fourPNO fits a four-parameter Bayesiean IRT model; it uses Rcpp and RcppArmadillo.
• rags2ridges computes ridge estimations of precision matrices from high-dimensional data; it uses Rcpp and RcppArmadillo.
• bigmemory manages massive matrices with share memory and memory-mapped files.
• 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.
• textreuse detects text reuse and document similarity.
• prclust implements penalized regression-based clustering methods.
• 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.
• 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 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.
• repolr fits linear models to repeated ordinal scores using GEE; it uses Rcpp and RcppArmadillo.
• rwfec simulates communications supporting forward error correction.
• 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.
• 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.
• mediaK calculates mean distance association by k-nearest neighbor; it uses Rcpp and RcppEigen.
• 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.
• 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.
• 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.
• easyVeryfication implements ensemble forecast verification for large data sets.
• 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.
• 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.
• 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.
• netdiffuseR models diffusion of innovations via network analysis; it uses Rcpp and RcppArmadillo.
• 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.
• RSpectra interfaces the Spectra library for large-scale eigenvalue and SVD problems; it use Rcpp and RcppEigen.
• biglasso extends the lasso to bigmemory matrices; it uses Rcpp and RcppArmadillo.
• rEDM does empiricial dynamic modeling of timeseries via time delay embedding for 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.
• 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.
• MiSPU provides microbiome based sum of powered score (MiSPU) tests.
• sitmo provides the parallel pseudo random number generator 'sitmo'.
• Countr estimates count process probabilities based on the Weibull distribution; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• LassoBacktracking efficiently models interactions in high-dimensions.
• blackbox performs black box optimization and exploration of parameter space; it uses Rcpp and RcppEigen.
• 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.
• protolite implements yet another serialization approach based on Protocol Buffers.
• RcppNumerical contains several libraries for numerical integration and optimization; it uses Rcpp and RcppEigen.
• grpSLOPE computes group-sorted L1 penalized estimation for adaptive selection in high-dimensions; it uses Rcpp and RcppEigen.
• 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.
• imputeMulti implements imputation methods for multivariate data.
• spduration fits split-population duration (cure) regression models; it uses Rcpp and RcppArmadillo.
• 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 (weighted or unweighted) correlation coefficients; 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).
• 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.
• flan provides inference for mutation models via fluctuation analysis of mutant cell calls.
• dtwclust clusters times series with optimization for dynamic time warping.
• 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.
• move visualizing and analyzing animal track data.
• 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.
• 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.
• 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.
• 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 round 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.
• rtk adds a rarefaction tool kit and allows normalization of very large abundance tables.
• btb estimates Kernel density 'beyond the border' dedicated to urban geography.
• wordspace implements an interactive laboratory for research on distributional semantic models.
• 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.
• GAS simulates, estimates and forecasts Generalized Autoregressive Score models; it uses Rcpp and RcppArmadillo.
• IHSEP simulates an inhomogeneous self-exciting process (IHSEP), or Hawkes process.
• 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.
• 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.
• ndjson implements a streaming JSON reader.
• 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.
• 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.
• 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.
• smooth provides forecasting using smoothing functions; it uses Rcpp and RcppArmadillo.
• recexcavAAR offers a toolset for 3-d reconstruction and analysis of excavations.
• dfphase1 plots phase I control charts with emphasis on distribution-free methods.
• combiter provides iterators for combinations, permutations, and subsets.
• MatchItSE computes standard errors for matched samples from 'MatchIt'; it uses Rcpp and RcppArmadillo.
• bio3d offers utilities to process, organize and explore protein structure, sequence and dynamics data.
• spass adds study planning and adaptation of sample size via sample size estimation and blinded sample size reestimation.
• 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.
• 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.
• moveWindSpeed estimates wind speeds from bird trajectories using maximum likelihood.
• 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; it uses Rcpp and RcppArmadillo.
• diagis creates a diagnostic plot and multivariate summary statistics from importance sampling; it uses Rcpp and RcppArmadillo.
• 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.
• bsearchtools exposes C++ binary search functions (std::lower_bound, std::upper_bound) plus other convenience functions.
• 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.
• flockimplements process synchronization using file locks.
• 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.
• 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.
• 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.
• strat provides the stratification index by Zhou (2012); 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).
• esaddle fits the Extended Empirical Saddlepoint (EES) density; 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.
• 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.
• 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.
• 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.
• ashr implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rates.
• 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.
• 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 a space-time 'Epidemic Type Aftershock Sequence' (ETAS) model to earthquake catalogs using stochastic declustering.
• joineRML jointly models multivariate longitudinal data and time-to-event 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.
• kdevine computes multivariate kernel density estimation with Vine copulas.
• pdSpecEst offers positive-definite wavelet-based multivariate spectral analysis; it uses Rcpp and RcppArmadillo.
• 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.
• Rlabkey exchanges data with a LabKey server.
• SpecsVerification collects routines for comparitive verification of ensemble forecast; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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.
• observer manipulates Microsoft Word and PowerPoint Documents.
• 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.
• 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.
• kohonen offers supervised and unsupervised self-organising maps (SOMs).
• 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.
• 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.
• 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.
• BETS downloads Brazilean time series; its use of Rcpp is spurious.
• 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.
• OpenMx provides extended structural equation modelling; it uses Rcpp and RcppEigen.
• 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.
• MCMCprecision calculates precision of discrete parameters in transdimensional MCMC; it uses Rcpp, RcppArmadillo and RcppEigen.
• ctsem adds continuous-time structural equation modeling.
• 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.
• PRIMME adds an interface to the PRIME eigenvalue and SVD library.
• mnis gives easy downloading capabilities for the members' name information service operated by the UK parliament.
• 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.
• 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.
• trackdem can obtain population density and body size structure from video material or image sequences; it uses Rcpp and RcppArmadillo.
• 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 '.dtable' or '.dtbin' files that can be read by DataGraph, a graphing and analysis application for macOS.
• 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.
• 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.
• 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.
• rangeBuilder implements occurrence filtering, geometric + taxonomic standardization and generation of species range polygons.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• rxylib provides access to the 'xylib' C library for to import xy data from powder diffraction, spectroscopy and other experimental methods.
• abcrf performs approximate Bayesian computation model choice and parameter inference via random forests; it uses Rcpp and RcppArmadillo.
• 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.
• RcppTN generate random deviates from and calculate moments of a Truncated Normal distribution using the algorithm of Robert (1995).
• 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.
• 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.
• 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.
• curstatCI computes the (smoothed) ml estimator and pointwise bootstrap CIs for the distribution function under current status data.
• 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 partition collections into a 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.
• 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'.
• 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.
• 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.
• 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.
• GBJ offers the Generalized Berk-Jones test for set-based inference in genetic association studies; it uses Rcpp and BH.
• rvinecopulib interfaces a high performance C++ version of 'VineCopula'; it uses Rcpp, RcppEigen and BH.
• 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.
• re2r provides an interface to the primarily deterministic finite automaton based regular expression engine RE2 from Google.
• scanstatistics detects anomalous space-time clusters using the scan statistics methodology; it uses Rcpp and RcppArmadillo.
• mclustcomp implements measures to compare clusters; it uses Rcpp and RcppArmadillo.
• 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.
• 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 for 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.
• RmecabKo interfaces the Eunjeon Project for part-of-speech tagging of Korean text.
• HistDAWass performs histogram-valued data analysis; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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.
• basad does Bayesian variable selection with shrinking and diffusing priors; it uses Rcpp and RcppEigen.
• PieceExpIntensity fits a Bayesian model to find changepoints based on rates and count data; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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.
• 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.
• 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.
• fDMA implements dynamic model averaging and dynamic model selection; it uses Rcpp and RcppArmadillo.
• lwgeom; 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.
• 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.
• 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.
• 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.
• bigsnpr brings tools for efficient, flexible and scalable analysis of massive SNP arrays; it uses Rcpp and RcppArmadillo.
• HMMEsolver implements a fast solver for Henderson Mixed Model Equations; it uses Rcpp and RcppArmadillo.
• 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.
• 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'.
• 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.
• reda implements recurrent event analysis; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• RcppCWB adds bindings for the 'Corpus Workbench'.
• 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.
• 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.
• gkmSVM adds gapped-Kmer support vector machine functionality.
• icr computes and plot Krippendorff's inter-coder reliability coefficient alpha.
• RcppGreedySetCover implementation of the greedy algorithm for the set cover problem; it uses Rcpp and BH.
• 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.
• colorednoise simulates temporally autocorrelated population time series.
• DataVisualizations visualizes high-dimensional data; 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.
• RJafroc offers modeling, analysis, validation and visualization of observer performance studies in diagnostic radiology.
• 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.
• specklestar obtains positional parameters for stellar systems from series of speckle images.
• 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.
• serrsBayes adds Bayesian modeling of Raman spectroscopy (SEERS); it uses Rcpp and RcppEigen.
• 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.
• 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.
• 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.
• 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.
• 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.
• understandBPMN calculates understandibility metrics for Business Process Modelling Notation (BPMN).
• 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.
• 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.
• 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.
• 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.
• gscounts implements design and analysis of group sequential designs with negative binomial outcomes.
• rres adds functions for studying realized genetic relatedness between people.
• 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.
• pcadapt implements fast principal component analysis for outlier detection; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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.
• 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.
• bnclassify adds alsgorithms for learning discrete Bayesian network classifiers; it uses Rcpp and BH.
• 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.
• 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.
• 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.
• 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.
• 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.
• mixdir clusters high-dimensional categorical datasets.
• RcppMeCab wraps the 'MeCab' part-of-speech and morphological analyser; it uses Rcpp, RcppParallel and BH.
• dynutils provides common functions for 'dynverse' packages for trajectory inference.
• glmmfields implements Bayesian spatial and spatialtemporal models; it uses Rcpp, RcppEigen and BH.
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• 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.
• 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.
• 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.
• lpirfs contains functions to estimate linear and nonlinear impulse responses; it uses Rcpp and RcppArmadillo.
• 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.
• pgdraw draws random samples from the Polya-Gama distribution.
• 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`.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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).
• mapi implemnts Mapping Average Pairwise Information to expression spatial variation of spatial metrics.
• 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.
• ggiraph creates interactive 'ggplot2' graphics via 'htmlwidgets'.
• 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.
• 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.
• mixsqp optimizes based on sequential quadratic programming for MLE of miture proportions; it uses Rcpp and RcppArmadillo.
• RCSF supports airborne LiDAR via Cloth Simulation Filter.
• 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.
• 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.
• metacard implements a flexible approach to identify moderators in meta-analysis.
• HMB provides hierarchical model-based estimation; it uses Rcpp and RcppArmadillo.
• 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.
• 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.
• 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'.
• 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.
• 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.
• 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.
• 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.
• apcf implements the adapted pair correct function for objects of finite size and irregular shape.
• 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.
• 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.
• swephR implements the high-precision Swiss Ephemeris based on the DE431 ephemerides from NASA's JPL.
• 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.
• qs implements quick serialization of R objects to and from disk with 'zstd'-based compression.
• 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.
• phenofit extracts remote sensing vegatation phenology; it uses Rcpp and RcppArmadillo.
• SMITIDvisu visualizes data for host and viral populations from 'SMITIDstruct'.
• telefit estimates and predicts remote effects spatial process models; it uses Rcpp, RcppArmadillo and RcppEigen.
• geometry provides the 'Qhull' library in a manner similar to 'Octave' / 'Matlab'; it uses Rcpp and RcppProgress.
• LongMemoryTS estimates, simulates and tests long memory processes; it uses Rcpp and RcppArmadillo.
• SAM offers computationally efficient tools for 'Sparse Additive Modeling'; it uses Rcpp and RcppEigen.
• segmenTier provides similarity-based segmentation of multidimensional signals.
• ScaleLink performs probabilistic linkage between two data sets; it uses Rcpp and RcppParallel.
• huge provides a framework for high-dimensional undirected graph estimation; it uses Rcpp and RcppEigen.
• Rlgt implements Bayesian global trend models for time series forecasting.
• UtilityFrailtyPH12 simulates phase 12 trial designs; it uses Rcpp and RcppArmadillo.
• landscapetools adds utility functions for taks in landscape analysis.
• mDAG infers causal networks from mixed observational data using a directed acyclic graph; it uses Rcpp and RcppArmadillo.
• qpdf splits, combine and compresses pdf files using the 'qpdf' API.
• SCCI implements the Stochastic Complexity-Based Conditional Independence test.
• tracerer permits parsing and analysis of 'BEAST2' input files from R.
• SHT provides a collection of statistical hypothesis testing procedures; it uses Rcpp and RcppArmadillo.
• fastglm fits generalized linear models efficiently; it uses Rcpp and RcppEigen.
• HMMmlselect determines the number of states in Hidden Markov Models via Maximum Likelihood.
• TSDFGS determines training sets for genomic selection via a genetic algorithm; it uses Rcpp and RcppEigen.
• apollo offers tools for choice model estimation and applications; it uses Rcpp, RcppArmadillo, and RcppEigen.
• earthtide supplies a parallel implementation of 'ETERNA 3.40'; it uses Rcpp, RcppArmadillo and RcppParallel.
• fssemR optimizes fused-sparse structural equation models; it uses Rcpp and RcppEigen.
• KONPsurv computes the K-sample omnibus non-proportional hazards tests for right-censored data.
• Lmoments estimates L-moments and trimmed L-moments; it uses Rcpp and RcppArmadillo.
• lavaSearch2 offers tools for latent variable model specificiations; it uses Rcpp and RcppArmadillo.
• oppr implements optimal project prioritization; it uses Rcpp and RcppArmadillo.
• gtfsrouter uses general transit feed specicifcation (GTFS) data for routing problems.
• Rfast2 is another collection of reimplementations of R function; it uses Rcpp and RcppArmadillo.
• ksNN predicts using the k* nearest neighbours algorithm.
• PolynomF implements univariate polynomial operations.
• BNPmix contains algorithms for Pitman-Yor process mixture models; it uses Rcpp and RcppArmadillo.
• unine implements 'light' stemmers similar to SolR and ElasticSearch.
• steps simulates population dynamics across space and time.
• tmt provides conditional maximum likelihood (CML) estimation of item parameters in multistage designs.
• opencv adds bindings to th 'OpenCV' library for computer vision.
• RNewsflow offers tools for measuring text similarity across time and media; it uses Rcpp and RcppEigen.
• armspp implements Adaptive Rejection Metropolis Sampling (ARMS).
• graphlayouts provides additional layout algorithms for network visualizations.
• hopit estimates hierarchical ordered Probit models; it uses Rcpp and RcppEigen.
• llbayesireg adds the L-Logistic Bayesian regression.
• mnlfa conducts moderated nonlinear factor analysis; it uses Rcpp and RcppArmadillo.
• uwot; it uses Rcpp and RcppArmadillo.
• BayesSenMC generates different posterior distributions of adjusted odds ratios.
• expperm computes expected permutation matrices given a matrix of likelihoods of assignments.
• mombf provides Bayesian model selection and averaging for non-local and local priors; it uses Rcpp and RcppArmadillo.
• bzinb estimates bivariate zero-inflated negative binomial models by maximum likelyhood; it uses Rcpp and BH.
• rsparse implements many algorithms for statistical learning on sparse matrices; it uses Rcpp and RcppArmadillo.
• sctransform adds variance stabilizing transformations for single cell UMI data; it uses Rcpp and RcppEigen.
• greybox implements functions and instruments for regression model building and its application to forecasting.
• bisque computes approximate Bayesian posterior inference; it uses Rcpp, RcppArmadillo and RcppEigen.
• DataViz gives access to statistically relevant data visualisation methods via 'd3'.
• inspectdf collects utilities for columnwise summary, comparison and visualisation of data frames.
• SplitReg computes split regularized estimators; it uses Rcpp and RcppArmadillo.
• stcos adds spatio-temporal change of support (STCOS) methods; it uses Rcpp and RcppArmadillo.
• pense provides a robust penalized elastic net S and MM estimator for linear regression; it uses Rcpp and RcppArmadillo.
• heuristicsmineR discovers process models with the heuristics miner algorithm; it uses Rcpp and BH.
• IOHanalyzer analyses data for the Iterative Optmization Heuristics Profiler ('IOHprofiler').
• rTRNG provides the TRNG advanced and parallel random number generator; it uses Rcpp and RcppParallel.
• abtest performs Bayesian A/B testing including prior elicitation.
• ivx draws roboust econometric inference on short- and long-horizon predictive regressions; it uses Rcpp and RcppArmadillo.
• kcpRS computes Kernel Change Point detection for running statistics; it uses Rcpp and RcppParallel.
• OTclust provides mean partitioning for ensemble clustering.
• SSOSVM streams suitable on-line support vector machines; it uses Rcpp and RcppArmadillo.
• empichar evaluates the empirical characteristic function for multivariate samples; it uses Rcpp and RcppArmadillo.
• HACSim iteratively explores species' Haplotype Accumulation Curves; it uses Rcpp and RcppArmadillo.
• SAGMM clusters ; it uses Rcpp and RcppArmadillo.
• volesti interfaces the 'volesti' C++ library to compute volume estimates of polytypes; it uses Rcpp, RcppEigen and BH.
• rotasym tests for rotational symmetry on the hypershere; it uses Rcpp and RcppArmadillo.
• multinomineq offers Bayesian inference for multinomial models with inequality constraints; it uses Rcpp, RcppArmadillo and RcppProgress.
• partition implements a fast and flexible framework for agglomerative partitioning; it uses Rcpp and RcppArmadillo.
• PLNmodels estimates and visualized Poisson-lognormal model and variants; it uses Rcpp and RcppArmadillo.
• tokenbrowser creates browsers for reading full texts from a token list format.
• mastif analyzes production and dispersal of seeds dispersed from trees and recovered in seed traps; it uses Rcpp and RcppArmadillo.
• gdalcubes processes collections of earth observation images as on-demand multispectral, multitemporal data cubes.
• genio implements readers and writers for genetics data file formats.
• RcppXsimd offers modern and portable wrappers for SIMD intrinsics and parallel math implementations.
• motmot fits models of trait evolution on phylogenies for continuous traits.
• rpact offers confirmatory adaptive clinical trial design and analysis.
• rstanemax perform sigmoidal Emax model fits using 'Stan' in a formula notation without writing 'Stan' model code.
• LeMaRns explores length-based multispecies models; it uses Rcpp and RcppArmadillo.
• jackalope provides a swift and versatile phylogenomics and sequencing simulator; it uses Rcpp and RcppArmadillo.
• promotionImpact analyses and measures promotion effectiveness.
• CircSpaceTime implements Bayesian modesl for spatio-temporal interpolation of circular data; it uses Rcpp and RcppArmadillo.
• spinBayes offers semi-parametric gene-environment interaction via Bayesian variable selection; it uses Rcpp and RcppArmadillo.
• missSBM handles missing data in stochastic block models; it uses Rcpp and RcppArmadillo.
• bvartools offers Bayesian inference for VAR models; it uses Rcpp and RcppArmadillo.
• pcFactorStan provides convenience functions for the pairwise comparison factor model; it uses Rcpp, RcppEigen and BH.
• TruncatedNormal has functions for the truncated normal and Student distributions; it uses Rcpp and RcppArmadillo.
• CGGP run experiments using composite grid gaussian processes; it uses Rcpp and RcppArmadillo.
• FisPro interfaces 'FisPro' to offer fuzzy inference system design and optimisation.
• rflexscan contains functions for the detection of spatial clusters.
• scModels fits discrete distribution models to count data.
• SimJoint simulates joint distrutions given nonparametric marginals and covariances; it uses Rcpp, RcppArmadillo and RcppParallel.
• EloRating quantifies animal dominance hierarchies; it uses Rcpp and RcppArmadillo.
• cusum provides functions for constructing and evaluating CUSUM charts and RA-CUSUM charts.
• AlphaPart partition and decomposes additive genetic values by information paths.
• splithalf estimates internal consistency of tasks with permutation based 'split-half' reliability approach.
• srm provides structural equations modeling for the social relations model; it uses Rcpp and RcppArmadillo.
• shrinkTVP does Bayesian estimation of time-varying parameter models with shrinkage priors via MCMC; it uses Rcpp and RcppArmadillo.
• SDMtune adds a user-friendly framework for species distribution models.
• cppRouting implements several variants of the Dijkstra algorithms for distances, shortest paths and isochrones.
• SeqNet generates RNA-Seq data from gene-gene association networks.
• bayes4psy contains several Bayesian models for data analysis of psychological tests; it uses Rcpp, BH and RcppEigen.
• GiniDistance adds a new Gini measure of dependence between categorical and numerical variables; it uses Rcpp and RcppArmadillo.
• psychonetrics implements multi-group (dynamical) structural equation models; it uses Rcpp and RcppArmadillo.
