diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 677 |
1 files changed, 674 insertions, 3 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 64b0b0e940..49bb24e594 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3227,14 +3227,17 @@ and tidyr provides no margins or aggregation.") (define-public r-hexbin (package (name "r-hexbin") - (version "1.27.1") + ;; The package tarball was updated in place, resulting in a change in the + ;; hash value. We decided to bump the version to 1.27.1-1 instead of + ;; keeping the version at upstream's 1.27.1. + (version "1.27.1-1") (source (origin (method url-fetch) - (uri (cran-uri "hexbin" version)) + (uri (cran-uri "hexbin" "1.27.1")) (sha256 (base32 - "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh")))) + "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -4170,3 +4173,671 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.") "This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.") (license license:gpl2+))) + +(define-public r-diptest + (package + (name "r-diptest") + (version "0.75-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "diptest" version)) + (sha256 + (base32 + "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/diptest") + (synopsis "Hartigan's dip test statistic for unimodality") + (description + "This package computes Hartigan's dip test statistic for unimodality, +multimodality and provides a test with simulation based p-values, where the +original public code has been corrected.") + (license license:gpl2+))) + +(define-public r-modeltools + (package + (name "r-modeltools") + (version "0.2-21") + (source + (origin + (method url-fetch) + (uri (cran-uri "modeltools" version)) + (sha256 + (base32 + "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/modeltools") + (synopsis "Tools and classes for statistical models") + (description + "This package provides a collection of tools to deal with statistical +models. The functionality is experimental and the user interface is likely +to change in the future.") + (license license:gpl2))) + +(define-public r-flexmix + (package + (name "r-flexmix") + (version "2.3-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexmix" version)) + (sha256 + (base32 + "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + (build-system r-build-system) + (propagated-inputs + `(("r-modeltools" ,r-modeltools))) + (home-page "http://cran.r-project.org/web/packages/flexmix") + (synopsis "Flexible mixture modeling") + (description + "This package implements a general framework for finite mixtures of +regression models using the EM algorithm. FlexMix provides the E-step and +all data handling, while the M-step can be supplied by the user to easily +define new models. Existing drivers implement mixtures of standard linear +models, generalized linear models and model-based clustering.") + (license license:gpl2+))) + +(define-public r-mclust + (package + (name "r-mclust") + (version "5.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "mclust" version)) + (sha256 + (base32 + "19cbg7p5h2b6h9mvcx9rjppyd3awma18ymaljakbnclpvhwbqpwd")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://www.stat.washington.edu/mclust/") + (synopsis "Gaussian mixture modelling for model-based clustering etc.") + (description + "This package provides Gaussian finite mixture models fitted via EM +algorithm for model-based clustering, classification, and density estimation, +including Bayesian regularization, dimension reduction for visualisation, +and resampling-based inference.") + (license license:gpl2+))) + +(define-public r-prabclus + (package + (name "r-prabclus") + (version "2.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "prabclus" version)) + (sha256 + (base32 + "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mclust" ,r-mclust))) + (home-page "https://cran.r-project.org/web/packages/prabclus") + (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") + (description + "This package provides a distance-based parametric bootstrap tests +for clustering with spatial neighborhood information. Some distance measures, +clustering of presence-absence, abundance and multilocus genetical data for +species delimitation, nearest neighbor based noise detection.") + (license license:gpl2+))) + +(define-public r-deoptimr + (package + (name "r-deoptimr") + (version "1.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "DEoptimR" version)) + (sha256 + (base32 + "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4")))) + (properties `((upstream-name . "DEoptimR"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/DEoptimR") + (synopsis "Differential evolution optimization in pure R") + (description + "This package provides a differential evolution (DE) stochastic +algorithms for global optimization of problems with and without constraints. +The aim is to curate a collection of its state-of-the-art variants that (1) do +not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) +can be efficiently implemented directly in the R language.") + (license license:gpl2+))) + +(define-public r-robustbase + (package + (name "r-robustbase") + (version "0.92-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "robustbase" version)) + (sha256 + (base32 + "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-deoptimr" ,r-deoptimr))) + (home-page "http://robustbase.r-forge.r-project.org/") + (synopsis "Basic robust statistics") + (description + "This packages allows to analyze data with robust methods such as +regression methodology including model selections and multivariate statistics.") + (license license:gpl2+))) + +(define-public r-trimcluster + (package + (name "r-trimcluster") + (version "0.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "trimcluster" version)) + (sha256 + (base32 + "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/trimcluster") + (synopsis "Cluster analysis with trimming") + (description + "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and +Matran (1997). This optimizes the k-means criterion under trimming a portion +of the points.") + (license license:gpl2+))) + +(define-public r-fpc + (package + (name "r-fpc") + (version "2.