R Core team

Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.

Identify peaks in ChIP-seq data with biological replicates using a one-sided quasi-likelihood ratio test in quasi-Poisson or quasi-negative binomial models.

Misc functions for training and plotting classification and regression models.

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.

Provides chronological objects which can handle dates and times.

Exploring fitted models by interactively taking 2-D and 3-D sections in data space.

Functions for handling dates.

Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.

Collection of package development tools.

S4-classes and methods for distributions.

Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.

EM algorithms and several efficient initialization methods for model-based clustering of finite mixture Gaussian distribution with unstructured dispersion in both of unsupervised and semi-supervised learning.

Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.

Useful tools for writing vector graphics devices.

Implements the Bayesian paradigm for fractional polynomials in generalized linear models, described by Held, Gravestock, Sabanes Bove (2015) <doi:10.1214/14-STS510>. See package 'bfp' for the treatment of normal models.

Read hierarchical fixed width files like those commonly used by many census data providers. Also allows for reading of data in chunks, and reading 'gzipped' files without storing the full file in memory.

Calculate comorbidities, medical risk scores, and work very quickly and precisely with ICD-9 and ICD-10 codes. This package enables a work flow from raw tables of ICD codes in hospital databases to comorbidities. ICD-9 and ICD-10 comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Common ambiguities and code formats are handled. Comorbidity computation includes Hierarchical Condition Codes, and an implementation of AHRQ Clinical Classifications. Risk scores include those of Charlson and van Walraven. US Clinical Modification, Word Health Organization, Belgian and French ICD-10 codes are supported, most of which are downloaded on demand.

Generates Rd files from R source code with comments. The main features of the default syntax are that (1) docs are defined in comments near the relevant code, (2) function argument names are not repeated in comments, and (3) examples are defined in R code, not comments. It is also easy to define a new syntax.

Obsolete: 'icd9' is replaced by CRAN package 'icd'. Calculate comorbidities, Charlson scores, perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9-CM (clinical modification) codes. ICD-9 codes appear numeric but leading and trailing zeroes, and both decimal and non-decimal "short" format codes exist. The package enables a work flow from raw lists of ICD-9 codes from hospital billing databases to comorbidities. ICD-9 to comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any other mapping of codes, such as ICD-10, to comorbidities can be used.

A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.

Two implementations of canonical correlation analysis (CCA) that are based on iterated regression. By choosing the appropriate regression algorithm for each data domain, it is possible to enforce sparsity, non-negativity or other kinds of constraints on the projection vectors. Multiple canonical variables are computed sequentially using a generalized deflation scheme, where the additional correlation not explained by previous variables is maximized. 'nscancor' is used to analyze paired data from two domains, and has the same interface as the 'cancor' function from the 'stats' package (plus some extra parameters). 'mcancor' is appropriate for analyzing data from three or more domains. See <http://sigg-iten.ch/learningbits/2014/01/20/canonical-correlation-analysis-under-constraints/> and Sigg et al. (2007) <doi:10.1109/MLSP.2007.4414315> for more details.

Two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function 'nsprcomp' computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function 'nscumcomp' jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the 'prcomp' function from the 'stats' package (plus some extra parameters), and both return the result of the analysis as an object of class 'nsprcomp', which inherits from 'prcomp'. See <https://sigg-iten.ch/learningbits/2013/05/27/nsprcomp-is-on-cran/> and Sigg et al. (2008) <doi:10.1145/1390156.1390277> for more details.

A set of classes for managing distributed matrices, and a collection of methods for computing linear algebra and statistics. Computation is handled mostly by routines from the 'pbdBASE' package, which itself relies on the 'ScaLAPACK' and 'PBLAS' numerical libraries for distributed computing.

An efficient interface to MPI by utilizing S4 classes and methods with a focus on Single Program/Multiple Data ('SPMD') parallel programming style, which is intended for batch parallel execution.

'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.

A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

Analysis of terms in linear, generalized and mixed linear models, on the basis of multiple comparisons of factor contrasts. Specially suited for the analysis of interaction terms.

Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.

Useful tools to pry back the covers of R and understand the language at a deeper level.

The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

Function to read and write the 'Stata' file format.

A set of utilities for client/server computing with R, controlling a remote R session (the server) from a local one (the client). Simply set up a server (see package vignette for more details) and connect to it from your local R session ('RStudio', terminal, etc). The client/server framework is a custom 'REPL' and runs entirely in your R session without the need for installing a custom environment on your system. Network communication is handled by the 'ZeroMQ' library by way of the 'pbdZMQ' package.

Base S4-classes and functions for robust asymptotic statistics.

We provide an outlier robust alternative of the function ets() in the 'forecast' package of Hyndman and Khandakar (2008) <DOI:10.18637/jss.v027.i03>. For each method of a class of exponential smoothing variants we made a robust alternative. The class includes methods with a damped trend and/or seasonal components. The robust method is developed by robustifying every aspect of the original exponential smoothing variant. We provide robust forecasting equations, robust initial values, robust smoothing parameter estimation and a robust information criterion. The method is described in more detail in Crevits and Croux (2016) <DOI:10.13140/RG.2.2.11791.18080>.

Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS.

A system contains easy-to-use tools as a support for time series analysis courses. In particular, it incorporates a technique called Generalized Method of Wavelet Moments (GMWM) as well as its robust implementation for fast and robust parameter estimation of time series models which is described, for example, in Guerrier et al. (2013) <doi: 10.1080/01621459.2013.799920>. More details can also be found in the paper linked to via the URL below.

Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.

Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences. This package is built for speed and runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of H�hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. 'hhh4' estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. 'twinSIR' models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by H�hle (2009) <doi:10.1002/bimj.200900050>. 'twinstim' estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2015) <http://arxiv.org/abs/1411.0416>.

Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.

A set of tools designed to facilitate easy adoption of R for students in introductory classes with little programming experience. Compiles output from existing routines together in an intuitive format, and adds functionality to existing functions. For instance, the regression function can perform linear models, generalized linear models, Cox models, or generalized estimating equations. The user can also specify multiple-partial F-tests to print out with the model coefficients. We also give many routines for descriptive statistics and plotting.

The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.