• svars implements data-driven identification for structural vector autoregressive models; it uses Rcpp and RcppArmadillo.
• jSDM fits joint species distribuion models in a hierarchical Bayesian framework; it uses Rcpp, RcppArmadillo and RcppGSL.
• socceR evaluates sport tournament predictions, simulating results from individual soccer matches and tournaments.
• modeLLtest compares models with cross-validated log-likelihoods; it uses Rcpp and RcppArmadillo.
• RKHSMetaMod estimates via ridge group sparse optimization; it uses Rcpp, RcppEigen and RcppGSL.
• Qtools calculates unconditional and conditional quantiles; it uses Rcpp and RcppArmadillo.
• intkrige offers a numerical implementation of interval-valued kriging; it uses Rcpp and RcppArmadillo.
• metaBMA computes the posterior model probabilities for standard meta-analysis models; it uses Rcpp, RcppEigen, and BH.
• svgViewR creates 3D animated, interactive visualizations that can be viewed in a web browser.
• ulid generates universally unique lexicographically sortable identifiers.
• DiscreteFDR implements multiple testing procedures with adaptation for discrete tests.
• MGDrivE provides a model for reliable tests of various gene drive interventions for mosquito-borne diseases control.
• lutz looks up time zones of point coordinates.
• CautiousLearning adds control charts with guaranteed performance and cautious parameters learning; it uses Rcpp and BH.
• mergeTrees aggregates a set of trees with the same leaves to create a consensus tree.
• offlineChange detects the number and location of change points.
• RRI does tests and inference using residual randomization models; it uses Rcpp and RcppArmadillo.
• borrowr estimates causal effects via borrowing betweeb data sources.
• simts contains time series analysis support; it uses Rcpp and RcppArmadillo.
• ShrinkCovMat provides nonparametric Steinian shrinkage estimators of the covariance matrix; it uses Rcpp and RcppArmadillo.
• NetMix implements variational EM estimation of mixed-membership stochastic blockmodel for networks.
• metadynminer3d implements biomolecular simulation analysis tools and visualizations.
• MixMatrix provides sampling and density functions for normal and t distributions; it uses Rcpp and RcppArmadillo.
• samurais offers statistical models for the unsupervised segmentation of time-series; it uses Rcpp and RcppArmadillo.
• outliertree implements explainable outlier detection through decision tree conditioning.
• baggr runs and compares meta-analyses of data with hierarchical Bayesian models in Stan, it uses Rcpp, RcppEigen and BH.
• bpgmm computes model-based clustering using Bayesian parsimonious Gaussian mixture models; it uses Rcpp and RcppArmadillo.
• DTDA.cif fits nonparemetric estimates of the cumulative incidence of competing risk under double truncation.
• exactextractr replaces the 'extract' function of the 'raster' package with one suitable for 'sf' polygons.
• RcppHungarian offers a header library and R functions to solve minimum cost bipartite matching using the 'Hungarian' algorithm.
• tfCox estimates piecemeal polynomial with data-adapative knots in in Cox model.
• tokenizers.bpe implements (unsupervides) byte pair encoding text tokenzation.
• whoa investigates the distribution of genotypes in genotypes-by-sequencing data.
• blavaan fits a variety of Bayesian latent variable models.
• exdex performs frequentist inference for the extremal index of a stationary time series; it uses Rcpp and RcppArmadillo.
• intsurv contains routines for integrative survial analysis models; it uses Rcpp and RcppArmadillo.
• RMixtCompIO adds mixture models with heterogenous and (partially) missing data; it uses Rcpp and RcppEigen.
• flamingos provides functional latent data models for clustering heterogeneous curves; it uses Rcpp and RcppArmadillo.
• GillespieSSA2 implements Gillespie's Stochastic Simulation Algorithms.
• scoper identifies B cell clones via spectral clustering methods; it uses Rcpp and RcppArmadillo.
• meteor adds functions for weather and climate data manipulation to support dynamic ecological modelling.
• PPMR implements efficient statistical inference of two-sample MR (Mendelian Randomization) analysis; it uses Rcpp and RcppArmadillo.
• thurstonianIRT fits Thurstonian item response theory (IRT) models.
• TestDesign use an optimal test design approach to fixed and adaptive test construction.
• disk.frame allows larger-than-RAM disk-based data manipulations for arbitrarily-large datasets.
• genodds calculates Agresti's generalized odds ratios.
• highfrequency provides functionality to manage, clean and match highfrequency trades and quotes; it uses Rcpp and RcppArmadillo.
• samc implements a framework for spatial absorbig Markov Chains; it uses Rcpp and RcppEigen.
• scorepeak offers peak detection in time series following Palshikar (2009).
• bigutilsr adds utility functions for large-scale data.
• Rirt focuses on item response theory modesl via parameter estimate, probability computation and visualization.
• dexter manages psychometric analysis of data from psychological and educational tests; it uses Rcpp and RcppArmadillo.
• gretel performs generalized path analysis for social networks.
• hpa computes distribution function and conditional and marginal densities for Hermite approximations; it uses Rcpp and RcppArmadillo.
• expectreg; fits expectile and quantile regression models with nonlinear effects.
• SimBIID uses state-space models in approximate Bayesian computation sequantial Monte Carlos (ABC-SMC); it uses Rcpp and RcppArmadillo.
• sprintr implements sparse reluctant interaction modeling; it uses Rcpp and RcppArmadillo.
• comat creates (weighted and integrated) co-occurence matricesfor spatial data; it uses Rcpp and RcppArmadillo.
• HBV.IANIGLA offers an decoupled hydrological model for research and education.
• visit implements a Bayesian phase i cancer vaccine trial design; it uses Rcpp, RcppEigen and BH.
• exceedProb computes confidence intervals for the exceedance probability of normally distributed estimators; it uses Rcpp and BH.
• symmetry tests for symmetry of data and model residuals; it uses Rcpp and RcppArmadillo.
• corrcoverage corrects the coverage of credible sets from Bayesian genetic fine-mapping; it uses Rcpp and RcppArmadillo.
• OwenQ evaluates the Owen-Q function for an integer valued degree of freedom; it uses Rcpp, RcppEigen and BH.
• sirus classifies based on random forests via short lists of rules; it uses Rcpp and RcppEigen.
• ddsPLS builds multi-data-driven sparse partial least squares models robust to missing samples for mono and multi-block data sets.
• hdbm performs 'high dimensional Bayesian mediation' analysis; it uses Rcpp and RcppArmadillo.
• IrishDirectorates adds a dynamic bipartite latent space model to analyse Irish company boards; it uses Rcpp and RcppArmadillo.
• OncoBayes2 provides Bayesian logistic regression for oncology dose-escalation trials; it uses Rcpp, RcppEigen and BH.
• avar implements the Allan variance and linear regression estimator; it uses Rcpp and RcppArmadillo.
• Phase12Compare simulates SPSO and Efftox Phase 12 trials with correlated outcomes; it uses Rcpp and RcppArmadillo.
• rMVP adds an efficient parallel tool for GWAS analysis; it uses Rcpp, RcppArmadillo, RcppEigen, and BH.
• wv provides tiiks to compute and plot classical and robust wavelet variance quantities; it uses Rcpp and RcppArmadillo.
• fixest offers fast and user-friendly estimation of econometric models with multiple fixed-effects.
• raceland provides pattern-based, zoneless analysis and visualization of (ethno)racial topography; it uses Rcpp and RcppArmadillo.
• bbl offers supervised learning via Boltzmann Bayes model inference.
• RPEGLMEN fits gamma and exponential GLMs with elastic net penalty via fast iterative shrinkage thresholding; it uses Rcpp and RcppEigen.
• selectiveInference adds tools for post-selection inference for use with stepwise, least angle, lasso and others.
• anomaly detects anomalies in time series data; it uses Rcpp and BH.
• readxlsb imports data from Excel binary workbooks.
• spnn implements scale invariant probabilistic Neural Networks; it uses Rcpp and RcppArmadillo.
• rstantools offers tools for developing R packages interfacing with 'stan'.
• RaceID identifies cell types and inference of lineage trees from single-cell RNA-Seq data.
• hsstan implements hierarchical shrinkage Stan models for biomarker selection; it uses Rcpp, RcppEigen and BH.
• fable provides a collection of univariate and multivariate time series forecasting models.
• freealg implements the free algebra of multivariate polynomials with non-commuting indeterminates.
• hans computes the Haversine distance between pairs of latitude and longitude points.
• TAG implements the transformed additive Gaussian (TAG) process ; it uses Rcpp and RcppArmadillo.
• bama offers Bayesian mediation analysis; it uses Rcpp and RcppArmadillo.
• goffda implements goodness-of-fit tests for functional data; it uses Rcpp and RcppArmadillo.
• Rquefts provides quantitative evaluation of native fertility of tropical soils.
• GPvecchia adds sclalable Gaussian Process approximations; it uses Rcpp, RcppArmadillo and BH.
• sfheaders converts R objects to Simple Features objects without using the 'sf' library.
• HTLR fits Bayesian Logistic regressions with heavy-tailed priors; it uses Rcpp and RcppArmadillo.
• ohenery models ordinal random variables via softmax regression.
• MPBoost performs treatment allocation in two-arm clinical trials; it uses Rcpp and BH.
• PCMBaseCpp provides a C++ backend for package 'PCMBase' for phylogenetic comparison; it uses Rcpp and RcppArmadillo.
• elfDistr computes the Kumaraswamy Complementary Weibull Geometric (Kw-CWG) lifetime probability distribution.
• GMKMcharlie uses Gaussian mixture and Minkowski K-Mean for clustering weighted dataa; it uses Rcpp, RcppArmadillo and RcppParallel.
• meteorits provides unified mixture-of-experts modeling and estimation; it uses Rcpp and RcppArmadillo.
• HypergeoMat evaluates the hypergeometric functions of a matrix argument; it uses Rcpp and RcppArmadillo.
• ltsspca implements robust and sparse PCA; it uses Rcpp and RcppArmadillo.
• mniw adds density evaluation and random number draws for the Matrix-Normal Inverse Wisihart distribution; it uses Rcpp and RcppEigen.
• rayrender builds and raytraces 3D scenes.
• Ryacas0 provides a legacy version of the Ryacas interfaces to the yacas computer-algebra system.
• YPPE fits semiparametric modesl of lifetime data with crossing survival curves; it uses Rcpp, RcppEigen and BH.
• locStra implement local population stratification methods; it uses Rcpp and RcppEigen.
• rocTree adds ROC-guided survival trees and ensemble methods; it uses Rcpp and RcppArmadillo.
• maotai supplies tools for matrix algebra, optimization and inference; it uses Rcpp and RcppArmadillo.
• spectralGraphTopology learns graph structure from data via spectral contraints; it uses Rcpp, RcppArmadillo and RcppEigen.
• BayesSUR offers Bayesian seemingly unrelated regression with general variable selection; it uses Rcpp and RcppArmadillo.
• robregcc estimates parameters of the robust regression model with compositional covariates; it uses Rcpp and RcppArmadillo.
• ALassoSurvIC implements the adaptive lasso for Cox regression with interval censored and possibly left truncated Data.
• WaveSampling samples weakly assicated vectors (WAVE) from spatial data; it uses Rcpp and RcppArmadillo.
• rbridge performs restricted bridge estimation, a special case of lasss / ridge / elastic net; it uses Rcpp and RcppArmadillo.
• cnaOpt optimizes consistency and coverage in configurational causal modeling by extending the 'cna' package.
• phyr collects functions to do model-based phylogenetic analysis; it uses Rcpp and RcppArmadillo.
• AntMAN fits finite Bayesian mixture models with random numbers of components; it uses Rcpp and RcppArmadillo.
• knn.covertree implements accurate k-nearest neighbours via cover trees; it uses Rcpp and RcppEigen.
• spBFA implements a spatial Bayesian non-parametric factor analysis model; it uses Rcpp and RcppArmadillo.
• tree.interpreter computes Random Forest prediction decomposition and feature importance measures; it uses Rcpp and RcppArmadillo.
• fplot offers easy ways to plot common types of graphics with moderators using formulas from.
• porridge does ridge-type estimation for a potpourri of modelse; it uses Rcpp and RcppArmadillo.
• hilbertSimilarity quantifies similarity between high-dimensional single cell samples.
• RobGARCHBoot adds bootstrap forecast denstities for GARCH models; it uses Rcpp and RcppArmadillo.
• tlrmvnmvt implements low-rank methods for multivariate Normal and t probabilities; it uses Rcpp, RcppEigen and BH.
• dipsaus offers a collection of helper functions; it uses Rcpp and RcppParallel.
• qtl2pleio tests pleiotropy in multiparental populations; it uses Rcpp and RcppEigen.
• BinSegBstrap computes piecewise smooth regression by bootstrapped binary segmentation.
• calculus implements optmized functions for numerical and symbolic calculus.
• mixl runs simulated maximum likelihood estimation for mixed logit models for large datasets.
• patternplot creates pie, ring and bar charts and box plots with colors, patterns, and images; it uses Rcpp and RcppParallel.
• RAINBOWR test mulitple SNPs via 'Reliable Association INference By Optimizing Weights with R'; it uses Rcpp and RcppEige.
• secr estimate density and size of spatially distributed animal populations; it uses Rcpp and RcppParallel.
• multbxxc contains auxiliary routines for the 'influx' software; it uses Rcpp and RcppArmadillo.
• rhoR tests inter-rater-reliability (IRR) statistics; it uses Rcpp and RcppArmadillo.
• AdaptGauss models mulitmodal distributions as Gaussian Mixture Models of components; it uses Rcpp and RcppArmadillo.
• penPHcure selects variables in PH Cure models with time-varying covariates; it uses Rcpp and RcppArmadillo.
• covafillr facilitates local polynomial regression in state-space models; it uses Rcpp and RcppEigen.
• fastshap computes fast approximate Shapley values for any supervised learning model; it uses Rcpp and RcppArmadillo.
• mmpca generalized principal component analysis for integrative analysis; it uses Rcpp and RcppEigen.
• DCEM implements the improved Expectation Maximisation EM* and traditional EM algorithm for clustering finite gaussian mixture models.
• rrcovHD adds robust multivariate methods for high-dimensional data.
• RScelestial offers Steiner Tree based single-cell lineage tree inference.
• treenomial compares trees using tree-defining polynomials; it uses Rcpp and RcppArmadillo.
• orf implements Ordered Random Forests for modesl with ordered categorical outcomes.
• FKSUM evaluates fast (univariate) kernel smothers based on recursive computations; it uses Rcpp and RcppArmadillo.
• vinereg implements D-vine quantile regression models with pair-copulas; it uses Rcpp, RcppEigen and BH.
• recurse computes revisitation metrics for trajectory data.
• ampir predicts antimicrobial peptides from protein sequences on a genomic-wide scale.
• BOSSreg performs best orthogonalized subset selection; it uses Rcpp and RcppArmadillo.
• SequenceSpikeSlab contains fast functions to calculate the exact Bayes posterior for the Sparse Normal Sequence Model.
• ttbary computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns.
• fastpos finds the critical sample size "point of stability" for a Pearson correlation; it uses Rcpp and RcppArmadillo.
• RLumModel solves ordinary differential equations to understand luminence; it uses Rcpp and RcppArmadillo.
• rpart.LAD recursively partitions least absolute deviation regression trees.
• LARisk estimates lifetime attributable risk of cancer from radiation exposure.
• isotree offers isolation-based outlier detection via fast multi-threaded implementations.
• TreeTools creates, modifies and analyses phylogenetic trees.
• BayesMFSurv estimates a split population survival model for misclassification probability of failure; it uses Rcpp and RcppArmadillo.
• fastmit estimates mutual information based on k-nearest neighbors; it uses Rcpp and RcppArmadillo.
• diversityForest implements diversity forests using a fork of ranger; it uses Rcpp and RcppEigen.
• publipha does Bayesian meta-analysis for publication bias and p-hacking; it uses Rcpp, RcppEigen and BH.
• r2sundials wraps the 'SUNDIALS' ODE solver; it uses Rcpp and RcppArmadillo.
• bggum implements Bayesian estimation of generalized graded unfolding model parameters.
• cbq estimates conditional binary quantile models; it uses Rcpp, RcppEigen and BH.
• MomTrunc computes arbitrary products moments for double truncated multivariate distributions; it uses Rcpp and RcppArmadillo.
• fcaR provides tools to perform fuzzy formal concept analysis.
• PRIMAL implements a parametric Simplex method for sparse learning; it uses Rcpp and RcppEigen.
• atakrig adds point-scale variogram deconvolution for area-to-area kriging.
• BinaryDosage creates, merges and read binary dosage VCF or GEN files.
• impactflu quantifies the population-level impact of vaccination.
• s2net implements the generalized semi-supervised elastic net; it uses Rcpp and RcppArmadillo.
• carat provies covariate-adaptive randomization for clinical trials.
• covglasso estimates sparse covariate matrices via the graphical lasso; it uses Rcpp and RcppArmadillo.
• policytree computes multi-action treatment effect estimation and policy learning; it uses Rcpp and BH.
• dscore quantifies child development 'D' scores; it uses Rcpp and RcppArmadillo.
• LassoNet estimates penalized regression models using the 3CoSE algorithm.
• statgenGWAS adds fast fits for single trait Genome Wide Association Studies (GWAS); it uses Rcpp and RcppArmadillo.
• PoissonBinomial implements exact and approximate methods for the Poisson binomial distribution; it uses Rcpp and BH.
• depcoeff computes coefficients measuring the dependence of two or more than two variables.
• flying simulates bird flight range via two ODE methods.
• fad does factor analysis via maximum likelihood in a Gaussian factor model using a the matrix-free methodology.
• gridtext provides improved text support for 'grid' graphics.
• santoku cuts data into intervals.
• signnet analyses signed networks via measures for structural balance; it uses Rcpp and RcppArmadillo.
• clifford handles Clifford algebras via routines using the 'Map' class of the STL; it uses Rcpp and BH.
• FSSF generates fully-sequential space-filling designs inside a unit hypercube; it uses Rcpp and RcppArmadillo.
• geodiv calculates gradient surface metrics for continuous analysis of landscape features; it uses Rcpp and RcppArmadillo.
• BayesReversePLLH fits Bayesian piecewise linear log-hazard model; it uses Rcpp and RcppArmadillo.
• ergmito simulates and estimations exponential random graph models; it uses Rcpp and RcppArmadillo.
• survPen fits hazard and excess hazard models with multidimensional penalized splines; it uses Rcpp and RcppEigen.
• conquestr implements an R front-end to' ACER ConQuest'.
• jmotif offers time series z-normalisations and pattern and anomaly discovery; it uses Rcpp and RcppArmadillo.
• owl estimates glm models regularized with the sorted L1-norm; it uses Rcpp and RcppArmadillo.
• RcppSimdJson connects R with the header-only 'simdjson' library for highly-performant JSON parsing.
• GofKmt tests goodness of fit via a Khmaladze martingale transformation; it uses Rcpp and RcppArmadillo.
• treestructure detects population structure from coalescent events in phylogenetic trees.
• BayesLN performs Bayesian inference under log-normality; it uses Rcpp and RcppArmadillo.
• mrf2d fits, samples and visualizes for (hidden) Markov random field models; it uses Rcpp and RcppArmadillo.
• mvrsquared computes the coefficient of determination for vector or matrix outcomes; it uses Rcpp and RcppArmadillo.
• SeqDetect learns and detects (latent) process sequences.
• ROptSpace reconstructs matrices from a few entries by inferring missing entries; it uses Rcpp and RcppArmadillo.
• matricks contains matrix creation and manipulation helper functions.
• superml builds machine learning models similar to Python's 'Scikit-Learn'; it uses Rcpp and BH.
• neatRanges collapse, partition, combine, fill gaps in and expand date/time ranges.
• psychrolib implements a library for psychrometric properties of moist and dry air in both metric (SI) and imperial (IP) units.
• quanteda.textmodels adds scaling models and classifiers for textual data; it uses Rcpp, RcppArmadillo and RcppParallel.
• SBmedian offers scalable Bayes with median of subset posteriors via median-of-means; it uses Rcpp and RcppArmadillo.
• IOHexperimenter provides the benchmarking module for the Iterative Optimization Heuristics Profiler; it uses Rcpp and BH.
• PanelMatch applies methods to time-series cross-sectional data; it uses Rcpp, RcppArmadillo, and RcppEigen.
• RestRserve create high-performance full featured HTTP APIs from R functions.
• tsmp implements the matrix profile concept that was created by CS-UCR; it uses Rcpp and RcppParallel.
• xrnet fits hierarchical regularized regression models to incorporate potentially informative external data; it uses Rcpp, RcppEigen, and BH.