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "fpc" version)) + (sha256 + (base32 + "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-diptest" ,r-diptest) + ("r-flexmix" ,r-flexmix) + ("r-kernlab" ,r-kernlab) + ("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-prabclus" ,r-prabclus) + ("r-robustbase" ,r-robustbase) + ("r-trimcluster" ,r-trimcluster))) + (home-page "http://cran.r-project.org/web/packages/fpc") + (synopsis "Flexible procedures for clustering") + (description + "This package provides various methods for clustering and cluster validation. +For example, it provides fixed point clustering, linear regression clustering, +clustering by merging Gaussian mixture components, as well as symmetric and +asymmetric discriminant projections for visualisation of the separation of +groupings.") + (license license:gpl2+))) + +(define-public r-vgam + (package + (name "r-vgam") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "VGAM" version)) + (sha256 + (base32 + "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3")))) + (properties `((upstream-name . "VGAM"))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM") + (synopsis "Vector generalized linear and additive models") + (description + "This package is an implementation of about 6 major classes of statistical +regression models. Currently only fixed-effects models are implemented, i.e., +no random-effects models. Many (150+) models and distributions are estimated +by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. +VGLMs can be loosely thought of as multivariate generalised linear models.") + (license license:gpl2+))) + +(define-public r-pbapply + (package + (name "r-pbapply") + (version "1.3-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbapply" version)) + (sha256 + (base32 + "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr")))) + (build-system r-build-system) + (home-page "https://github.com/psolymos/pbapply") + (synopsis "Adding progress bar to apply functions") + (description + "This lightweight package that adds progress bar to vectorized R +functions apply. The implementation can easily be added to functions where +showing the progress is useful e.g. bootstrap.") + (license license:gpl2))) + +(define-public r-fnn + (package + (name "r-fnn") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "FNN" version)) + (sha256 + (base32 + "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj")))) + (properties `((upstream-name . "FNN"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/FNN") + (synopsis "Fast nearest neighbor search algorithms and applications") + (description + "This package provides cover-tree and kd-tree fast k-nearest neighbor +search algorithms and related applications including KNN classification, +regression and information measures.") + (license license:gpl2+))) + +(define-public r-minqa + (package + (name "r-minqa") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "minqa" version)) + (sha256 + (base32 + "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (inputs + `(("gfortran" ,gfortran))) + (home-page "http://optimizer.r-forge.r-project.org") + (synopsis "Derivative-free optimization algorithms by quadratic approximation") + (description + "This package provides a derivative-free optimization by quadratic approximation +based on an interface to Fortran implementations by M. J. D. Powell.") + (license license:gpl2))) + +(define-public r-rcppeigen + (package + (name "r-rcppeigen") + (version "0.3.2.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppEigen" version)) + (sha256 + (base32 + "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5")))) + (properties `((upstream-name . "RcppEigen"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "http://eigen.tuxfamily.org") + (synopsis "Rcpp integration for the Eigen templated linear algebra library") + (description + "This package provides an integration of Eigen in R using a C++ template +library for linear algebra: matrices, vectors, numerical solvers and related algorithms. +It supports dense and sparse matrices on integer, floating point and complex numbers, +decompositions of such matrices, and solutions of linear systems.") + (license license:gpl2+))) + +(define-public r-modelmetrics + (package + (name "r-modelmetrics") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ModelMetrics" version)) + (sha256 + (base32 + "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8")))) + (properties `((upstream-name . "ModelMetrics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "http://cran.r-project.org/web/packages/ModelMetrics") + (synopsis "Rapid calculation of model metrics") + (description + "Written in C++ using @code{Rcpp}, this package provides a collection of +metrics for evaluating models.") + (license license:gpl2+))) + +(define-public r-matrixmodels + (package + (name "r-matrixmodels") + (version "0.4-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "MatrixModels" version)) + (sha256 + (base32 + "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) + (properties `((upstream-name . "MatrixModels"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/MatrixModels") + (synopsis "Modelling with sparse and dense matrices") + (description + "This package models with sparse and dense matrix matrices, +using modular prediction and response module classes.") + (license license:gpl2+))) + +(define-public r-quantreg + (package + (name "r-quantreg") + (version "5.29") + (source + (origin + (method url-fetch) + (uri (cran-uri "quantreg" version)) + (sha256 + (base32 + "098gy8xv9kcl5y0cm93b8chr5sm6crrdxi20bkx9lmwmybl3himv")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-matrixmodels" ,r-matrixmodels) + ("r-sparsem" ,r-sparsem))) + (home-page "http://www.r-project.org") + (synopsis "Quantile regression") + (description + "This package provides an estimation and inference methods for models +of conditional quantiles: linear and nonlinear parametric and non-parametric +models for conditional quantiles of a univariate response and several methods +for handling censored survival data. Portfolio selection methods based on +expected shortfall risk are also included.") + (license license:gpl2+))) + +(define-public r-nloptr + (package + (name "r-nloptr") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nloptr" version)) + (sha256 + (base32 + "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089")))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("nlopt" ,nlopt))) + (home-page "http://cran.r-project.org/web/packages/nloptr") + (synopsis "R interface to NLopt") + (description + "This package is interface to NLopt, a library for nonlinear +optimization. NLopt is a library for nonlinear optimization, providing a +common interface for a number of different free optimization routines +available online as well as original implementations of various other +algorithms.") + (license license:lgpl3))) + +(define-public r-lme4 + (package + (name "r-lme4") + (version "1.