• tergmLite does fast simulations of simple temporal exponential random graph models.
• hsrecombi estimates recombination rate and maternal LD in half-sibs.
• DCPO estimates latent public opinion variables cross-nationally and over time from sparse survey data; it uses Rcpp, RcppEigen and BH.
• ipaddress implements classes and functions for working with IP addresses and networks; it uses Rcpp and AsioHeaders.
• hal9001 adds the highly adaptive lasso via sparse matrices of basis functions; it uses Rcpp and RcppEigen.
• symengine interfaces from R to the 'SymEngine' library for fast symbolic manipulations.
• ctgt implments closed testing for large-scale pathwat analysis; it uses Rcpp and BH.
• evgam fits various extreme value distributions with parameters of GAM form; it uses Rcpp and RcppArmadillo.
• rayimage uses convolution-based techniques to generate camera bokeh, depth of field, and other effects; it uses Rcpp and RcppArmadillo.
• processmapR visualizes event logs using directed graphs ('process maps'); it uses Rcpp and BH.
• maxnodf computes approximate maximisation of nestedness in bipartite graphs.
• BoostMLR jointly models the multivariate longitudinal response and multiple covariates and time; it uses Rcpp and RcppArmadillo.
• dann implements discriminant adaptive nearest neighbor classification; it uses Rcpp and RcppArmadillo.
• CatReg solves linear and logistic regression models with a nonconvex penalty (SCOPE) efficiently.
• gtfs2gps converts general transit feed specification (GFTS) data to GPS records.
• registr registers (functional data) curves from exponential family functions; it uses Rcpp and RcppArmadillo.
• collapse offers advanced and fast data transformations.
• errum performs Bayesian estimation of the ErRUM model; it uses Rcpp and RcppArmadillo.
• FDX adds multiple testing procedures for heterogeneous and discrete tests.
• MCPModPack implements the multiple comparison and modeling method; it uses Rcpp and RcppEigen.
• netcontrol adds various control theory methods for use in brain and psychological networks; it uses Rcpp and RcppArmadillo.
• Radviz projects multidimensional data in 2d space; it uses Rcpp and RcppArmadillo.
• dbnR implements dynamic Bayesian network learning and inference.
• eNchange uses ensemble methods for multiple changepoint detection.
• parzer parses 'messy' geographic coordinates from various formats to decimal degree numeric values.
• terra adds classes and methods for spatial data, especially raster data.
• eimpute efficiently imputes large scale matrices; it uses Rcpp and RcppEigen.
• FaultTree constructs and displays fault trees for risk and reliability analysis; it uses Rcpp and RcppArmadillo.
• GridOnClusters does joint discretization of data on a grid which preserves clusters.
• MLModelSelection helps with model selection in multivariate longitudinal data analysis; it uses Rcpp and RcppArmadillo.
• Rwofost implements the World Food Studies crop growth model.
• SSLR; it uses Rcpp and RcppArmadillo.
• edina perform a Bayesian estimation of the exploratory deterministic input, noisy and gate (EDINA) model; it uses Rcpp and RcppArmadillo.
• eddington computes a cyclist's Eddington number including efficiently cumputing E over a vector.
• nlmm fits linear mixed models based on convolutions of general Laplace distributions; it uses Rcpp, RcppArmadillo and BH.
• provides Reinert text clustering methods.
• SpatialBSS adds blind source separation for multivariate spatial data; it uses Rcpp and RcppArmadillo.
• Bestie offers Bayestiam estimation of intervention effects for directed acyclic graphs learned from binary data.
• RTCC adds the randomized trait community clustering method.
• spsurv eases semiparametric survival regression modelng based on Bernstein polynomials; it uses Rcpp, RcppEigen and BH.
• text.alignment find text similarities using the Smith-Waterman algorithm.
• zcurve implements z-curve to estimate discovery and replicability rates based on published studies.
• PINSPlus provides a robust approach for omics data integration and disease subtyping; it uses Rcpp, RcppArmadillo, and RcppParallel.
• datasailr interfaces with the 'Sailr' language and library for fast row by row data processing.
• infinitefactor implements a semi-parametric Bayesian infinite factor model; it uses Rcpp and RcppArmadillo.
• mokken conducts Mokken scale analysis on test and questionnaire data.
• ConsReg fits regression and ARMA models subject to constraints on coefficients.
• VUROCS calculate the volume under the ROC surface for multi-class ROC analysis; it uses Rcpp and RcppArmadillo.
• binGroup2 addresses the group testing identication problem via several methods; it uses Rcpp and RcppArmadillo.
• dgumbel offers the Gumble distribution functions and gradients; it uses Rcpp and RcppEigen.
• finity tests for finiteness of moments in a distribution; it uses Rcpp, RcppArmadillo and BH.
• bigsparser stores sparse matrices (in dgCMatrix format) on disk; it uses Rcpp and RcppArmadillo.
• GGClassification implements a binary large margin classifier based on the Gabriel Graph; it uses Rcpp and RcppEigen.
• gear implements common geostatistical analysis methods.
• lodr fits linear regression models accounting for covariates with lower limit of detection (LOD); it uses Rcpp and RcppArmadillo.
• conquer computes fast and accurate convolution-type smoothed quantile regression; it uses Rcpp and RcppArmadillo.
• FMCCSD efficiently estimates clustered current status data; it uses Rcpp and RcppArmadillo.
• fits keyword-assisted topic models using collapsed Gibbs samplers; it uses Rcpp and RcppEigen.
• catsim computes a structural similarity metric for binary and categorical 2D and 3D images.
• regmed offeres mediation analysis by penalized structural equation models; it uses Rcpp and RcppArmadillo.
• terrainmeshr triangulates and simplifies 3-dimensional terrain meshes.
• bayescopulareg fits Bayesian copule generalized linear models; it uses Rcpp and RcppArmadillo.
• cnum processes Chinese numerals; it uses Rcpp and BH.
• fstcore provides R bindings to the Fstlib library for multithreaded serialization in fst format.
• ldsr reconstructs linear dynamical systems; it uses Rcpp and RcppArmadillo.
• surbayes offers Bayesian analysis of seemingly unrelated regression (SUR) models; it uses Rcpp and RcppArmadillo.
• m2r interfaces with the Macaulay2 system for algebraic geometry and commutative algebra.
• RcppUUID generates universally unique identifiers in either version 4 or 5.
• cenROC estimates time-dependent ROC and AUC for censored survival data; it uses Rcpp and RcppEigen.
• CLVTools offers tools for customer live value estimates; it uses Rcpp and RcppArmadillo.
• nnlib2Rcpp provices a collection of neural networks including BP, Autoencodere, LVQ and MAM.
• targeted implements methods for targeted and semiparanetric inference.
• DeCAFS detects abrupt change in time series with local random walk fluctuations and AR(1) noise.
• roben offers robust Bayesian variable selection for gene-environment interactions; it uses Rcpp and RcppArmadillo.
• covsim provides VITA and IG simulation support for given covariance and marginals.
• stringfish implements strings and string functions using an alternative representation.
• immunarch is a framework for bulk analyses of single-cell and T-cell receptor and antibody reprtoires.
• TransPhylo infers transmission trees from dated phylogeny to simulate and analyse outbreaks.
• wbsd implements the 'theta' wild bootstrap size diagnostic; it uses Rcpp and RcppEigen.
• seqest solves binary classification problems via sequential methods; it uses Rcpp and RcppArmadillo.
• sensitivity undertakes global sensitivity analysis of model outputs.
• ess implements efficient stepwise selection in decomposable modes.
• REndo fits linear models with endogenous regressors using latent instrumental variables; it uses Rcpp and RcppEigen.
• higlasso estimates via the hierarchical integrative group lassso; it uses Rcpp and RcppArmadillo.
• rbiom reads, write, transforms and summarizes 'BIOM' data files.
• glca fits latent class analysis models with group variable and covariates.
• mrbayes does Bayesian summary data models for Medeloan randomization; it uses Rcpp, BH and RcppEigen.
• BGGM fits Bayesian Gaussian Graphical Models; it uses Rcpp and RcppArmadillo.
• CausalQueries makes, updates, or queries binary causal models; it uses Rcpp, RcppEigen, BH.
• gif recovers the precision matrix for Gaussian graphical models efficiently; it uses Rcpp and RcppEigen.
• grpCox fits penalized Cox models with non-overlapping and overlapping grouped penalities; it uses Rcpp and RcppEigen.
• nametagger wraps the 'nametag' library to find and extract entities in raw text.
• sentencepiece does unsupervised text tokenization using byte pair encoding and unigram modelling.
• tsfknn forecasts time series using neareast neighbors regression.
• word2vec learns vector representation of words by continuous bag of words and skip-gram implementation of the 'word2vec' algorithm.
• corels offers the 'Certifiably Optimal Rule Lists' (Corels) learner.
• lowpassFilter creates lowpass filters for use in ion channel recordings.
• mashr implements multivariate adaptive shrinkage (mash); it uses Rcpp, RcppArmadillo and RcppGSL.
• UComp offers automatic unobserved components models; it uses Rcpp and RcppArmadillo.
• dmbc adds model-based clustering of binary dissimilarity measures; it uses Rcpp and RcppArmadillo.
• RLumCarlo simulates luminiscence production in dosimetric materials; it uses Rcpp and RcppArmadillo.
• krige estimates geospatial kriging models for geographical point-referenced data.
• BGVAR estimates Bayesian Global Vector Autoregression models; it uses Rcpp and RcppArmadillo.
• rLFT assists in the manipulation and processing of linear features with the help of the 'sf' package.
• drf implements distributional random forests; it uses Rcpp and RcppEigen.
• gRim adds graphical Gaussian models for multivariate normal data and mixed interaction models; it uses Rcpp, RcppArmadillo and RcppEigen.
• CamelUp implements the board game 'CamelUp' via a shiny app.
• lazyarray persists large data arrays with lazy-loading on demand.
• dcov implements fast distance covariance and relevant statistics; it uses Rcpp and RcppArmadillo.
• dynmix estimates dynamic finite mixtures with state-space components; it uses Rcpp and RcppArmadillo.
• DysPIA identifies dysregulated pathways based on a pre-ranked gene pair list.
• malan implement male lineage analysis by simulating genealogies backwards; it uses Rcpp and RcppArmadillo.
• peppm fits a piecewise exponential distribution with random time grids.
• rBMF provides four boolean matrix factorization methods.
• bootUR performs bootstrap unit root tests for individual and multiple time series and panel data; it uses Rcpp and RcppArmadillo.
• dnapath integrates pathway information into the differential network analysis; it uses Rcpp and RcppArmadillo.
• flexpolyline integrates with the flexible polyline encoding of HERE.
• qtl2 provides quantitative trait locus mapping in experimental crosses; it uses Rcpp and RcppEigen.
• RMPSH optimizes any black-box non-convex function on hyper-rectangular parameter spaces.
• bellreg offers count regression models with overdispersion based on the Bell distribution; it uses Rcpp and RcppEigen.
• ibdsim2 simulates chromosomal regions shared by family members.
• springer models sparse group variable selection for gene-environment interactions; it uses Rcpp and RcppArmadillo.
• YPBP implements the Yang and Prentice model; it uses Rcpp, RcppEigen and BH.
• lfmm adds inference for GEAs via latent factor models; it uses Rcpp and RcppEigen.
• LOPART implements labeled optimal partitioning with constraints and penalties.
• multinma offers Bayesnian network meta-analysis of individual and aggregate data; it uses Rcpp, RcppEigen and BH.
• TreeDist computes distances between phylogenetic trees.
• clustermq evaluates arbitrary function calls on HPC schedulers.
• DMCfun computes a diffusion model of conflict (DMC) in reaction time tasks.
• qtl2convert converts data between QTL mapping packages.
• SITH implements a three-dimensional stochastic model of cancer growth and mutation.
• TBRDist calculates rearrangement distances between unrooted phylogenetic trees.
• backbone extracts the signed or binary backbone retaining only significant edges from a weighted graph.
• ivdoctr ensures mutuallu consistent beliefs when using instrumental variables; it uses Rcpp and RcppArmadillo.
• vcpen performs penalizes variance components analysis; it uses Rcpp and RcppArmadillo.
• iCellR analyses high-throughput single cell sequencing data.
hadron analyses correlation function from Lattice Monte Carlo simulations in physics. -->
• GGMncv estimates Gaussian graphical models with non-convex penailties; it uses Rcpp and RcppArmadillo.
• netClust clusters unilayer and multilayer network data; it uses Rcpp and RcppArmadillo.
• paropt optimizes parameters of ordinary differential equations; it uses Rcpp and RcppArmadillo.
• specs implements a single-equation penalized error-correction selector; it uses Rcpp and RcppArmadillo.
• EFAtools implements fast and flexible exploratory factor analysis; it uses Rcpp and RcppArmadillo.
• Keyboard designed single-agent, drug-combination, or phase I/II dose-finding clinical trials.
• sbm offers tools and functions for a variety of stochastic blockmodels (SBM); it uses Rcpp and RcppArmadillo.
• ARCokrig models autoregressive co-kriging for multifidelity codes; it uses Rcpp, RcppArmadillo and RcppEigen.
• rbscCI provides a fast calculation of the Blyth-Still-Casella confidence interval; it uses Rcpp and BH.
• fddm implements a probability density function for the diffusion decision model.
• splines2 constructs B-splines, M-splines, I-splines, C-splines and Bernstein polynomials; it uses Rcpp and RcppArmadillo.
• ssdtools computes species sensitivity distributions for toxicity concentrations.
• gen3sis offers a general engine for eco-evolutionary simulations; it uses Rcpp and BH.
• PAsso assesses partial association between ordinal variables; it uses Rcpp and RcppArmadillo.
• IFC works with imaging flow cyometry data from 'ImageStream' and 'FlowSlight'..
• multivar simulates, estimates and forecasts multi-subject VAR models; it uses Rcpp and RcppArmadillo.
• statespacer estimates time series state-space models following Durbin and Koopmans; it uses Rcpp and RcppArmadillo.
• fastkmedoids adds R wrappers for faster k-medoids clustering algorithms.
• crandep analyses the network of CRAN packages; it uses Rcpp, RcppArmadillo and RcppGSL.
• ImpactEffectsize calculates and visualizes the impact effect size measure.
• reReg offers a collection of regression models for recurrent event process and failure time data; it uses Rcpp and RcppArmadillo.
• intervalaverage computes time-weighted averages for interval data.
• waspr computes Wasserstein barycenters of subset posteriors; it uses Rcpp, RcppArmadillo and BH.
• ztpln provides density, random variates and ML estimates for the Zero-truncated Poisson Lognormal distribution; it uses Rcpp and RcppEigen.
• image.binarization improves optical character recognition by binarizing images.
• image.ContourDetector implements unsupervised smooth contour detection.
• image.CornerDetectionF9 uses the 'FAST-9' corner detection algorithm.
• image.CornerDetectionHarris implements the Harris Corner Detection methods.
• image.dlib wraps around the image processing functionality of 'Dlib'.
• image.libfacedetection uses a pretrained convolutional neural network to detect faces in images.
• image.LineSegmentDetector detects line segments in images.
• image.Otsu implements Otsu's image segmentation method.
• dracor decodes meshes and points encoded by the Draco mesh compression library by Google.
• genieclust retakes the Genie algorithm for robust hierarchical clustering.
• wkutils adds utilities for well-known geometry vectors.
• mhazard computes multivariate survival and Cox regression estimates with multiple censored outcomes; it uses Rcpp and RcppArmadillo.
• image.CannyEdges implements the Canny Edge Detector for detecting edges in images.
• ldsep estimates gametic or composite pairwise linkage disequilibrium in polyploids; it uses Rcpp and RcppArmadillo.
• gasper provides standard operations for signal processing on graphs; it uses Rcpp and RcppArmadillo.
• lefko3 creates (a)historical population projection matrices for population ecological analyses; it uses Rcpp and RcppArmadillo.
• rmsb offers a Bayesian companion to 'Regression Modeling Strategies (rms)'; it uses Rcpp and RcppEigen.
• HDLSSkST computes distribution-free exact high-dimensional low sample size k-sample tests.
• qpmadr intrefaces to the 'qpmad' quadratic program solver; it uses Rcpp and RcppEigen.
• torch defines and trains neural networks using the 'libtorch' library.
• Benchmarking offers benchmark and frontier analysis via DEA and SFA.
• nanotime support nanosecond-resolution time calculations.
• geometries converts between R objects and geometric structures.
• dpseg computes piecewise linear segmentation (for time series data) by dynamic programmic.
• Signac offers a framework for analysis adn exploration of single-cell Chromatin Data.
• ebmstate implements an empiricial Bayes multi-state Cox model for survival analysis.
• fable.prophet connects 'fable' with a 'prophet' modeling interface.
• MGMM estimates Gaussian Mixture Models in the presence of missing data; it uses Rcpp and RcppArmadillo.
• mixedCCA uses a semi-parametric approach for sparse canonical correlation analysis.
• sigminer extracts, analyzes and visualizes signatures for genomic variations.
• microclass implements methods for taxonomic classification of prokaryotes; it uses Rcpp, RcppEigen, and RcppParallel.
• glow makes plots that 'glow' and contain glowing points.
• sdetorus offers statistical tools for toroisal diffussions; it uses Rcpp and RcppArmadillo.
• oneclust implements maximum homegeneity clustering for one-dimensional data via dynamic programming.
• agtboost does adaptive and automatic gradient boosting; it uses Rcpp and RcppEigen.
• EpiNow2 estimates real-time case counts and time-varying epidemiological parameters; it uses Rcpp, RcppEigen, and BH.
• leontief computes input/output analysis as developed by Leontief; it uses Rcpp and RcppArmadillo.
• mcmcsae fits multi-level models with possibly correlated random effects MCMC; it uses Rcpp and RcppEigen.
• RobKF implements a series of robust Kalman Filtering approaches; it uses Rcpp and RcppEigen.
• simplextree provides an interface to the Simplex Tree data structure.
• spGARCH fits spatial and spatiotemporal ARCH models; it uses Rcpp and RcppEigen.
• starvz add visualization techniques for task based applications.
• fmf detects noise 'fast' via multi-factor based learning; it uses Rcpp and RcppArmadillo.
• fracture converts decimals to fractions.
• shapr predicts explanation with dependence-aware Shapley values; it uses Rcpp and RcppArmadillo.
• ExactMultinom computes exact p-values for multinomial goodness-of-fit tests based on multiple test statistics.
• tiledb adds a data science storage engine for sparse and dense multi-dimensional arrays.
• dsmisc contains miscellaneous Data Science utility functions.
• personalized2part; it uses Rcpp and RcppArmadillo.
• seededlda implemened seeded-LDA for semi-supervised topic modeling; it uses Rcpp, RcppArmadillo, and RcppParallel.
• hermiter estimation of the full pdf, cdf and quantile function using Hermite series based estimators.; it uses Rcpp and BH.
• qbld implements Bayesian quantile regression for binary longitudinal data; it uses Rcpp and RcppArmadillo.
• SimSurvNMarker simulates joint survival and marker models; it uses Rcpp and RcppArmadillo.
• binsegRcpp implements efficient binary segmentation with a log-linear average runtime and a quadratic worst-case.
• ripserr calculates persistent homology with Ripser-based engines.
• image.textlinedetector segments images in text lines and words.
• onlineforecast fits adaptive forecasting models using forecases as model inputs; it uses Rcpp and RcppArmadillo.
• rater fits models of repeated categirical rating data; it uses Rcpp, RcppEigen, and BH.
• CNVRG implements Dirichlet multinomial modelling of relative abundance; it uses Rcpp, RcppEigen, and BH.
• RcppSpdlog provides the 'spdlog' C++ header library for logging.
• bmgarch fit Bayesian multivariate GARCH models; it uses Rcpp, RcppEigen, and BH.
• MAPITR computes 'marginal epistasis tests for regions' in genomic analysis; it uses Rcpp and RcppArmadillo.
• gitear interfaces the 'gitea' API for repositories hosting in 'gitea'.
• splmm fits high-dimensionality linear mixed-effects models with fixed and random effects penalities; it uses Rcpp and RcppArmadillo.
• bravo performs Bayesian variable selection with embedded screening for ultra-high dimensional Gaussian linear regression models.
• mrregression implements frequentist and Bayesian linear regression for large data sets via Merge and Reduce.
• Riemann learns from data via Riemannian Manifolds; it uses Rcpp and RcppArmadillo.
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• sanic solves larges systems of linear equations 'nimbly' via C++ solvers from Eigen; it uses Rcpp and RcppEigen.
• MABOUST conducts and simulates 'Multi-Armed Bayesian Ordinal Utility-Based Sequential Trials'; it uses Rcpp and RcppArmadillo.
• RJcluster implements a clustering algorithm for high-dimensional data where n << p; it uses Rcpp and RcppArmadillo.
• T4cluster provides a variety of algorithms from clustering to partition space learning; it uses Rcpp and RcppArmadillo.
• irt adds psychometric Item Response Theory functions.
• simcross simulates experimental crosses in genotypes.
• ggip visualizess IP addresses and networks.
• o2geosocial reconstructs transmission chains from surveillance data.
• BayesProject computes projection direction for multivariate changepoint detections; it uses Rcpp and RcppEigen.
• GxEScanR runs GWAS/GWEIS scans using binary dosage files; it uses Rcpp and RcppArmadillo.
• mrMLM conducts multi-locus genome-wide association studies in a random-SNP-effect mixed linear model (mrMLM) framework (spurious depends).
• mrMLM.GUI conducts multi-locus genome-wide association studies with a GUI; it uses Rcpp, RcppEigen, and RcppArmadillo.
• N2R implements fast and scalable approximate k-nearest neightbours using 'N2'; it uses Rcpp and RcppEigen.
• densEstBayes estimates densities using the Bayesian inference engines paradigm; it uses Rcpp, RcppArmadillo, RcppEigen, and BH.
• sccore offers core utilities for single-cell RNA-Seq data analysis; it uses Rcpp, RcppArmadillo, and RcppEigen.
• bigSurvSGD fits large datasets with a the Cox model using Stochastic Gradient Descent.
• stfit adds a general spatiotemporal satellite image imputation method.
• smerc implements statistical methods for regional counts using spatial scan methods.
• T4transport offers some tools for computational optimal transport problems; it uses Rcpp and RcppArmadillo.
• mappoly constructs genetic maps in autopolyploid full-sub populations.
• gsisdecoder decodes identifiers of National Football League players.
• bayesmove models animal movement from telemetry and biologging data using non-parametric Bayesian methods;it uses Rcpp and RcppArmadillo.
• sparta multiplies and divides sparse tables fast; it uses Rcpp and RcppArmadillo.
• survivalmodels has a collection of classical and machine learning models for survival analysis.
• IBMPopSim simulates the random evolution of structured population dynamics; it uses Rcpp and RcppArmadillo.
• StempCens implements spatio-temporal estimation and prediction for censored/missing responses; it uses Rcpp and RcppArmadillo.
• klsh implements a k-means variant of locality sensitive hashing.
• imbibe provides a set of fast, chainable image-processing operations.
• psqn offers quasi-Newton methods ot minimize partially separable functions.
• ivsacim uses instrumental variables under a structural cumulative additive intensity model.
• rlfsm enables simulation and inference for linear fractional stable motions.
• interleave converts matrices and lists of matrices into a single vector by interleaving their values.
• GCSM implements a Generic Composite Similarity Measure (GCSM); it uses Rcpp and RcppArmadillo.
• msce calculates hazard and survival function of multi-stage clonal expansion models.
• geoFKF provides a kriging method for functional datasets with spatial dependency.
• breakfast contains computationally efficient multiple change-point detection and estimation methods.
• viscomplexr creates phase portraits of functions in the complex number plane.
• epinetr adds epistatic network modelling with forward-time simulation.
• FlexReg fits regression models for bounded responses, such as rates and proportions; it uses Rcpp, RcppEigen and BH.
• poolfstat computes F-statistics from Pool-Seq data in population genomics studies.
• sbo builds and evaluates text prediction functions based on Stupid Back-Off n-gram models.
• FlyingR simulates the flight range of birds.
• gfilmm simulates the generalized fiducial distribution for normal linear mixed models with interval data; it uses Rcpp and RcppEigen.
• LassoGEE fits generalized estimating equations with L1 regularization to longitudinal data; it uses Rcpp and RcppArmadillo.
• lineup2 adds tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data.
• tfarima has customized transfer function and ARIMA models with multiple operators and parameter restrictions; it uses Rcpp and RcppArmadillo.
• hdpGLM uses MCMC to estimate the Hierarchical Dirichlet Process Generalized Linear Model (hdpGLM); it uses Rcpp and RcppArmadillo.
• sureLDA implements a novel multi-disease automated phenotyping method for the EHR; it uses Rcpp and RcppArmadillo.
• Bayesrel adds the most common Bayesian single test reliability estimators; it uses Rcpp and RcppArmadillo.
• QF computes quadratic form (QF) distributions and ratios of QFs.
• Ravages does rare variant assocation tests; it uses Rcpp, RcppEigen and BH.
• leidenAlg implements an R interface to the Leiden algorithm for iterative community detection; it uses Rcpp, RcppArmadillo, and RcppEigen.
• RMSNumpress connects R to MS Numpress for compression of numeric data from mass spectrometers.
• SCORNET does consistent, semi-supervised, non-parametric survival curve estimations of EHR data; it uses Rcpp and RcppArmadillo.
• dismo models species distribution by predicting the environmental similarity of sites to locations of known occurrences of a species.
• bayesGAM fit multivariate response Generalized Additive Models using Hamiltonian Monte Carlo; it uses Rcpp, RcppEigen and BH.
• evolqg provides functions for evolutionary quantitative generics; it uses Rcpp and RcppArmadillo.
• gbeta computes d/q/p/r functions of the generalized Beta and Beta Prime distribution; it uses Rcpp, RcppArmadillo, and RcppEigen.
• jti implements junction tree inference; it uses Rcpp and RcppArmadillo.
• adheRenceRX assesses medication adherence from pharmaceutical claims data.
• ciu implements contextual importance and utility (CIU) for explainable AI (XAI).
• slopeOP partitions data optimally to detect change-in-slop with continuity constraints.
• BCT implements tools for exact Bayesian inference for discrete time series.
• cpss detects change points by sample splitting; it uses Rcpp and RcppArmadillo.
• fctbases offers easy-to-use fast implementations of various functional bases; it uses Rcpp and RcppArmadillo.
• GWmodel adds techniques for geographically-weighted models; it uses Rcpp and RcppArmadillo.
• pda contains a collection of privacy-preserving distributed algorithms; it uses Rcpp and RcppArmadillo.
• WinRatio calculates the win ration for prioritized outcomes and 95% confidence intervals.
• WRI implements Wasserstein regression inference methods; it uses Rcpp and RcppArmadillo.
• eBsc adds empirical Bayes smoothing splines for correlated errors; it uses Rcpp and RcppArmadillo.
• EigenR supports real and complex matrix operations; it uses Rcpp and RcppEigen.
• gfiExtremes performs generalized fiducial inference on generalized Pareto distribution quantiles; it uses Rcpp, RcppArmadillo, and BH.
• latentgraph estimates graphical models with latent variables; it uses Rcpp and RcppArmadillo.
• SurrogateRegression; it uses Rcpp and RcppArmadillo.
• clevr does clustering and link prediction evaluation; it uses Rcpp and BH.
• RecAssoRules recursively mines for frequent patterns and confident association rules.
• quanteda.textstats computes textual statistics for characterizing and comparing data; it uses Rcpp and RcppArmadillo.
• blatent estimates latent variable models using Bayesian methods.
• GreedyExperimentalDesign computes experimental designs for two-arm experiments with covariates.
• PRDA conducts prospective or retrospective design analysis; it uses Rcpp and RcppArmadillo.
• mlpack offers fast and flexible machine learning written in C++; it uses Rcpp and RcppArmadillo.
• OptCirClust clusters circular, periodic, or framed data fast, optimally, and reproducibly.
• comparator compares strings, sequences, and numeric vectors for clustering and record linkage applications.
• doc2vec learns vectors representations of sentences, paragraphs or documennts using 'Paragraph Vector' algorithms.
• chillR provides statistical methods for phonology analysis in temperate fruit trees.
• biClassify implements binary classification using discriminant analysis; it uses Rcpp and RcppArmadillo.
• quanteda.textplots visualizes textual data and extends 'quanteda'.
• rminizinc interfaces 'MiniZinc' constraint programming solver.
• SUNGEO integrates spatially-misaligned GIS data and part of the sub-national geospatial data archive system.
• polyqtlR does quantitative trait loci (QTL) analysis in polyploid bi-parental F1 populations; it uses Rcpp and RcppArmadillo.
• sparkwarc loads WARC (Web ARChive) files into Apache Spark allowing to read files from the Common Crawl project.
• foreSIGHT creates hydroclimate scenarios, stress tests systems and visualizes system performance.
• SPARSEMODr implements spatially-explicit, stochastic disease models with customizable time windows.
• GLMcat fits Generalized Linear Models for categorical responses; it uses Rcpp, RcppEiegn, and BH.
• CoMiRe computes posterior inference under the convex mixture regression model; it uses Rcpp and RcppArmadillo.
• SAMGEP implements a semi-supervised method for prediction of phenotype event times; it uses Rcpp and RcppArmadillo.
• matrixdist computes statistics for matrix distributions.
• mgss offers a matrix-free multigrid preconditioner for spline smoothing.
• read.gt3x efficiently parses 'Actigraph' 'GT3X'/'GT3X+' accelerometer data.
• sfcr simulate stock-flow consistent models; it uses Rcpp and RcppArmadillo.
• MSEtool helps develop, simulate, test, and implement management procedures for fisheries; it uses Rcpp and RcppArmadillo.
• DSWE adds data science for wind energy applications; it uses Rcpp and RcppArmadillo.
• GPFDA implements Gaussian process regression for functional data analysis; it uses Rcpp and RcppArmadillo.
• JMbayes2 extends joint models for longitudinal and time-to-event data; it uses Rcpp and RcppArmadillo.
• mixture implements 14 parsimonious mixture models for model-based clustering or classification; it uses Rcpp and RcppArmadillo.
• vectorwavelet computes vector wavelet coherence for multiple time series.
• bmabasket implements Bayesian model averaging for basket trials; it uses Rcpp and RcppArmadillo.
• ExhaustiveSearch provide an easy to use, fast and scalable exhaustive search framework; it uses Rcpp and RcppArmadillo.
• SeuratObject defines S4 classes for single-cell genomic data and associated information.
• sparsevb implements spike-and-slab variational Bayes for linear and logistic regression; it uses Rcpp and RcppArmadillo.
• spNetwork performs spatial analysis on network data; it uses Rcpp and RcppArmadillo.
• ubms run Bayesian models for data from unmarked animals using 'Stan'.
• GenomeAdmixR simulate admixture of genomes; it uses Rcpp and RcppArmadillo.
• bayesforecast models Bayesian time series with Stan; it uses Rcpp, RcppEigen and BH.
• SPlit optimally splits a dataset for training and testing using support points; it uses Rcpp and RcppArmadillo.
• iGraphMatch offers graph matching methods and analysis.
• multibridge evaluates multinomial order restrictions with bridge sampling.
• rliger does linked inference of genomic experimental relationships; it uses Rcpp, RcppArmadillo, and RcppEigen.
• gfilogisreg implements generalized fiducial inference for binary logistic regression models.
• gplite implements the most common Gaussian process (GP) models; it uses Rcpp and RcppArmadillo.
• idem offers inference in randomized controlled trials with death and missingness; it uses Rcpp, RcppEigen, and BH.
• robslopes has Fast algorithms for the Theil-Sen estimator and Siegel's repeated median slope estimator; it uses Rcpp and RcppArmadillo.
• sensobol computes, bootstraps and plots up to third-order Sobol'-based sensitivity indices; it uses Rcpp and RcppArmadillo.
• warbleR streamlines bioacoustic analysis.
• pagoda2 analyzes and interactively explores large-scale single-cell RNA-seq datasets.
• rgeoda provides several spatial data analysis functionalities.
• fmerPack implements heterogeneity pursuit via finite mixture effects models; it uses Rcpp and RcppArmadillo.
• FamilyRank grows and ranks families of features via graphical knowledge; it uses Rcpp and RcppArmadillo.
• motif describes spatial patterns of categorical raster data for any defined regular and irregular areas; it uses Rcpp and RcppArmadillo.
• RcppFastFloat interfaces the 'fastfloat' library for gigabyte per second character parsing.
• wowa introduces weights into ordered weighted averages and extend bivariate means based on n-ary tree construction.
• mlsbm fit Bayesians (multi-level) stochastic block models using efficient Gibbs sampling; it uses Rcpp and RcppArmadillo.
• patentr accesses USPTO bulk data in tidy rectangular format.
• PoolTestR implements prevalence and regression for pool-tested (group-tested) data; it uses Rcpp, RcppEigen, and BH.
• PHSMM fits hidden semi-Markov models (HSMMs) with flexible state dwell-time distributions via penalised ML; it uses Rcpp and RcppArmadillo.
• SplitGLM computes generalized linear models that split the covariates into groups; it uses Rcpp and RcppArmadillo.
• blaster implements an efficient BLAST-like sequence comparison algorithm.
• ipmr fits integral projection models using an expression based framework.
• fipp computes implicitly induced quantities from prior/hyperparameter specifications for mixture models; it uses Rcpp and RcppArmadillo.
• matrixprofiler implements core functions of the Matrix Profile used by 'tsmp'.
• CoOL implements computational phase of 'Causes of Outcome Learning'; it uses Rcpp and RcppArmadillo.
• kgrams has tools to train and evaluate k-gram language models.
• POSetR provides a set of tools for generating, analysing, and visualizing finite partially ordered sets.
• PheVis adds automatic phenotyping of electronic health record at visit resolution.
• lavacreg estimates multi-group count regression models with latent covariates.
• fwildclusterboot implements fast wild cluster bootstrap inference for linear models.
• bestridge finds best subset ridge regression in glm and Cox proportional hazard models; it uses Rcpp and RcppEigen.
• mdgc imputes missing data usnig Gaussian copulas; it uses Rcpp, RcppArmadillo, and BH.
• metapack performs Bayesian inference for (network) meta-analytic models through MCMC; it uses Rcpp, RcppArmadillo and BH.
• survidm offers estimation of several probabilities in an illness-death model.
• CDatanet models count data with peer effects; it uses Rcpp and RcppArmadillo.
• lingmatch offers a processing tools and similarity metrics to facilitate flexible representation of texts and matching.
• spacefillr generates random and quasi-random space-filling sequences.
• xutils collects utility functions by Fangzhou Xie.
• MIRES offers Measurement Invariance assessment using Random Effects models and Shrinkage; it uses Rcpp, RcppEigen, and BH.
• conos implements clustering on networks of (single-cell RNA) samples; it uses Rcpp, RcppArmadillo, and RcppEigen.
• fHMM fits Hidden Markov Models to financial data; it uses Rcpp and RcppArmadillo.
• localScore calculates the local score and statistical relevance in sequences of given distributions.
• communication offers feature extraction and model estimation for audio of human speech; it uses Rcpp and RcppArmadillo.
• econetwork analysis ecological networks; it uses Rcpp, RcppEigen, and RcppGSL.
• RespirAnalyzer processes and analyses respiratory data via linear and nonlinear statistics.
• ccrtm uses coupled chain radiative transfer models to describe absorption, reflectance and transmission of solar energy in vegetation.
• twangContinuous provides functions for propensity score estimation and weighting for continuous exposures.
• qad quantifies asymptotic dependence using copulas.
• FORTLS processes Terrestrial Laser Scanner (TLS) point cloud data derived from single scans; it uses Rcpp and RcppEigen.
• Sshaped estimates S-shaped functions and inflection points; it uses Rcpp and RcppArmadillo.
• ph2rand assists with phase II oncology design trials with Bernoulli outcome variables.
• ICSKAT computes interval-censored sequence kernel association resrs; it uses Rcpp and RcppEigen.
• smartsnp offers fast multivariate analyses of genotype data; it uses Rcpp and RcppArmadillo.
• smmR estimates and simulates multi-state discrete semi-Markov processes; it uses Rcpp and RcppArmadillo.
• implements an l1-version of spectral clustering; it uses Rcpp and RcppArmadillo.
• ondisc offers fast, universal and intuitive large-scale single-cell data computing.
• ATAforecasting add automatic time series analysis and forecasting; it uses Rcpp and RcppArmadillo.
• gigg adds group inverse-gamma gamma shrinkage for sparse regression with grouping structure; it uses Rcpp, RcppArmadillo, and BH.
• tsfgrnn forecasts timeseries using general regression neural networks.
• markerpen implements marker gene detection via penalized principal components; it uses Rcpp and RcppEigen.
• TDAkit adds a toolkit for topological data analysis; it uses Rcpp and RcppArmadillo.
• LMMELSM fits latent multivariate mixed effects location scale models; it uses Rcpp, RcppEigen, and BH.
• tidysq processes and analyses biological sequence data efficiently.
• dccmidas fits DCC models with GARCH-MIDAS specifications in the univariate step; it uses Rcpp and RcppArmadillo.
• gghilbertstrings offers a fast 'ggplot2'-based implementation of Hilbert curves.
• snpsettest tests set-based associations using GWAS summary statistics; it uses Rcpp and RcppArmadillo.
• pleiotest performs a fast multi-trait GWAS analysis based on seemingly unrelated regressions; it uses Rcpp and RcppArmadillo.
• thunder computates and visualises atmospheric convective parameters.
• microsimulation does event-oriented and process-oriented discrete simulation.
• Dire fits linear regressions with a latent outcome variable.
• isodistrreg computes distributional regression under stochastic order restrictions for numeric and binary response variables.
• MultOrdRS models multivariate ordinal responses including response styles; it uses Rcpp and RcppArmadillo.
• sdpdth implements an M-estimator for threshold and non-threshold spatial dynamic panel data model; it uses Rcpp and RcppArmadillo.
• strucchangeRcpp tests, monitors, and dates structural changes via C++; it uses Rcpp and RcppArmadillo.
• BSSprep whitens data as preparation for blind source separation; it uses Rcpp and RcppArmadillo.
• BayesRGMM implements Bayesian Robust Generalized Mixed Models for longitudinal data; it uses Rcpp and RcppArmadillo.
• ClustAssess adds a set of tools to assess clustering similarity across methods and method stability.
• hawkesbow estimates Hawkes processes from binned data; it uses Rcpp, RcppArmadillo, and BH.
• SpatialKWD computes spatial Kantorovich-Wasserstein distances for large spatial maps.
• bbdetection implements two bull and bear market states detection methods for financial markets.
• ProcData provides tools for exploratory process data analysis.
• Rforestry has fast implementations of Honest and Linear random forests and gradient boosting; it uses Rcpp and RcppArmadillo.
• sasfunclust implements the sparse and smooth functional clustering; it uses Rcpp and RcppArmadillo.
• gRc offers estimation, model selection and other aspects of statistical inference in Graphical Gaussian models; it uses Rcpp and RcppArmadillo.
• fcci supports building Feldman-Cousins confidence intervals.
• gwpcormapper interactively maps geographically weighted correlation and partial correlation.
• readsparse reads and writes labelled sparse matrices in various text formats.
• bmggum does full Bayesian estimation of Multidimensional Generalized Graded Unfolding Model; it uses Rcpp, RcppEigen, and BH.
• SBCK implements several recent multivariate bias correction methods; it uses Rcpp and RcppEigen.
• diffmatchpatch wraps Google's 'diff-match-patch' library.
• bigalgebra provides 'BLAS' and 'LAPACK' for R matrices and 'big.matrix' objects; it uses Rcpp and BH.
• ForestTools analyses remotely sensed forest data.
• mistral regroups varias reliability analysis methods for rare events analysis.
• modesto models and analyses stochastic systems.
• abess selects adaptive best subsets; i in polynomial time, it uses Rcpp and RcppEigen.
• greed clusters and selects models with integrated classification likelihood; it uses Rcpp and RcppArmadillo.
• grpsel performs group subset selection for sparse models with grouped predictors; it uses Rcpp and RcppArmadillo.
• braggR calculate the revealed aggregator of probability predictions.
• ganGenerativeData creates generative data using Generative Adversarial Networks.
• UPCM computes uncertainty in partial credit models; it uses Rcpp and RcppArmadillo.
• hrt implements linear model tests robust to heteroscedasticity; it uses Rcpp and RcppEigen.
• purgeR implements inbreeding-purging estimation in pedigreed populations.
• bfast detects time series breaks in additive season and trend components.
• scINSIGHT interprets heterogenous single-cell gene expression data; it uses Rcpp and RcppArmadillo.
• bayesZIB fits Bayesian zero-inflated Bernoulli regression models; it uses Rcpp, RcppEigen, and BH.
• dga performans capture-recapture estimation via Bayesian model averaging; it uses Rcpp and RcppArmadillo.
• Recocrop estimates environmental suitability for plants.
• TriDimRegression computes Bayesian statistics for 2d/3d transformations; it uses Rcpp, RcppEigen, and BH.
• vasicekreg supports regression modeling using Vasicek distribution.
• BayesPPD computes Bayesian power prior designs for glm models; it uses Rcpp, RcppArmadillo, and RcppEigen.
• CPGLIB generates ensembles of generalized linear models using competing proximal gradients; it uses Rcpp and RcppArmadillo.
• MAGEE offers mixed model association test for gene-environment interactions; it uses Rcpp and RcppArmadillo.
• parsermd implements a formal parser (and related tools) for R Markdown.
• rtrend estimates linear models under autocorrelated errors and trends.
• smoots estimates time series trend and its derivative nonparametricsally; it uses Rcpp and RcppArmadillo.
• MatrixExtra offers additional methods for sparse matrices.
• BosonSampling implements Boson sampling ; it uses Rcpp and RcppArmadillo.
• fastText interfaces the 'fastText' library for efficient work representation and sentence classification.
• multgee adds a GEE solver for correlated nominal or ordinal multinomial response.
• netgsa carries out network-based gene set analysis by incorporating external information about interactions among genes.
• RprobitB fits latent class mixed multinomial probit models; it uses Rcpp and RcppArmadillo.
• autocart adds autocorrelation regression trees for spatial data with coordinate information; it uses Rcpp and RcppArmadillo.
• bliss fits Bayesian functional linear regression models with sparse step functions; it uses Rcpp and RcppArmadillo.
• glamlasso penalizes in large scale generalized linear array models; it uses Rcpp and RcppArmadillo.
• legion forecasts using multivariate space-space model; it uses Rcpp and RcppArmadillo.
• VARDetect implements multiple change point detection in structural VAR models; it uses Rcpp and RcppArmadillo.
• einsum implements summation over n-dimensional array indices as suggested by Einstein (1916).
• gsignal offers an R implementation of the Octave package 'signal' for signal processing.
• Rcatch22 implements 22 functions for calculations of canonical time-series characterics.
• HDSpatialScan detects spatial clusters of abnormal data on multivariate or functional data; it uses Rcpp and RcppArmadillo.
• spectre predicts regional community composition.
• xplorerr offers tools for interactive data explorations.
• jsonStrings manipulates strings in JSON documents: extract, delete, merge and more.
• robsel estimates via graphical lasso regularization; it uses Rcpp and RcppEigen.
• qtl2ggplot visualizes quantitative trait loci (QTL) experiments.
• conleyreg runs estimationses using Conley (1999) standard errors; it uses Rcpp and RcppArmadillo.
• surveyvoi implements a decision support tool for prioritizing sites for ecological surveys; it uses Rcpp and RcppEigen.
• mdendro offers extended agglomerative hierarchical clustering.
• hhsmm fits, predicts, and simulates hidden hybrid (semi-)Markov models.
• dpcc solves L1 convex clustering problems with identical weights via dynamic programming.
• harmony provides fast, sensitive, and accurate integration of single cell data; it uses Rcpp and RcppArmadillo.
• HDTSA adds procedures for high-dimensional time series analysis; it uses Rcpp and RcppEigen.
• gesso induces main-effect-before-interaction hierarchical structure for single environmental exposure; it uses Rcpp, RcppEigen, and BH.
• betaBayes implements Bayesian beta regression; it uses Rcpp and RcppArmadillo.
• ecotraj analyses temporal ecosystems changes as trajectories on a chosen multivariate space.
• scDHA provides a fast and accurate pipeline for single-cell analyses via hierarchical autoencoding, it uses Rcpp and RcppArmadillo.
• BINtools forecasts via Bayesian BIN (Bias, Information, Noise); it uses Rcpp, RcppEigen, and BH.
• meshed fits Bayesian spatiotemporal multivariate regression models via latent meshed Gaussian processes; it uses Rcpp and RcppArmadillo.
• QFASA estimates predator diets via quantitative fatty acid signature analysis; it uses Rcpp and RcppEigen.
• admix fits two-component admixtutre (aka contamination) models.
• geomader helps to study gerrymandering focusing on the geographic tools.
• individual adds a framework for specifying and simulating individual based models.
• rmarchingcubes calculates 3d contour meshes via the marching cubes algorithm; it uses Rcpp and RcppArmadillo.
• rayvertex rasterizes images using a 3d software renderer.
• ClusPred estmates regression models with fixed group effects where variable is missing; it uses Rcpp and RcppArmadillo.
• MultSurvTests implements permutation tests for multivariate survival analysis; it uses Rcpp and RcppArmadillo.
• fmtr contains a set of functions to apply formats to data frames and vectors.
• lgpr offers nonparametric modeling of longitudinal data using additive Gaussian processes; it uses Rcpp, RcppEigen, and BH.
• hrqglas conducts group variable selection for quantile and robust mean regression.
• rim the 'R Interface to Maxima' brings symbolic computation into R.
• ahMLE fits additive hazard models; it uses Rcpp and RcppArmadillo.
• CKMRpop wraps the 'spip' program to simulate pedigree from age-structured populatons with user-specified life histories.
• RDP implements Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2d curve.
• strawr reads and dumps .hic files.
• TensorClustering performs model-based tensor-clustering.
• ugomquantreg adds quantile regression modeling for unit-Gompertz responses.
• libr creates data libraries, generates data dictionaries, and simulates a data step.
• impactr reads, processes, and analyses accelorometers data from 'ActiGraph' for mechanical loading variables.
• greeks calculates option price sensitivities for European and Asian and American options in the Black Scholes model.
• dcortools provides fast and flexible functions for distance correlation analysis; it uses Rcpp, RcppArmadillo, and RcppEigen.
• hydrotoolbox reads, plots, manipulates and processes hydro-meteorological data records.
• MedianaDesigner calculates power and sample size for late-stage clinical trials via simulation.
• nomclust implements hierarchical cluster analysis of nominal data.
• natcpp offers fast C++ primitives for 'NeuroAnatomyToolbos'.
• DCLEAR computes distance-based cell lineage reconstruction; it uses Rcpp and RcppArmadillo.
• recometrics calculates evaluation metrics for implicit-feedback recommender systems.
• MNARclust clusters data with non-ignorable missingness using Semi-Parametric Mixture Models; it uses Rcpp and RcppArmadillo.
• SC.MEB spatially clusters via Hidden Markov Random Field using Empirical Bayes; it uses Rcpp and RcppArmadillo.
• DDD implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process.
• fedmatch provides a flexible set of tools for matching two un-linked data sets.
• sdcHierarchies creates and (interactively) modifies nested hierarchies.
• SMME efficiently solves the soft maximin problem for large scale heterogeneous data; it uses Rcpp and RcppArmadillo.
• tidylda implements an algorithm for Latent Dirichlet Allocation; it uses Rcpp and RcppArmadillo.
• CARlasso fits Bayesian Conditional Autoregressive LASSO with automatic and adaptive shrinkage; it uses Rcpp and RcppArmadillo.
• AovBay computes classic, nonparametric and Bayesian one-way analysis of variance panels; it uses Rcpp, RcppEigen, and BH.
• CausalGPS matches on generalized propensity scores with conitnuous exposure.
• RcppFarmHash provides access to the FarmHash family of hash functions.
• adjclust implements a constrained version of hierarchical agglomerative clustering; it uses Rcpp and RcppArmadillo.
• magi provides inference for estimation of ordinary differential equations parameters; it uses Rcpp, RcppArmadillo, and RcppEigen.
• profoc combines probabilistic forecasts using CRPS learning algorithms; it uses Rcpp and RcppArmadillo.
• RcppML implements high-performance machine learning algorithms; it uses Rcpp and RcppEigen.
• didimputation fits two-way fixed effect difference-in-difference/event-study models via imputation; it uses Rcpp and RcppArmadillo.
• edgebundle contains algorithm to detect bundling edges in networks, flow and metro layouts.
• sorcering offers a soil organic carbon and CN ratio driven nitrogen modelling framework; it uses Rcpp and RcppArmadillo.
• SPSP computes selection by partitioning of the solution paths.
• crctStepdown does univariate analysis of cluster trials with multiple outcomes; it uses Rcpp and RcppArmadillo.
• EmiR adds an evolutionary minimizer following different evolutionary algorithms; it uses Rcpp and RcppArmadillo.
• robustcov collects methods for robust covariance estimation; it uses Rcpp and RcppArmadillo.
• handwriter processes handwriting documents into letters, words and lines.
• symphony implements Syphony single-cell reference building algorithms; it uses Rcpp and RcppArmadillo.
• PLFD computes portmanteau local feature discrimination for matrix-variate data; it uses Rcpp and RcppArmadillo.
• DCSmooth implements nonparametric regression for spatial models; it uses Rcpp and RcppArmadillo.
• aRtsy offers generative art with ggplot2; it uses Rcpp and RcppArmadillo.
• statgenIBD calculates 'Idendity by Descent' probabilities; it uses Rcpp and RcppArmadillo.
• tci implements target-controlled infusion algorithms; it uses Rcpp and RcppArmadillo.
• fastqq helps to computes quantile-quantile plots from large samples.
• GUniFrac add a suite of methods for microbiome analysis.
• geocmeans provides functions for spatial fuzzy unsupervised classification; it uses Rcpp and RcppArmadillo.
• RVCompare offers a framework to compare two random variables.
• flipr adds a flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing.
• simfam simulates and models family pedigree with structured founders.
• sphunif computes uniformity tests on the circle and (hyper)sphere; it uses Rcpp and RcppArmadillo.
• flintyR implements flexible and interpretable non-parametric tests of exchangeability; it uses Rcpp and RcppArmadillo.
• shrinkDSM provides efficient Bayesian inference for dynamic survival models with shrinkage; it uses Rcpp and RcppArmadillo.
• DOVE implements maximum likelihood methods for evaluating the durability of vaccine efficacy; it uses Rcpp and RcppArmadillo.
• filearray supports file-backed arrays for out-of-memory computations.
• penppml fits penalized Poisson Pseudo Maximum Likelihood regressions; it uses Rcpp and RcppEigen.
• TiPS generates stochastic time series and genealogies associated with a population dynamics model.
• VIC5 offers the variable infiltration capacity (VIC) hydrological model.
• GPBayes offers tools for Gaussian process modeling in uncertainty quantification; it uses Rcpp and RcppEigen.
• iDOVE adds a nonparametric maximum likelihood method for assessing potentially time-varying vaccine efficacy; it uses Rcpp and RcppArmadillo.
• relliptical generates random numbers from a truncated multivariate elliptical distribution; it uses Rcpp, RcppArmadillo, and RcppEigen.
• baskexact implements exact calculations of basket trial operating characteristics; it uses Rcpp and RcppArmadillo.
• rbioacc provides inference and prediction for toxico-kinetic (TK) models; it uses Rcpp, RcppEigen, and BH.
• rmBayes performs Bayesian inference for repeated-measures designs; it uses Rcpp, RcppEigen, and BH.
• staggered adds efficient estimation under staggered treatment timing; it uses Rcpp and RcppEigen.
• quadtree works with raster-like quadtrees allowing for variable-sized cells.
• sglg fits semi=parametric generalized log-Gamma regression models.
• multiblock support multi-block data fusion for statistics and machine learning; it uses Rcpp and RcppEigen.
• PoDBAY estimates vaccine efficacy using the PoDBAY method.
• bpr fits Bayesian Poisson regression models; it uses Rcpp, RcppArmadillo, and BH.
• RcppCensSpatial adds spatial esimation and prediction for censored/missing responses; it uses Rcpp and RcppArmadillo.
• rethnicity predicts ethnic groups from names; it uses Rcpp and RcppEigen.
• MazamaRollUtils implements rolling mins, means, maxes for environmental time series.
• RavenR processes and outputs files for the Raven Hydrogolical Modelling Framework.
• nevada offers a network-value data analysis framework; it uses Rcpp and RcppArmadillo.
• isotracer implements Bayesian models to analyze data from tracer addition experiments; it uses Rcpp, RcppEigen, and BH.
• aspline implements spline regression with adaptive know selection.
• bistablehistory applies cmulative history analysis to bistable perception times series; it uses Rcpp, RcppEigen and BH.
• EmpiricalCalibration add routines for performing empirical calibration of observational study estimates.
• ICvectorfields constructs vector fields from spatial population abundancen time series.
• ZIPBayes offers Bayesian analysis for zero-inflated Poisson models.
• mclustAddons extends the 'mclust' package fpor Gaussian finite mixture modelling; it uses Rcpp and RcppArmadillo.
• melt runs multiple empiricial likelihood tests in a general block design; it uses Rcpp and RcppEigen.
• nodeSub simulates DNA alignments using node substitutions.
• predtools evaluates predictive models via calibration curves and model-based ROC.
• tabularMLC applies a maximum likelihood classifier (MLC) to tabular data; it uses Rcpp and RcppArmadillo.
• pecora performas permutation conditioal random one- and two-sample tests; it uses Rcpp and RcppArmadillo.
• StanMoMo estimates Bayesian mortality models; it uses Rcpp, RcppEigen, and BH.
• discretefit simulates Goodness-of-Fit tests for discrete distributions.
• niaidMI implements Markov Model Multiple Imputation with application to NIAID OS.
• igcop adds computational tools for the IG and IGL copula families.
• clhs offers conditioned latin hypercube sampling; it uses Rcpp and RcppArmadillo.
• slasso implements a smooth LASSO estimator for function-on-function linear regression; it uses Rcpp and RcppArmadillo.
• transmdl helps with the application of semiparametric transformation models; it uses Rcpp and RcppEigen.
• CensSpatial fits linear models for censored spatial data.
• bayesPO models presence-only data with a point process model; it uses Rcpp and RcppEigen.
• GCPBayes implements Bayesian meta-analysis of pleiotropic effects using group structure.
• permuco computes permutatins tests for regressions, repeated masures AN(C)OVA and comparis of signals.
• rcbayes estimates Rogers-Castro migration age schedules with Bayesian models; it uses Rcpp, RcppEigen, and BH.
• linconGaussR samples the multivariate normal distribution under linear constraints; it uses Rcpp and RcppArmadillo.
• geoFourierFDA implements ordinary functional kriging methods; it uses Rcpp and RcppArmadillo.
• rsvddpd computes robust singular value decomposition using density power divergence; it uses Rcpp and RcppArmadillo.
• pedmod estimates mixed probit models using pedigree data in liability threshold models; it uses Rcpp and RcppArmadillo.
• rema implements a permutation-based approach for binary meta-analyses of 2x2 tables in the presence of heterogeneity.
• LMMsolver solves sparse mixed model equations for use in statistical genetics.
• glmnet adds extremely efficient procedures for fitting lasso or elastic-net regularization paths for GLMs; it uses Rcpp and RcppEigen.
• RcppClock times execution of overlapping or unique Rcpp code chunks.
• scITD offers single-cell interpretable tensor decomposition; it uses Rcpp and RcppArmadillo.
• wehoop accesses woman's basketball play by play data.
• cuda.ml interfaces the RAPIDS cuML suite of libraries for GPU-accelerated machine learning.
• nlmeVPC adds visual model checking for nonlinear mixed effect models; it uses Rcpp and RcppArmadillo.
• VEwaningVariant implements methods for inference on potential waning of vaccine efficacy; it uses Rcpp and RcppArmadillo.
• fractalRegression adds functions for fractal and multifractal analysis; it uses Rcpp and RcppArmadillo.
• lddmm implements the drift-diffusion mixed model for category learning; it uses Rcpp and RcppArmadillo.
• dateutils offers utilities for mixed-frequency data to aggregate and normalize; it uses Rcpp and RcppArmadillo.
• desla calculates the de-sparsified lasso; it uses Rcpp and RcppArmadillo.
• EpiModel simulates mathematical models of infectious disease dynamics.
• hoopR accesses men's basketball play-by-play data.
• missSOM implements self-organizing maps with built-in missing data imputation.
• qtlpoly performs random-effect mulitple interval mapping; it uses Rcpp and RcppArmadillo.
• surveil adds time series models for disease surveillance; it uses Rcpp, RcppEigen, and BH.
• mwcsr solves maximum weight connected subgraph problems and its variants.
• zoid fits Dirichlet regression and zero-and-one inflated Dirichlet regression; it uses Rcpp, RcppEigen, and BH.
• pARI computes permutation-based all-resolutions inference; it uses Rcpp and RcppArmadillo.
• DR.SC offers joint dimention reduction and spatial clustering for single-cell RNA sequencing; it uses Rcpp and RcppArmadillo.
• mapscanner prints maps, draws on them and scans them back in.
• o2plsda implements multiple omics data integration; it uses Rcpp, RcppArmadillo, and RcppEigen.
• sweater evaluates implicit biases in word embeddings via different tests.
• stan4bart fits semiparametric linear and multilevel models with BART components; it uses Rcpp, RcppEigen, and BH.
• SIRmcmc provides a Susceptible-Infectious-Recovered model of household and community infection.
• deepgp implements design for deep gaussian processes using MCMC; it uses Rcpp and RcppArmadillo.
• sumSome adds sum-based tests with permutation true disovery guarantee.
• minMSE performs treatment assigment for (field) experiments for one or multiple treatment groups.
• diffudist evaluates diffusion distances for complex single-layer networks; it uses Rcpp and RcppEigen.
• opera combines user-supplied forecasts to create create 'online prediction by expert aggregation'; it uses Rcpp and RcppEigen.
• qlcal brings the QuantLib calendering functionality to R.
• BMisc regroups miscellaneous functions for panel data, quantiles, and printing results; it uses Rcpp and RcppArmadillo.
• fastRhockey accesses Premier Hockey Federation and National Hockey League play by play data; it uses Rcpp and RcppParallel.
• hibayes computes individual-level, summary-level and single-step Bayesian regression models; it uses Rcpp and RcppArmadillo.
• changepoints collects several change-point detection methods; it uses Rcpp and RcppArmadillo.
• pema conducts penalized meta-analysis; it uses Rcpp, RcppEigen, and BH.
• prioriactions uses mixed integer programming for multi-action planning problems; it uses Rcpp, RcppArmadillo, and BH.
• adjSURVCI estimates parameters and adjusted probabilities for right-censored data; it uses Rcpp and RcppArmadillo.
• bayMDS offers Bauesian multidimensional scaling and choice of dimension; it uses Rcpp and RcppArmadillo.
• brmsmargins computes Bayesian marginal effects for 'brms' models; it uses Rcpp and RcppArmadillo.
• survival.svb fits high-dimensional proportional hazards models; it uses Rcpp and RcppEigen.
• lrstat computers power and sample size for non-proportional hazards models.
• PLSiMCpp adds methods for partial linear single index models; it uses Rcpp and RcppArmadillo.
• redistmetrics scores redistring plans unsing common measures; it uses Rcpp and RcppArmadillo.
• sleev implements semiparametric likelihood estimation with errors in variables; it uses Rcpp, RcppArmadillo, and RcppEigen.
• EpiLPS add Bayesian estimates of the instantaneous reproduction number via Laplacian P-splines; it uses Rcpp and RcppArmadillo.
• rego automates time series forecasts including imputation; it uses Rcpp and RcppArmadillo.
• SoyNAM adds the soybean nested association mapping dataset for genome-wide analysis; it uses Rcpp and RcppEigen.
• FastJM offers semi-parametric joint modeling of survival and longitudinal data; it uses Rcpp and RcppEigen.
• ILSE fits linear models using 'ILSE' imputation for block missing data and covariate correlation.
• RcppCGAL provifes the Computational Geometry Algorithms Library headers.
• free offers a unified regularized estimating equation solver; it uses Rcpp and RcppArmadillo.
• approxOT implments approximate and exact optimal transport methods; it uses Rcpp, RcppEigen, and BH.
• tmvtnsim simulates with truncated multivariate Normal and t random vectors; it uses Rcpp and RcppArmadillo.
• edlibR integrates with the Edlib library for pairwise exact sequence alignment using Edit / Levenshtein distance.
• ALUES evaluates land suitability for different crop production uses.
• intRinsic performs likelihood-based intrinsic dimension estimations; it uses Rcpp and RcppArmadillo.
• PoissonMultinomial adds methods to compute the Poisson-Multinomial distribution; it uses Rcpp and RcppArmadillo.
• dynatop implements and enhances the dynamic TOPMODEL hydrological model.
• plotHMM suppports modeling sequential data via Hidden Markov Models; it uses Rcpp and RcppArmadillo.
• gamselBayes offers Bayesian Generalized Additive Model Selection; it uses Rcpp and RcppArmadillo.
• TreeDimensionTest tests for trajectory presence and heterogenity in multivariate data.
• BEKKs add multivariate conditional volatility modeling and forecasting; it uses Rcpp and RcppArmadillo.
• glmmPen fits high-dimensional penalized generalized linear mixed models; it uses Rcpp, RcppArmadillo, RcppEigen, and BH.
• nebula deploys negative binomial mixed mpdels using large-sample approximations; it uses Rcpp and RcppEigen.
• aphylo analyzes and predicts gene-functional annotations in phylogenetic trees.
• rofanova implements robust functional analysis of variance; it uses Rcpp and RcppArmadillo.
• penAFT fits regularized Gehan estimator with elastic and sparse group lasso penalites; it uses Rcpp and RcppArmadillo.
• twinning offers an efficient algorithm for data twinning.
• ATNr runs allometric throphic network models; it uses Rcpp and RcppArmadillo.
• fcirt provides Bayesian estimation of forced choice models in Item Response Theory; it uses Rcpp, RcppEigen, and BH.
• fdacluster implements joint clustering and alignment of functional data; it uses Rcpp and RcppArmadillo.
• PCObw implements bandwidth selection with penalized comparison to overfitting criterions; it uses Rcpp and RcppEigen.
• representr creates representative records after entity resolution.
• netcmc implements spatio-network GLM models for areal unit and network data; it uses Rcpp and RcppArmadillo.
• asteRisk computes satellite positions given a state vector.
• aum computes the area under minimum of false positves and negatives.
• RMCC adds airborne LiDAR filtering methods based on multiscale curvature.
• geostan implements Bayesian spatial analysis inference methods; it uses Rcpp, RcppEigen, and BH.
• fastadi implements self-tuning data adaptive matrix imputation; it uses Rcpp and RcppArmadillo.
• tipsae adds tools for handling indices and proportions in small area estimations.
• LMN does efficient frequentist profiling and Bayesian marginalization of parameters; it uses Rcpp and RcppEigen.
• tabulate creates pretty console output for tables.
• fido fits Bayesian multinomial logistic normal regression models; it uses Rcpp, RcppEigen, and BH.
• clustAnalytics evaluates the stability and significance of clusters of 'igraph' graph objects.
• ghcm implements a statistical hypothesis tests for conditional independence.
• rgraph6 represents graphs as 'graph6', 'digraph6' or 'sparse6' strings.
• lsirm12pl analyses dichotomous and continuous response data using latent factors; it uses Rcpp and RcppArmadillo.
• nbfar fits negative binomial factor regression models; it uses Rcpp, RcppArmadillo, and RcppParallel.
• LOMAR reads, registers and compares point sets from single molecule localization microscopy.
• ohoegdm perform a Bayesian estimation of the ordinal exploratory Higher-order General Diagnostic Model; it uses Rcpp and RcppArmadillo.
• opa implements ordinal pattern analysis for repeated measures observations and time-series data; it uses Rcpp and RcppArmadillo.
• qqconf creates simultaneous testing bands for QQ-plots; it uses Rcpp and RcppArmadillo.
• prome offers patient-reported outcome data analysis via Stan; it uses Rcpp, RcppEigen, and BH.
• autoRasch performs semi-automated Rasch analysis; it uses Rcpp and RcppArmadillo.
• FIESTAutils offers a set of utility functions for forest inventory estimation and analysis.
• dccpp support fast computation of distance correlations; it uses Rcpp and RcppArmadillo.
• gofar enables generalized co-sparse factor regression; it uses Rcpp and RcppArmadillo.
• rbmi implements reference based multiple imputation; it uses Rcpp, RcppEigen, and BH.
• abclass adds multi-category angle-based large-margin classifiers; it uses Rcpp and RcppArmadillo.
• stepSplitReg performs stepwise split regulariszed regression; it uses Rcpp and RcppArmadillo.
• torchvisionlib adds operators for image segmentation and object detection for computer vision models.
• adaHuber performs adaptive Huber estimation and regression; it uses Rcpp and RcppArmadillo.
• dtts offers high-frequency time-series operators via nanotime and data.table.
• RCDT performs fast constrained 2D Delaunay triangulation; it uses Rcpp and RcppArmadillo.
• PSGD generate ensembles of generalized linear models using greedy projected subset gradient descent; it uses Rcpp and RcppArmadillo.
• rrMixture estimates full-ranked, rank-penalized, and adaptive nuclear norm penalized models; it uses Rcpp and RcppArmadillo.
• sentopics offers tools for joint sentiment and topic analysis of textual data.
• cpop detects multiple changes in slope in univariate time series.
• rlemon provides access to LEMON graph algorithms.
• ast2ast translates R functions into external pointer C++ functions for use in ODE or optimization; it uses Rcpp and RcppArmadillo.
• bspline adds b-spline interpolation and regression; it uses Rcpp and RcppArmadillo.
• causalOT uses optimal transport weights for causal inference; it uses Rcpp, RcppEigen, and BH.
• bootCT bootstraps the autoregressive distributed lags test for cointegration; it uses Rcpp and RcppArmadillo.
• combinIT offers a combined interaction test for unpreplicated two-way tables; it uses Rcpp and RcppArmadillo.
• rts2 implements real-time disease surveillance; it uses Rcpp, RcppEigen, and BH.
• PPSFS adds partial profile score feature selection in high-dimensional generalized linear interaction models; it uses Rcpp and RcppArmadillo.
• svines fits and simulates stationary vine copula models for time series; it uses Rcpp, RcppEigen, and BH.
• QWDAP models and predicts time-series based continuous-time quantum walks; it uses Rcpp and RcppEigen.
• JFM extracts joint planes from 3d triangular messhes derived from point cloud data; it uses Rcpp and RcppArmadillo.
• SheetReader parses xlsx files efficiently.
• saeMSPE computes MSPE estimates for the Fay Herriot model and nested error regression model; it uses Rcpp and RcppArmadillo.
• semicmprskcoxmsm uses inverse probability weighting to estimate treatment effects for semi-competing risks data.
• spFW estimates and predicts using Bayesian Hierarchical Spatial Finlay-Wilkinson model; it uses Rcpp and RcppArmadillo.
• PKPDsim performs pharmacokinetic-pharamcodynamic simulations; it uses Rcpp and BH.
• iAR fits irregularly-observed autoregressive models; it uses Rcpp and RcppArmadillo.
• iq implements protein quantification in mass spectometry-based proteomics; it uses Rcpp and RcppEigen.
• networkscaleup analyzes aggregated relational data mostly through 'stan'; it uses Rcpp, RcppEigen, RcppParallel, and BH.
• bmstdr implements Bayesian modeling of spatia-temporal data; it uses Rcpp, RcppEigen, and BH.
• coxrobust fit proportional hazards models robustlt; it uses Rcpp and RcppArmadillo.
• BipartiteModularityMaximization partitions networks into non-overlapping biclusters.
• clusterHD clusters in high-dimensional data; it uses Rcpp and RcppArmadillo.
• zebu estimates local (and global) association measures.
• tglkmeans implements the k-means++ algorithm efficiently.
• baseballr acquires and analyses baseball data.
• rolog embeds SWI Prolog permitting R to query Prolog.
• CircularSilhouette calculates silhouette information for clusters on circular or linear data.
• rminqa offers derivative-free optimizations; it uses Rcpp and RcppArmadillo.
• numberofalleles compute the probability distribution of the number of alleles in a DNA mixture.
• biosensors.usc offers distributional data analysis techniques for biosensor data; it uses Rcpp and RcppArmadillo.
• lpcde estimates via boundary adaptive local polynomial conditional density; it uses Rcpp and RcppArmadillo.
• glmmLasso adds variable selection for generalized linear mixed models via L1-shrinkage; it uses Rcpp and RcppEigen.
• LA adds the Lioness Algorithm (LM) for optimal designs over continuous design space; it uses Rcpp and RcppArmadillo.
• RMM models revenue management using robust demand estimation.
• rxode2 simulates from OSE-based models; it uses Rcpp, RcppArmadillo, RcppEigen, and BH.
• COMIX fits Dirichlet process mixtures with hierarchical multivariate skew kernels; it uses Rcpp, RcppArmadillo, and RcppEigen.
• mnorm calculates and differentiates probabilities and density of (conditional) multivariate normals; it uses Rcpp and RcppArmadillo.
• pwlmm estimates two-level multilevel linear model and two-level multivariate linear multilevel models; it uses Rcpp and RcppEigen.
• FRESHD does fast and robust estimation of signals in heterogenous data; it uses Rcpp, RcppArmadillo, and RcppEigen.
• nlmixr2est fits nonlinear mixed-effects models in population pk/pd; it uses Rcpp, RcppArmadillo, RcppEigen and BH.
• simer offers data simulation for life sciences and breeding; it uses Rcpp, RcppArmadillo, and BH.
• terminaldigits tests for uniformity and independency of terminal digits.
• ycevo nonparametrically estimates the yield curce evolution; it uses Rcpp and RcppArmadillo.
• TAM estimates unidimensional and multudimensional item response models; it uses Rcpp and RcppArmadillo.
• gyro computes hyperbolic geometry for hyperboloid and Poincare models; it uses Rcpp, RcppEigen, and BH.
• epm facilitates aggregation of species' geographic ranges from vector or raster spatial data.
• nlmixr2extra extra support functions for nonlinear mixed-effects models in population PK/PD; it uses Rcpp and RcppArmadillo.
• habCluster detects spatial clustering based on connections between graids.
• BranchGLM offers GLM fitting and variable selection; it uses Rcpp and RcppArmadillo.
• EpiInvert estimates time varying reprpoduction numbers and restored incidence curves using variational techniques.
• grwat implements river hydrograph separation and analysis methods.
• hgwrr estimates via hierarchical and geographically weighted regression; it uses Rcpp and RcppArmadillo.
• markets adds estimation methods for market equilibrium and disequilibrium; it uses Rcpp and RcppGSL.
• RTL offers a risk tool library for trading and commodity risk.
• ScaleSpikeSlab adds a scalable Gibbs sampler implementation for high-dimensional Bayes regression; it uses Rcpp and RcppEigen.
• sits provides satellite image time series analysis for earth observation data cubes.
• eurodata adds fast and easy Eurostat data import and search.
• FGLMtrunc fits truncated functional generalized linear models; it uses Rcpp and RcppArmadillo.
• bbknnR performs batch-balanced K-nearest neighbours.
• binspp fits Bayesian inference for Neyman-Scott point processes; it uses Rcpp, RcppArmadillo, and RcppEigen.
• dynConfiR fits dynamic models for confidence and response time distributions.
• fastTopics adds fast algorithms for fitting topic models; it uses Rcpp and RcppArmadillo.
• IRon solves unbalanced regression tasks.
• deformula integrates one-dimensional functions with double exponential formulas.
• fasano.franceschini.test implements a multidimensional KS test.
• portvine estimates vine-based (un)conditional portfolio risk; it uses Rcpp and RcppEigen.
• CERFIT fits causal effects random forest of interaction tress (CERFIT); it uses Rcpp and RcppArmadillo.
• ASV uses MCMC for a stochastic volatility model with or without leverage; it uses Rcpp and RcppArmadillo.
• DAISIE simulates maximum likelihood of a dynamical model of island biota; it uses Rcpp, RcppEigen, and BH.
• DSSP implementats the direct sampling spatial prior; it uses Rcpp and RcppArmadillo.
• kissmig simulates species migration and range dynamics under stable or changing environmental conditions.
• MagmaClustR clusters and predicts using multi-task Gaussian Processes with common mean.
• sketching sketches data via random subspace embeddings.
• CRTConjoint offers conditional randomization testing (CRT) for conjoint analysis.
• VMDecomp implements 'Variational Model Decomposition'; it uses Rcpp and RcppArmadillo.
• kerSeg offers a new kernel-based changepoint detection suitable for high-dimensional data.
• concom computes connected components on a graphs; it uses Rcpp and BH.
• ipsecr estimates the density of spatially distributed animal population; it uses Rcpp and BH.
• qmd quantifies multivariate dependence usinga copula-based approach; it uses Rcpp and BH.
• batchmix fits semi-supervised and unsupervised Bayesian mixture models with cluster/class structure; it uses Rcpp and RcppArmadillo.
• phacking performns sensitivity analysis for p-hacking in Meta-Analyses; it uses Rcpp, RcppEigen, and BH.
• espadon processes and visualizes 2d-3d DICOM-RT files for use in oncology.
• GeneralizedWendland implements the fully parameterized generalized Wendland covariance function.
• jacobi evaluates Jacobi theta functions and related functions.
• mvnimpute simultaneously imputes missing and censored values; it uses Rcpp and RcppArmadillo.
• PRECAST offers embedding and clustering with alignment for spatial datasets; it uses Rcpp and RcppArmadillo.
• Sieve adds nonparametric estimation by the method of sieves; it uses Rcpp and RcppArmadillo.
• wdnet implementats network analysis of weighted and directed networks; it uses Rcpp and RcppArmadillo.
• PFIM evaluates or optimizes designs for nonlinear mixed effects models using the Fisher information matrix.
• RGMM robustly estimates parameters of a Gaussian, Student, or Laplace Mixture Model; it uses Rcpp and RcppArmadillo.
• mmcif computes mixed multivariate cumulate incidence functions; it uses Rcpp and RcppArmadillo.
• qgg efficiently samples gaussian linea regression with arbitrary priors; it uses Rcpp, RcppArmadillo, and RcppParallel.
• RcppColors helps with color conversion and color mappings.
• GPCERF provides a non-parametric Bayesian framework based on Gaussian process priors; it uses Rcpp and RcppArmadillo.
• itp offers an 'interpolate, truncate, project' root finder.
• bsnsing builds decision trees with optimal multivariate splits; it uses Rcpp and RcppArmadillo.
• RDSsamplesize adds functionality for sample size estimation and power calculation in Respondent-Driven Sampling.
• StrucDiv quantifies spatial structural diversity in continuous remote sensing data.
• tlars computes the solution path of the Terminating-LARS (T-LARS) algorithm; it uses Rcpp and RcppArmadillo.
• DySS implements a dynamic screening system; it uses Rcpp and RcppArmadillo.
• ganDataModel create a hierarchical, categorical data model for a data source.
• InteRD computes the integrated and robust deconvolution.
• qsplines provides routines to create quaternions and other splines; it uses Rcpp and BH.
• bartcs fits Bayesian Regression Additive Trees (BART) to select relevant confounders.
• fiberLD estimates tree fiber (tracheid) length distributions; it uses Rcpp, RcppArmadillo, and BH.
• lnmCluster perform logistic normal multinomial clustering for microbiome compositional data.
• NNS implements nonlinear nonparametrics statistics using partial moments; it uses Rcpp and RcppParallel.
• TMTI computes joint tests controlling the Familywise Error Rate (FWER).
• BeeGUTS calibrates, validates, and predicts survival adapted for bee species; it uses Rcpp, RcppEigen, and BH.
• calibrationband calibrates of probabilistic classifiers using confidence bands for monotonic functions.
• narray adds subset- and name-aware array utility functions.
• bws interfaces a Bayesian weighted sum model; it uses Rcpp, RcppEigen, and BH.
• SpaceTimeBSS adds blind-source separation for multivariate spatio-temporal data; it uses Rcpp and RcppArmadillo.
• gmwmx estimates functional parameters of linear models with correlated residuals; it uses Rcpp and RcppArmadillo.
• VAJointSurv estimates joint marker and survival outcomes using variational approximations; it uses Rcpp, RcppArmadillo, and RcppEigen.
• fastGLCM implemens 'Gray Level Co-occurence Matrix' texture featires; it uses Rcpp and RcppArmadillo.
• gena implements Genetic Algorithm and Particle Swarm optimization; it uses Rcpp and RcppArmadillo.
• GGIRread reads data from wearable acceleratometers used in sleep and physical activity research; it uses Rcpp and RcppArmadillo.
• copre adds tools for nonparametric martingale posterior sampling; it uses Rcpp, RcppArmadillo, and BH.
• hwep computes Hardy-Weinberg equilibrium in polyploids; it uses Rcpp, RcppEigen, and BH.
• roboBayes implements robust Bayesian online changepoint detection; it uses Rcpp and RcppArmadillo.
• EloSteepness obtains Bayesian posterior distributions of dominance hierarchy steepness; it uses Rcpp, RcppEigen, and BH.
• mHMMbayes implements multilevel (mixed / random effects) hidden Markov models using Bayesian estimation.
• ambit simulates and estimates ambit processes.
• rSpectral adds spectral modularity clustering for networks; it uses Rcpp and RcppArmadillo.
• disbayes estimates incidence and case fatality for a chronic disease; it uses Rcpp, RcppEigen, and BH.
• hlt offers higher-order item response theory functionality.
• TDAvec provides tools for vector summaries of persistence diagrams.
• multinomialLogitMix clusters multinomial count data under the presence of covariates; it uses Rcpp and RcppArmadillo.
• singR implements simultaneous non-Gaussian component analysis; it uses Rcpp and RcppArmadillo.
• truncnormbayes estimates moments for a truncated Normal distribution; it uses Rcpp, RcppEigen, and BH.
• VARSELECTEXPOSURE adds variable selection methods including an exposure variable; it uses Rcpp and RcppArmadillo.
• aorsf fits, interprets and predicts from oblique random survival forests; it uses Rcpp and RcppArmadillo.
• covdepGE applies a covariate-depdendent approach to Gaussian graphical modeling; it uses Rcpp and RcppArmadillo.
• goldfish fits statistical network models for dynamic network data; it uses Rcpp and RcppArmadillo.
• prcbench evaluate tools that calculate precision-recall curves.
• evalR evaluates unverified code by parsing statements into trees.
• netUtils adds miscellaneous functions for network analysis; it uses Rcpp and RcppArmadillo.
• hmcdm fits hidden Markov cognitive diagnosis models for learning; it uses Rcpp and RcppArmadillo.
• iNEXT provides functions to compute and plot rarefaction and extrapolation curces for species diversity.
• qris fits quantile regression models for residual lifetime using an induced smoothing approach; it uses Rcpp and RcppArmadillo.
• afttest offers model diagnostics for accelerated failure time models; it uses Rcpp and RcppArmadillo.
• highs interfaces the 'HIGHS' mixed integer optimization solver; it uses Rcpp and RcppArmadillo.
• BSPBSS offers Bayesian spatial blind source separation; it uses Rcpp and RcppArmadillo.
• bsvars adds Bayesian estimation of structural vector autoregressive models; it uses Rcpp and RcppArmadillo.
• kalmanfilter implements a multivariate Kalman filter for state-space models; it uses Rcpp and RcppArmadillo.
• multiview implements cooperative learning for multi-view analysis; it uses Rcpp and RcppEigen.
• rPBK adds inference and prediction of generic physiologically-based kinetic models; it uses Rcpp, RcppEigen, and BH.
• paws.common provides low-level access to Amazon Web Services including S3.
• eyelinkReader imports gaze data for the EyeLink eye trackcr by SR Research.
• BHMSMAfMRI performs Bayesian hierarchical multi-subject multiscale analysis of fMRI data; it uses Rcpp and RcppArmadillo.
• elections.dtree adds ranked voting election audits with Dirichlet-trees prior distributions.
• GWASinlps offers non-local prior based iterative variable selection for GWAS; it uses Rcpp and RcppArmadillo.
• historicalborrowlong computes longitudinal Bayesian historical borrowing models.
• kimfilter implements the multivariate Kim filter for state probability inference; it uses Rcpp and RcppArmadillo.
• vglmer estimates hierarchical models using mean-field variational Bayes; it uses Rcpp and RcppEigen.
• EthSEQ offers reliable and rapid ethnicity annotation from whole exome and targeted sequencing data.
• numbat runs haplotype-aware CNV analysis from scRNA-Seq; it uses Rcpp, RcppArmadillo, and RcppParallel.
• Ease simulates explicit population genetics models.
• SparseChol adds sparse Cholesky LDL decomposition of symmetric matrices.
• unitquantreg fits parametric quantile regression for bounded data.
• alqrfe adds quantile regression with fixed effects solves longitudinal data; it uses Rcpp and RcppArmadillo.
• RoBTT implements a Bayesian model-averaged t-tests; it uses Rcpp, RcppEigen, and BH.
• saccadr extract saccades via an ensemble of methods approach.
• SiPhyNetwork simulates reticulate evolution under a birth-death-hybridization process.
• RPhosFate implements a soil and chemical substance emission and transport model; it uses Rcpp and RcppArmadillo.
• binaryMM fits flexible marginalized models for binary correlated outcomes.
• rlibkriging interfaces the 'libKriging' library to process Kriging models; it uses Rcpp and RcppArmadillo.
• glmmrBase specifies generalized linear mixed models using R6 classes; it uses Rcpp and RcppArmadillo.
• pompp estimates presence-only for marked point processes; it uses Rcpp and RcppEigen.
• squat computes statistics for quaternion data; it uses Rcpp, RcppArmadillo, and RcppEigen.
• watson fits and simulates mixtures of Watson distributions; it uses Rcpp and RcppArmadillo.
• rxode2ll provides log-likelihoods with gradients for 'rxode2'; it uses Rcpp, RcppEigen, and BH.
• openxlsx2 reads, writes and edits 'xslx' files.
• mclm reads, inspects and processes corpus files for quantitative corpus linguistics.
• manifold implements operations for Riemannian manifolds; it uses Rcpp and RcppArmadillo.
• MultiscaleDTM calculates multi-scale geomorphometric terrain attributes from digital terrain models; it uses Rcpp and RcppArmadillo.
• GLCMTextures calculates grey level co-occurrence matrix (GLCM) based texture measures; it uses Rcpp and RcppArmadillo.
• rxode2parse provides the parsing needed for 'rxode2'; it uses Rcpp, RcppEigen, and BH.
• deforestable classifies RGB images into 'forest or non-forest'; it uses Rcpp and RcppArmadillo.
• EcoEnsemble offers a general framework for combining ecosystem models; it uses Rcpp, RcppEigen, and BH.
• missoNet fits with missingness in multi-task regression with network estimation; it uses Rcpp and RcppArmadillo.
• bakR analyzes and compares nucleotide recoding RNA sequencing datasets; it uses Rcpp, RcppEigen, and BH.
• rxode2random provides (parallel) RNGs 'rxode2'; it uses Rcpp, RcppArmadillo, and BH.
• SVDNF offers discrete nonlinear filtering for stochastic volatility models.
• dfms efficiently fits dynamic factor models using EM or 2S also supporting missing data; it uses Rcpp and RcppArmadillo.
• R2sample supports two sample problems using permutation.
• SoftBart implements the SoftBart model with an optional sparsity-inducing prior; it uses Rcpp and RcppArmadillo.
• fect estimates causal effects with panel data using counterfactual methods; it uses Rcpp and RcppArmadillo.
• LDAandLDAS computes Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS).
• rxode2et adds event table functions for 'rxode2'.
• gridOT approximates optimal transport between two-dimensional grids; it uses Rcpp and RcppArmadillo.
• pqrfe fits penalized quantile regression with fixed effects; it uses Rcpp and RcppArmadillo.
• NestMRMC calculates between-cases AUC estimates in nested data problems.
• datefixR standardizes dates in different formats or with missing data.
• fastWavelets compute maximal overlap discrete wavelet transforms.
• mtdesign implements Mander and Thompson methods for two-stage designs; it uses Rcpp and BH.
• babelmixr2 uses 'nlmixr' to interact with open source and commerical software; it uses Rcpp, RcppArmadillo, and RcppEigen.
• FBCRM offers phase I optimal dose assignment using FBCRM and MFBCRM methods; it uses Rcpp and RcppArmadillo.
• mrfse implements three algorithms for estimating Markov random field structure.
• pcaone adds randomized singular value decomposition methods; it uses Rcpp and RcppEigen.
• fdaPDE implements regression with partial differntial regularization using finite element methods; it uses Rcpp and RcppEigen.
• jmatrix reads and writes to and from disk with any type of binary matrix format.
• adaptIVPT uses a mixed scaling approach for bioequivalence design for in-vitro tests; it uses Rcpp and RcppArmadillo.
• ggbrain creates images of volumetric brain data in NIfTI format using 'ggplot' syntax; it uses Rcpp and RcppArmadillo.
• iotarelr adds iota inter code reliability for content analysis.
• mas offers membership association studies for GWAS; it uses Rcpp and RcppEigen.
• nett implements network analysis and community detection; it uses Rcpp and RcppArmadillo.
• rswipl interfaces 'SWI Prolog' to provide 'Prolog' for use in other packages.
• NPCirc adds nonparametric smoothing methods for density and regression estimation involving circular data; it uses Rcpp and RcppArmadillo.
• geosphere computes spherical trigonometry for geographic applications.
• robusTest implements corrected two-sample tests where rejection under the null is asymptotically equal to the test level.
• vol2birdR generates vertical profiles of birds and other biological signals in weather radar data; it uses Rcpp and RcppGSL.
• ClusROC adds ROC analysis in three-class classification problems for clustered data; it uses Rcpp and RcppArmadillo.
• blindedrecalc computes key characteristics and plots for blinded sample size recalculation.
• scistreer adds fast maximum-likelihood phylogeny inference from noisy single-cell data; it uses Rcpp, RcppArmadillo, and RcppParallel.
• vMF samples fom the von Mises-Fisher distribution; it uses Rcpp, RcppArmadillo, and BH.
• mapfit estimates phase-type distribution (PH) and Markovian arrival process (MAP) from empirical data.
• parallelpam adds parallel partitioning-around-medoids (PAM) for big sets of data.
• GAGAs fits via a global adaptive generative adjustment algorithm for glm; it uses Rcpp and RcppEigen.
• scellpam partitions around medoids to single cell data with high number of cells.
• wav reads and writes waveform (WAV) audio files.
• brif builds decision trees and random forests for classification and regression.
• mccca computes several multi-category classification accurations evaluation measures.
• HTT offers a novel decision tree algorithm in the hypothesis testing framework.
• netdiffuseR analyses, visualises and simulates diffusion and contagion on networkds; it uses Rcpp and RcppArmadillo.
• endogeneity fits recursive two-stage models to address endogeneity; it uses Rcpp and RcppArmadillo.
• finalsize calculate the final size of an epidemic; it uses Rcpp and RcppEigen.
• mvMAPIT computes a multivariate genome wide marginal epistasis test; it uses Rcpp and RcppArmadillo.
• secrdesign implements sampling design for spatially explicit capture-recapture; it uses Rcpp, RcppArmadillo, and BH.
• gmvjoint fits joint models of survival and multivariate longitudinal data; it uses Rcpp and RcppArmadillo.
• oncomsm implements Bayesian multi-state models for early oncology; it uses Rcpp, RcppEigen, and BH.
• reservr fits distributions and neural networks to censored and truncated data; it uses Rcpp, RcppArmadillo, and BH.
• rSRD computes the Sum of Ranking Differences test.
• qspray symbolically calculates and evaluates multivariate polynomials with rational coefficients; it uses Rcpp, RcppEigen, and BH.
• bamm estimates the area of distribution of a species using biotic, abiotic and movement factors; it uses Rcpp and RcppArmadillo.
• mmrm fits mixed models for repeated measures; it uses Rcpp and RcppEigen.
• SIT computes 'sliced independence test' (sit) coefficient between two vectors; it uses Rcpp and RcppArmadillo.
• coreCollection creates custom-sized core collection based on distance matrix and different methods.
• PPtreeregViz implements projection pursuit regression tree visualization; it uses Rcpp and RcppArmadillo.
• ridgetorus computes PCA in the torus via density ridge estimation; it uses Rcpp and RcppArmadillo.
• CARME offers CAR-MM modeling via 'stan'; it uses Rcpp, RcppEigenm and BH.
• enerscape computes energy landscapes using a digital elevation model raster and body mass of animals.
• em implements a generic 'expectations-maximization' within a maximum likelihood framework; it uses Rcpp and RcppArmadillo.
• BCClong implements Bayesian consensus clustering for multiple longitudinal features; it uses Rcpp and RcppArmadillo.
• AllelicSeries offers gene-level rare variant association tests targeting allelic series; it uses Rcpp and RcppArmadillo.
• gravmagsubs computes gravitational and magnetic attraction of 3-d verticular rectangular prisms.
• ldt offers methods and tools to 'let data talk'; it uses Rcpp and BH.
• glmmrOptim fits approximate optimal experimental designs using generalised linear mixed models; it uses Rcpp and RcppEigen.
• multilink implements multifile record linkage and duplicate detection; it uses Rcpp and RcppArmadillo.
• hbal offers hierarchically regularized entropy balancing; it uses Rcpp and RcppEigen.
• pomdp adds infrastructure for partially observable Markov decision process models.
• StochBlock implements stochastic blockmodeling of one-mode and linked networks; it uses Rcpp and RcppArmadillo.
• BayesDLMfMRI analyses task-based functional magnetic resonance data; it uses Rcpp and RcppArmadillo.
• SK4FGA implements the Scott-Knott method for forensic glass analysis.
• templateICAr estimates brain networks and connectivity with ICA and empirical priors; it uses Rcpp and RcppEigen.
• jack implements symbolic calculation of Jack, zonal, amd Schur polynomials.
• RationalMatrix implements exact matrix algebra for rational matrices; it uses Rcpp, RcppEigen, and BH.
• baygel implements a Bayesian graphical ridge data-augmented block Gibbs sampler; it uses Rcpp and RcppArmadillo.
• RcppArray interoperates with C++11 (or later) `std::array` types.
• echoice2 implements choice models from economic theory; it uses Rcpp and RcppArmadillo.
• GFDmcv performs general hypothesis tesing for multivariate coefficients of variation.
• mateable assesses mating potential in space and time.
• PROsetta links patient-reported outcome measures according to PROsetta Stone methodologyOA; it uses Rcpp and RcppArmadillo.
• blockCV creates spatially or environmentally separated folds for cross-validation; it uses Rcpp and RcppArmadillo.
• synMicrodata fits a non-parametric Bayesian HCMM model to generate synthetic data; it uses Rcpp and RcppArmadillo.
• ade4 analyses multivariate environmental data; it uses Rcpp and RcppArmadillo.
• datazoom.amazonia download and treat data regarding the Brazilian Amazon region from a variety of official sources.
• expertsurv incorporate expert opinion with parametric survival models; it uses Rcpp, RcppEigen, and BH.
• rcontroll interfaces with the individual-based forest growth simulator 'TROLL'; it uses Rcpp and RcppGSL.
• GFM fits a generalized factor model implemented for ultra-high dimensional data with mixed-type variables; it uses Rcpp and RcppArmadillo.
• MAZE offers mediation analysis for zero-inflated mediators containing true zeros and false zeros.
• tfevents provides a convenient way to log scalars, images, audio, and histograms in the 'tfevent' record file format.
• aniSNA performs statistical network analysis of animal social networks.
• pemultinom fits L1-penalized multinomial regression supporting statistical inference.
• netcox fits and cross-validates the overlapping group Lasso for Cox models with time-dependent covariates.
• DTRKernSmooth estimates optimal treatment regimes among all linear regimes; it uses Rcpp, RcppArmadillo, and RcppEigen.
• statgenQTLxT offers fast multi-trait and multi-trail genome wide association studies; it uses Rcpp and RcppArmadillo.
• RDM quantifies dependence using the 'Rearranged Dependence Measure'.
• tame implements agglomerative hierarchical clustering with a bespoke distance measure.
• RcppFastAD offers an interface to the FastAS automatic differentiation library.
• tetrascatt compute the acoustic backward scattering from tetrahedrons; it uses Rcpp and RcppArmadillo.
• LorenzRegression adds inference for (penalized) Lorenz regressions; it uses Rcpp and RcppArmadillo.
• ODRF offers oblique decision random forest for classification and regression; it uses Rcpp and RcppArmadillo.
• rvMF provides fast generation of von Mises-Fisher distributed pseudo-random vectors.
• aihuman experimentally evaluates algorithm-assisted human decision-making; it uses Rcpp, RcppArmadillo, and RcppEigen.
• satdad offers tools to analyze tail dependence in any sample or in particular theoretical models.; it uses Rcpp, RcppArmadillo, and BH.
• ecr adds a framework for building evolutionary algorithms for single and multi-objective; it uses Rcpp and RcppArmadillo.
• FuncDiv uses contributional diversity metrics to link taxonomic + functional microbiome data; it uses Rcpp, RcppArmadillo, and RcppParallel.
• TapeS compute tree taper curves based on the 'TapeR' model; it uses Rcpp and RcppArmadillo.
• ABM implements agent-based model simulations.
• marginaleffects computes and plot predictions, slopes, marginal means, and comparisons; it uses Rcpp and RcppEigen.
• coconots fits, validates, and forecasts convolution-closed time series models for low counts.
• sparvaride implements variance identification in sparse factor analysis; it uses Rcpp and RcppArmadillo.
• banditpam offers almost linear time k-medoids clustering; it uses Rcpp and RcppArmadillo.
• greencrab.toolkit models and interprets green crab monitoring assessments; it uses Rcpp, RcppEigen, and BH.
• multilevLCA estimates and plots single- and multi-level latent class models; it uses Rcpp and RcppArmadillo.
• hbamr performs hierarchical Bayesian Aldrich-McKelvey scaling; it uses Rcpp, RcppEigen, and BH.
• BayesianPlatformDesignTimeTrend simulates and analyses Bayesian platform trials; it uses Rcpp, RcppEigen, and BH.
• Carlson computes Carlson elliptic integrals and incomplete elliptic intergrals.
• qfratio evaluates moments of ratios and products of quadratic forms; it uses Rcpp and RcppEigen.
• gsDesign2 implements group sequential design with non-constant effect.
• jfa provides statistical methods for auditing; it uses Rcpp, RcppEigen, and BH.
• dcm2 computes the M2 model fit statistics for diagnostic classification models.
• htetree offers causal inference with tree-based machine learning algorithms; it uses Rcpp and RcppArmadillo.
• sox adds structured learning in time-dependent Cox models.
• causaloptim helps to specify causal graphs and compute bounds on causal effects.
• sparseDFM estimates dynamic factor models with sparse loadings; it uses Rcpp and RcppArmadillo.
• frailtyMMpen fits penalized and non-penalized Minorize-Maximization (MM) frailty models; it uses Rcpp and RcppGSL.
• Rgof can run many goodness-of-fit tests in parallel.
• simmr fits stable isotope mixing models (SIMMs); it uses Rcpp and RcppArmadillo.
• mmconvert converts mouse genome positions between the build 39 map and the genetic map of Cox et al.
• rrandvec generates random vectors whose components sum to one.
• measr implements Bayesian psychometric measurement; it uses Rcpp, RcppEigen, and BH.
• interpolation interpolates bivariate functions; it uses Rcpp and BH.
• lessSEM offers non-smooth regularization for structural equation models; it uses Rcpp, RcppArmadillo, and RcppParallel.
• pureseqtmr predicts transmembrane protein topologies using 'PureseqTM' from R.
• countSTAR models count data for Bayesian and classical inference; it uses Rcpp and RcppArmadillo.
• disclapmix2 computes mixtures of discrete Laplace distributions using numerical optimisation.
• gibasa offers an alternative wrapper of 'MeCab' to segment Chinese, Japanese, and Korean text; it uses Rcpp and RcppParallel.
• hclust1d implements hierarchical clustering of univariate (1d) data.
• QuickJSR interfaces (and supplies) the 'QuickJS' Javascript engine.
• bioregion compares bioregionalisation methods based on clustering and network algorithms.
• CCMMR minimizes the convex clustering loss function; it uses Rcpp and RcppEigen.
• asmbPLS predicts and classified patient phenotypes with multi-omics data; it uses Rcpp and RcppArmadillo.
• gKRLS provides generalized kernel regularized least squares; it uses Rcpp and RcppEigen.
• intmap provides ordered containers with integer keys an 'R6' class; it uses Rcpp and BH.
• bgms adds Bayesian variable selection for networks of binary and/or ordinal variables.
• rivnet extracts and analyses rivers from elevation data.
• rpm models revealed preference maychings; it uses Rcpp and RcppArmadillo.
• markovmix fits mixtures of Markov chains of higher orders from multiple sequences.
• MHD computes metric halfspace depth for object data.
• rcccd fits class cover catch digraph classification models; it uses Rcpp and RcppArmadillo.
• OCNet generates and analyzes Optimal Channel Networks (OCNs) which are oriented spanning trees wuth real river network features.
• stockR identifies stocks in genetic data using a mixture model for clustering.
• mixedBayes fits Bayesian longitudinal regularized quantile mixed models; it uses Rcpp and RcppArmadillo.
• marble offers robust marginal Bayesian variable selection for gene-environment interactions; it uses Rcpp and RcppArmadillo.
• MDEI impements the method of direct estimation and inference; it uses Rcpp and RcppArmadillo.
• secsse infers state-dependent diversification simulataneously across states of one or more traits; it uses Rcpp, RcppParallel and BH.
• switchSelection adds endogeneous switching and sample-selection regression models; it uses Rcpp and RcppArmadillo.
• flps simulates and analyses fully-latent principal stratification with measurement models.
• survstan fits survival regression models via 'stan'; it uses Rcpp, RcppEigen, and BH.
• robStepSplitReg performs robust stepwise split regularized regression; it uses Rcpp and RcppArmadillo.
• FLORAL fits log-ratio lasso regressions for compositional data; it uses Rcpp and RcppArmadillo.
• RTSA implements 'trial sequential analysis' for error contraol in sequential meta-analyses.
• intrinsicFRP efficiently computes (adaptive) initrinsic factor risk premia; it uses Rcpp and RcppArmadillo.
• baldur fits Bayesian hierarchical models for label-free proteomics; it uses Rcpp, RcppEigen, RcppParallel, and BH.
• navigation analyzes the impact of sensor error modelling on navigation performance; it uses Rcpp and RcppArmadillo.
• Bernadette implements Bayesian inference and model selection for stochastic epidemics; it uses Rcpp, RcppEigen, and BH.
• emBayes provides robust Bayesiab variable selection via Expectation-Maximization; it uses Rcpp and RcppArmadillo.
• sgs adds sparse-group SLOPE, an adaptive bi-level selection with FDR-control; it uses Rcpp and RcppArmadillo.
• Bayenet fits a Bayesian quantile elastic net for genetic studies; it uses Rcpp and RcppArmadillo.
• gdalraster binds to the 'Geospatial Data Abstraction Library' Raster API.
• JUMP aids replicability analysis of high-throughput experiments; it uses Rcpp and RcppArmadillo.
• pgenlibr wraps the PLINK 2 core library to read .pgen files.
• spfa estimates, scores and plots functions for a semi-parametric factor model; it uses Rcpp and RcppArmadillo.
• nonmem2rx; it uses Rcpp and RcppArmadillo.
• matrixset creates and manipulates matrix ensembles (where matrices share common properties).
• RITCH lets R parse ITCH files; it uses Rcpp and RcppArmadillo.
• ScatterDensity combines density estimation and visualization of 2-d scatter plot; it uses Rcpp and RcppArmadillo.
• MetricGraph creates and amnipulates metrix graphs such as street or river networks; it uses Rcpp and RcppEigen.
• sphereTessellation implements Delaunay and Voronoi tesselation on the sphere; it uses Rcpp, RcppEigen, and BH.
• htsr manages hydrological and meteorological time-series in a 'SQLite; data base.
• RcppJagger interfaces the morphological analyzer 'jagger' for tokenization, POS tagging and lemmatization.
• BayesfMRI offers spatial bayesian methods for task functional MRI studies; it uses Rcpp and RcppEigen.
• ProFAST implements probabilistic factor analysis for spatially-aware dimension reductions; it uses Rcpp and RcppArmadillo.
• RMSS generates ensembles of robust, sparse and diverse models via robust multi-model subset selection; it uses Rcpp and RcppArmadillo.
• mop computes multiple versions of the Mobility Oriented Parity metric; it uses Rcpp and RcppArmadillo.
• CptNonPar implements a nonparametric moving sum procedure for detection of changes in joint characteristic functions.
• hdflex computes high-dimensional aggregate density forecasts; it uses Rcpp and RcppArmadillo.
• MSCquartets anakysis gene tree quartets under the multi-species coalescent.
• msentropy adds functionality for spectral entropy for mass spectometry data.
• STAREG offers an empirical Bayes approach for replicability analysis across two studies; it uses Rcpp and RcppArmadillo.
• tdata provides tools for managing time-series data and frequency conversion.
• ebTobit implements empirical Bayesian Tobit matrix estimation; it uses Rcpp, RcppArmadillo, and RcppParallel.
• JMH jointly models heterogeneous repeated measures and survival data; it uses Rcpp and RcppEigen.
• OSFD generates design in the input space sequentially filling output space of a black-box function; it uses Rcpp and RcppArmadillo.
• remaCor adds random-effect meta analysis for correlated test statistics; it uses Rcpp and RcppArmadillo.
• bennu fits Bayesian modesl for total naloxone kit numbers; it uses Rcpp, RcppEigen, and BH.
• maq implements multi-armed Qini to evaluate costly and mutually exclusive treatments.
• ReAD offers powerful replicability analysis of genome-wide association studies; it uses Rcpp and RcppArmadillo.
• rflashtext implements the FlashText algorithm for finding and replacing words in one pass.
• MendelianRandomization encodes methods for Mendelian randomization for summarised data; it uses Rcpp and RcppArmadillo.
• hystar firs the hystereric threshold autoregressive model.
• bbmix models RNA-seq data using mixtures of three beta-binomial distributions; it uses Rcpp, RcppEigen, and BH.
• SNSeg implements self-normalizing change-point detection in univariate and multivariate timeseries.
• fastLogisticRegressionWrap provides very fast logistic regression with inferences; it uses Rcpp and RcppEigen.
• jrSiCKLSNMF performs regularized single-cell matrix factorization; it uses Rcpp and RcppArmadillo.
• MissCP implements change-point detection with missing values; it uses Rcpp and RcppArmadillo.
• eummd computes efficient univariate maximum mean discrepance.
• mixvlmc estimates variable length Markov chain models.
• twdtw implements time-weighted dynamic warping for time-series similarity.
• pliman adds tools for single and batch plant image analysis; it uses Rcpp and RcppArmadillo.
• APackOfTheClones visualizes T-cell clonal expansion via circle-packing.
• MCARtest implements optimal nonparametric testing of missing completely at random.
• frab offers an alternative interpretation of named vectors.
• BET nonparametrically detects nonuniformiity and dependence with binary expansion testion (BET).
• pg implements a Polya Gamma Distribution sampler; it uses Rcpp and RcppArmadillo.
• ranktreeEnsemble fits ensemble methods of rank-based trees with extracted decision rules.
• boodist makes some distributions provided by Boost available as R6 classes; it uses Rcpp, RcppEigen, and BH.
• invgamstochvol computes the likelihood of an inverse gamma stochastic volatility model; it uses Rcpp and RcppArmadillo.
• mxsem specifies OpenMx models with a lavaan-style syntax.
• RTMB interfaces TMB so that models can be written in R; it uses Rcpp and RcppEigen.
• slcm offers Bayesian estimation of sparse latent class modesl for binary data; it uses Rcpp and RcppArmadillo.
• libstable4u adds tools for fast and accurate evaluation of skew stable distributions; it uses Rcpp and RcppGSL.
• piqp interfaces a proximal interior point quadratic programming solver; it uses Rcpp and RcppEigen.
• lit implements latent interaction testing for genome-wide studies; it uses Rcpp, RcppArmadillo, and RcppEigen.
• Apollonius computes 2-d Apollonius diagrams of given 2-d points; it uses Rcpp, RcppEigen, and BH.
• aifeducation provides a unified interface for 'keras' and 'tensorflow', it uses Rcpp and RcppArmadillo.
• stpphawkes fits marked Hawkes process with missing data; it uses Rcpp, RcppArmadillo, and RcppGSL.
• psp implements an n-dimensional parameter space partitioning algorithm for evaluating global model behaviour; it uses Rcpp and RcppArmadillo.
• heterogen adds spatial functions for heterogeneity and climate variability; it uses Rcpp, RcppArmadillo, and RcppEigen.
• fmesher generates triangle meshes and related geometry tools.
• Rmodule supports automated Markov chain Monte Carlo for arbitrarily structured correlation matrices; it uses Rcpp and RcppArmadillo.
• PartialNetwork estimates peer effects using partial network data; it uses Rcpp, RcppArmadillo, and RcppEigen.
• countsplit splits a count matrix into independent folds for training/test or cross-validation; it uses Rcpp and RcppArmadillo.
• phylter detects and remove outliers in phylogenomics datasets; it uses Rcpp, RcppArmadillo, and RcppEigen.
• lamle implements maximum likelihood estimation of latent variable models; it uses Rcpp and RcppArmadillo.
• segregation computes entropy-based segregation indices; it uses Rcpp and RcppArmadillo.
• TrialEmulation does causal analysis of observational time-to-event data.
• stringmagic performs complex string operations compactly and efficiently.
• Rlibkdv offers a versatile kernel density visualization library for geospatial analytics.
• ARCensReg fits univariate censored linear regression model with autoregressive errors; it uses Rcpp and RcppArmadillo.
• keyperm implements efficient permutation tests for keyword analysis in corpus linguistics.
• seqtrie adds Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances.
• HDJM fits penalized high-dimensional joint models; it uses ses Rcpp, RcppArmadillo, and RcppEnsmallen.
• VBJM implements variational inference for joint modeling; it uses Rcpp, RcppArmadillo, and RcppEnsmallen.
• FLOPART computes optimal segmentation model with Poisson loss, up-down constraints, and label constraints.
• Racmacs making antigenic maps from immunological assay data; it uses Rcpp, RcppArmadillo, and RcppEnsmallen.
• RcppInt64 helps to pass integer64 values between R and C++.
• SurvivalClusteringTree implements clustering using survival tree and forest algorithms; it uses Rcpp and RcppArmadillo.
• zlib provides compression and decompression functions for gzip, zlib and deflate formats.
• dropout offers robust tools to identify and manage incomplete responses in survey datasets.
• eDITH models transport of environmental DNA in river networks.
• fastcpd implements fast changepoint detection via sequential gradient descent; it uses Rcpp and RcppArmadillo.
• NAIR provides tools for network analysis of immune repertoire; it uses Rcpp and RcppArmadillo.
• ocf offers a nonparametric estimator for ordered non-numeric outcome; it uses Rcpp and RcppEigen.
• pqrBayes fits penalized Bayesian quantile regression models; it uses Rcpp and RcppArmadillo.
• fdaSP offers sparse functional data analysis methods; it uses Rcpp and RcppArmadillo.
• remotePARTS runs spatiotemporal autoregressive analyses for large data sets; it uses Rcpp and RcppEigen.
• kmBlock provides k-means like blockmodeling of one-mode and linked networks; it uses Rcpp and RcppArmadillo.
• PEPBVS does Bayesian variable selection using power-expected-posterior priors; it uses Rcpp, RcppArmadillo, and RcppGSL.
• Euclimatch implements the Euclidean 'Climatch' algorithm for climate matching.
• evinf does inferences with extreme value inflated count data; it uses Rcpp and RcppArmadillo.
• miniPCH computes survival distributions with piece-wise constand hazards.
• cloneRate estimates growth rates from phylogenic trees; it uses Rcpp, RcppEigen, and BH.
• ICSClust implements tandem clustering with invariant coordinate selection; it uses Rcpp and RcppArmadillo.
• adaR offers a fast 'WHATWG' compliant URL parser.
• aftgee estimates accelerated failure time models with generalized estimating equations; it uses Rcpp and RcppArmadillo.
• treeshap computes SHAP values for tree-based models using the 'TreeSHAP' algorithm.
• psbcSpeedUp runs penalized semiparametric Bayesian survival models; it uses Rcpp and RcppArmadillo.
• clubpro implements classification using binary procrustes rotation; it uses Rcpp and RcppArmadillo.
• UniExactFunTest adds a uniform exact functional test for continency tables.
• galamm estimates generalized additive latent and mixed models using maximum marginal likelihood; it uses Rcpp and RcppEigen.
• SMR computes the studentized midrange distribution (pdf, cdf, quantile, random numbers).
• SANple fits shared atoms nested models via Markov Chains Monte Carlo; it uses Rcpp and RcppArmadillo.
• SANvi fits shared atoms nested models via Variational Bayes; it uses Rcpp and RcppArmadillo.
• inferCSN infers cell-specific gene regulatory networks; it uses Rcpp and RcppArmadillo.
• lingdist adds fast linguistic distance and alignment computations.
• surtvep fits Cox non-proportional hazards model with time-varying coefficients; it uses Rcpp and RcppArmadillo.
• deform fits nonstationary Gaussian process models by spatial deformation; it uses Rcpp and RcppArmadillo.
• drugDemand performs drug demand forecasting.
• oeli collects seveal general utility functions; it uses Rcpp and RcppArmadillo.
• spam adds functions for sparse matrix algebra.
• bayesWatch offers Bayeian change-point detection for process monitoring with fault detection; it uses Rcpp, RcppArmadillo, and RcppEigen.
• cophescan runs a Bayesian method for Phonome-wide assocations studies (PheWAS); it uses Rcpp and RcppArmadillo.
• hahmmr implements a haplotype-aware hidden Mmarkov model for RNA; it uses Rcpp and RcppArmadillo.
• DMQ estimates, predicts, and simulates using the Dynamic Multiple Quantile model; it uses Rcpp and RcppArmadillo.
• probe implements sparse high-dimensional regression with partitioned empirical Bayes Ecm (PROBE); it uses Rcpp and RcppArmadillo.
• Rnanoflann offers extremely fast nearest neighbor search via 'nanoflann'; it uses Rcpp and RcppArmadillo.
• simRestore simulates the effects of management policies on restoration efforts.
• bvhar fits Bayesian vector heterpgenous autoregressive models; it uses Rcpp and RcppEigen.
• interpolators implements several interpolation methods; it uses Rcpp and BH.
• remify processes and transforms relational event history data; it uses Rcpp and RcppArmadillo.
• GWEX fits multi-site stochastic models for daily precipitation and temperature; it uses Rcpp and RcppArmadillo.
• deseats adds data-driven locally weighted regression for trend and seasonality in time series; it uses Rcpp and RcppArmadillo.
• mlrv adds plug-in and difference-based long-run covariance matrix estimation for time series regression; it uses Rcpp and RcppArmadillo.
• BayesGmed performa Bayesia causal mediation analysis using 'stan'.
• longevity analsys excess lifetimes with collection of parametric and non-parametric methods; it uses Rcpp and RcppArmadillo.
• mase adds a set of model-assisted survey estimators; it uses Rcpp and RcppEigen.
• PANPRSnext builds polygenic risk prediction models based on summary statistics of GWAs; it uses Rcpp and RcppArmadillo.
• remstats computes statistics for relational event history data; it uses Rcpp, RcppArmadillo, and RcppProgress.
• SGDinference provides estimation and inference methods for large-scale mean and quantile regression; it uses Rcpp and RcppArmadillo.
• simStateSpace simulates data from state space models; it uses Rcpp and RcppArmadillo.
• BayesGrowth estimate fish length-at-age models using MCMC analysis with 'rstan' models; it uses Rcpp, RcppEigen, and BH.
• dartR.sim simulates SNP data uing genlight objects.
• FlexVarJM estimate joint models with subject-specific variance; it uses Rcpp and RcppArmadillo.
• Mhorseshoe provides an approximate algorithm for the horseshoe estimator used in Bayesian linear models.
• semidist measures dependence between categorical and continuous variables; it uses Rcpp and RcppArmadillo.
• metaRange adds a framework for mechanistic and metabolic constrained species distribution models; it uses Rcpp and RcppArmadillo.
• multipleDL addressing detection limits by cumulative probability models (CPMs); it uses Rcpp, RcppEigen, and BH.
• ggdist visualizes distributions and uncertainty in either a frequentist or Bayesian manner.
• MJMbamlss estimates multivariate joint longitudinal and time-to-event models with 'bamlss'; it uses Rcpp and RcppEigen.
• nuggets implements an extensible data pattern searching framework.
• rnndescent provides a nearest neighbor descent method for approximate nearest neighbors.
• spatialising performs simulations of binary spatial raster data using the Ising model.
• HDMAADMM implements ADMM for high-dimension mediation models; it uses Rcpp and RcppEigen.
• enmpa performs ecological niche modeling using presence-absence data.
• MarZIC estimates and tests marginal mediation effects for zero-inflated compositional mediators; it uses Rcpp and RcppArmadillo.
• regmhmm fits hidden Markov models with regularization to longitudinal data; it uses Rcpp and RcppArmadillo.
• pmartR offers quality control processing and statistical analysis of mass spectrometry (MS) omics data; it uses Rcpp, RcppArmadillo, and BH.
• TDApplied offers machine learning and inference for topological data analysis.
• BTtest estimates the number of factors in large nonstationary datasets; it uses Rcpp and RcppArmadillo.
• simtrial provides some basic routines for simulating a clinical trial.
• CytoSimplex provides simplex visualizations of cell fate similarity in single-cell data; it uses Rcpp and RcppArmadillo.
• tdROC fits nonparametric estimation of time-dependent ROC, Brier score, and survival difference with or with competing risks.
• WeightedTreemaps generates and plots Voronoi or sunburst treemaps from hierarchical data; it uses Rcpp and BH.
• Glarmadillo solves the graphical lasso problem with Armadillo; it uses Rcpp and RcppArmadillo.
• vcfppR rapidly manipulates Variant Call Format (VCF) files via bindings to htslib.
• extBatchMarking runs batch-marking analysis for marked and unmarked individuals; it uses Rcpp and RcppArmadillo.
• L1centrality analyses graph/network data based on L1 centrality.
• BPrinStratTTE estimates causal effects in principal strata defined by antidrug antibodies; it uses Rcpp, RcppEigen and BH.
• remstimate adds an optimization framework for tie-oriented and actor-oriented relational event models; it uses Rcpp and RcppArmadillo.
• FBMS implements flexible Bayesian model selection and model averaging.
• localboot adds local bootstrap methods for various networks; it uses Rcpp and RcppEigen.
• giniVarCI estimates Gini index and computes variances and confidence intervals for finite and infinite populations.
• timeDF subsets and flags data frames with times by the use of periods.
• Apoderoides prioritizes and deleted errorneous taxa in a large phylogenetic tree.
• arcgisutils add developer-oriented utility functions for working with ArcGIS location services.
• BayesPPDSurv offers Bayesian power prior design calculations for survival data; it uses Rcpp and RcppArmadillo.
• tinycodet contains functions to help in coding etiquette.
• rgm implements advanced inference with random graphical models.
• treestatsadds a collection of phylogenetic tree statistics written to maximize computation speed.
• bayesianVars adds efficient MCMC estimation for fully Bayesian VAR models; it uses Rcpp and RcppArmadillo.
• ktaucenters implements clustering similar to K-Means but resistant to outliers, and efficient.
• robustmatrix robustly estimates covariance matrices using MMCD; it uses Rcpp and RcppArmadillo.
• QuantRegGLasso fits adaptively weighted group Lasso for semiparametric quantile regression models; it uses Rcpp and RcppArmadillo.
• TCHazaRds generates modelled parametric Tropical Cyclone (TC) spatial hazard fields and time series output from TC tracks.
• SpaTopic integrate cell type and spatial information to identify the complex spatial tissue architecture; it uses Rcpp and RcppArmadillo.
• speedytax rapidly imports classifier results into 'phyloseq'.
• distops provides the usual operations for distance matrices in a parallelised implementation.
• ionet computes network analysis for input-output tables.
• WpProj performs Wasserstein projections for predictive distributions of any linear model; it uses Rcpp and RcppEigen.
• nn2poly builds polynomial model performing almost equivalently to given (densely connected) neural network; it uses Rcpp and RcppArmadillo.
• indexthis quickly indexes any type of vector or combination of those as a building block for other algorithms.
• VeccTMVN computes multivariate normal probabilities using the Vechia approximation; it uses Rcpp and RcppArmadillo.
• fastglmpca implements fast, scalable optimization algorithms for fitting generalized PCA models; it uses Rcpp and RcppArmadillo.
• SKFCPD offers fast online changepoint detection for temporally correlated data; it uses Rcpp and RcppEigen.
• SurrogateBMA flexibly evaluates surrogate markers with Bayesian model averaging; it uses Rcpp and RcppEigen.
• TFRE adds a tuning-free robust and efficient approach to high-dimensional regression; it uses Rcpp and RcppEigen.
• elgbd computes the empirical likelihood for general block designs; it uses Rcpp and RcppEigen.
• viewscape provides functions for viewscape analysis and viewscape metrics.
• fastliu efficiently computes Liu regression coefficient paths and related statistics; it uses Rcpp and RcppArmadillo.
• md4r wraps the 'MD4C' markdown parser covering commonmark, Github-flavoured markdown and latex equations.
• cramer computes the multivariate nonparametric Cramer-test for the two-sample-problem.
• pgKDEsphere fits parametrically-guided kernel density estimates for spherical data; it uses Rcpp and RcppArmadillo.
• psBayesborrow adds Bayesian Information borrowing with propensity score matching; it uses Rcpp, RcppEigen and BH.
• iNEXT.3D interpolates and extrapolates for three dimensions of biodiversity.
• LTFHPlus implements LT-FH++ extending the liability threshold family history (LT-FH) model.
• saeczi runs small area estimation for continuous zero inflated data; it uses Rcpp and RcppEigen.
• bigergm fits, simulates and diagnoses hierarchical exponential family models for big networks; it uses Rcpp and RcppArmadillo.
• PAGFL offers joint estimation and identification of latent groups in panel data models; it uses Rcpp and RcppArmadillo.
• Colossus performs survival analysis using general non-linear models; it uses Rcpp and RcppEigen.
• QuadratiK implements methods constructed using kernel-based quadratic distances; it uses Rcpp and RcppEigen.
• rstanbdp runs Bayesian Deming Regresion for Method Comparisons; it uses Rcpp, RcppEigen, and BH.
• bigrquerystorage interfaces the Google 'BigQuery Storage' API.
• HDNRA implements high-dimensional location testing with normal-reference approaches; it uses Rcpp and RcppArmadillo.
• Rapi interfaces the multiple data providers 'EDDS' and 'FRED'.
• sanketphonetictranslator facilitates phonetic translation between Hindi and English.
• tsnet fits, compares and visualizes networks based on time series data; it uses Rcpp and RcppEigen.
• MR.RGM supports multivariate bidirectional Mendelian randomization netwroks; it uses Rcpp and RcppArmadillo.
• COAP fits a high-dimensional covariate-augmented overdispersed Poisson factor model; it uses Rcpp and RcppArmadillo.
• fdarep offers two-dimensional FPCA, marginal FPCA, and product FPCA for repeated functional data; it uses Rcpp and RcppEigen.
• agcounts calculates 'ActiGraph' counts from accelerometer data; it uses Rcpp and RcppArmadillo.
• chouca implements an engine for stochastic cellular automata; it uses Rcpp and RcppArmadillo.
• TestsSymmetry tests for symmetry when the center of symmetry is unknown.
• LikertMakeR synthesises and correlates rating-scale data; it uses Rcpp and RcppArmadillo.
• EMgaussian fits the expectations-maximization algorithm for multivariate Normal data with missingness; it uses Rcpp and RcppArmadillo.
• rcpptimer implements a 'tic-toc' timer with OpenMP support.
• MultiCOAP fits a high-dimensional covariate-augmented overdispersed multi-study Poisson factor model; it uses Rcpp and RcppArmadillo.
• noisysbmGGM adds a Bayesian algorithm to fit a noisy stochastic block model to an observed sparse graph; it uses Rcpp and RcppArmadillo.
• lconnect provides functions to upload vectorial data and derive landscape connectivity metrics in habitat or matrix systems.
• rid implements multiple change-point detection in multivariate time series; it uses Rcpp and RcppEigen.
• survey analyses complex survey samples; it uses Rcpp and RcppArmadillo.
• clusterMI enables cluster analysis with missing values by multiple imputation; it uses Rcpp and RcppArmadillo.
• geeVerse offers comprehensive analysis of high-dimensional longitudinal data; it uses Rcpp and RcppEigen.
• dnn builds deep neural networks with flexible user-defined loss functions and probability models; it uses Rcpp and RcppArmadillo.
• MSmix fits and analyses finite mixtures of Mallows models with Spearman distance for full and partial rankings with missing positions.
• modsem estimates interaction (i.e., moderation) effects between latent variables in structural equation models (SEM).
• tensorMiss handles missing data in higher-order tensor data; it uses Rcpp and RcppEigen.
• gamstransfer offers a data interface between GAMS and R.
• coglasso reconstructs networks from multi-omics data sets with the collaborative graphical lasso; it uses Rcpp and RcppEigen.
• qch provides functions for the joint analysis of Q sets of p-values obtained for the same list of items; it uses Rcpp and RcppArmadillo.
• DPTM fits dynamic panel multiple threshold models with fixed effecrs; it uses Rcpp and RcppEigen.
• nonprobsvy provides statistical inference with non-probability samples; it uses Rcpp and RcppArmadillo.
• CARMS offers continuous time Markov rate modeling for reliability analysis.
• YatchewTest implements a linearity test improved for heteroscedasticity.
• stcpR6 implements a sequential test- and change-point algorithm.
• complex offers time-series analyses and forecasting using complex variables; it uses Rcpp and RcppArmadillo.
• spaths computes shortest paths between points in grids.
• DIFM fits dynamic ICAR spatiotemporal factor models; it uses Rcpp and RcppArmadillo.
• tclust implements robust trimmed clustering; it uses Rcpp and RcppArmadillo.
• rqPen performs penalised quantile regression with different penalties; it uses Rcpp and RcppArmadillo.
• BayesSurvive implements Bayesian survival models for high-dimensional data; it uses Rcpp and RcppArmadillo.
• drclust provides methods for simultaenous clustering and dimensionality reduction; it uses Rcpp and RcppArmadillo.
• RobRegression adds robust methods to estimate the parameters of multivariate Gaussian linear models; it uses Rcpp and RcppArmadillo.
• slca provides comprehensive tools for the implementation of Structural Latent Class Models (SLCM).

Last modified: Tue Apr 23 10:12:19 CDT 2024