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "lme4" version)) + (sha256 + (base32 + "0j60l5kgx1wvw2wm3jwfqwi63hammaq8gfcxzwa4h552likvaxi9")))) + (build-system r-build-system) + (native-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (propagated-inputs + `(("r-minqa" ,r-minqa) + ("r-nloptr" ,r-nloptr))) + (home-page "http://cran.r-project.org/web/packages/lme4") + (synopsis "Linear mixed-effects models using eigen and S4") + (description + "This package provides fit linear and generalized linear mixed-effects +models. The models and their components are represented using S4 classes and +methods. The core computational algorithms are implemented using the Eigen +C++ library for numerical linear algebra and RcppEigen glue.") + (license license:gpl2+))) + +(define-public r-pbkrtest + (package + (name "r-pbkrtest") + (version "0.4-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbkrtest" version)) + (sha256 + (base32 + "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4))) + (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/") + (synopsis "Methods for linear mixed model comparison") + (description + "This package implements a parametric bootstrap test and a Kenward Roger +modification of F-tests for linear mixed effects models and a parametric +bootstrap test for generalized linear mixed models.") + (license license:gpl2+))) + +(define-public r-car + (package + (name "r-car") + (version "2.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "car" version)) + (sha256 + (base32 + "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-pbkrtest" ,r-pbkrtest) + ("r-quantreg" ,r-quantreg))) + (home-page "https://r-forge.r-project.org/projects/car/") + (synopsis "Companion to applied regression") + (description + "This package provides functions and datasets from book Companion +to Applied regression, Second Edition, Sage, 2011.") + (license license:gpl2+))) + +(define-public r-caret + (package + (name "r-caret") + (version "6.0-73") + (source + (origin + (method url-fetch) + (uri (cran-uri "caret" version)) + (sha256 + (base32 + "1jzaqwv4glyqqnfbpalgajd0ag866247vvdh5i83ffqs1yhs984h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-modelmetrics" ,r-modelmetrics) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/topepo/caret") + (synopsis "Classification and regression training") + (description + "This package provides misc functions for training and plotting +classification and regression models.") + (license license:gpl2+))) + +(define-public r-rcppprogress + (package + (name "r-rcppprogress") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppProgress" version)) + (sha256 + (base32 + "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x")))) + (properties `((upstream-name . "RcppProgress"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/kforner/rcpp_progress") + (synopsis "Interruptible progress bar for C++ in R packages") + (description + "This package allows to display a progress bar in the R console for long running +computations taking place in C++ code, and support for interrupting those computations +even in multithreaded code, typically using OpenMP.") + (license license:gpl3+))) + +(define-public r-mnormt + (package + (name "r-mnormt") + (version "1.5-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mnormt" version)) + (sha256 + (base32 + "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") + (synopsis "Multivariate normal and \"t\" distributions") + (description + "This package provides functions for computing the density and the +distribution function of multivariate normal and \"t\" random variables, and +for generating random vectors sampled from these distributions. Probabilities +are computed via non-Monte Carlo methods.") + (license license:gpl2+))) + +(define-public r-numderiv + (package + (name "r-numderiv") + (version "2016.8-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "numDeriv" version)) + (sha256 + (base32 + "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v")))) + (properties `((upstream-name . "numDeriv"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/numDeriv") + (synopsis "Accurate numerical derivatives") + (description + "This package provides methods for calculating accurate numerical +first and second order derivatives.") + (license license:gpl2))) + +(define-public r-sn + (package + (name "r-sn") + (version "1.5-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sn" version)) + (sha256 + (base32 + "0fh7xjsfd2x8d9lbnss7raldh24b72b3pvcv7zqa1qprzg7zfr01")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mnormt" ,r-mnormt) + ("r-numderiv" ,r-numderiv))) + (home-page "http://azzalini.stat.unipd.it/SN") + (synopsis "The skew-normal and skew-t distributions") + (description + "This packages provides functionalities to build and manipulate +probability distributions of the skew-normal family and some related +ones, notably the skew-t family, and provides related statistical +methods for data fitting and diagnostics, in the univariate and the +multivariate case.") + (license license:gpl2+))) + +(define-public r-tclust + (package + (name "r-tclust") + (version "1.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tclust" version)) + (sha256 + (base32 + "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mclust" ,r-mclust) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sn" ,r-sn))) + (home-page "http://cran.r-project.org/web/packages/tclust") + (synopsis "Robust trimmed clustering") + (description + "This package implements different robust clustering +algorithms (@code{tclust}) based on trimming and including some graphical +diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") + (license license:gpl3))) + +(define-public r-ranger + (package + (name "r-ranger") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ranger" version)) + (sha256 + (base32 + "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/imbs-hl/ranger") + (synopsis "Fast implementation of random forests") + (description + "This package provides a fast implementation of Random Forests, +particularly suited for high dimensional data. Ensembles of classification, +regression, survival and probability prediction trees are supported. Data from +genome-wide association studies can be analyzed efficiently.") + (license license:gpl3))) + +(define-public r-tsne + (package + (name "r-tsne") + (version "0.1-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tsne" version)) + (sha256 + (base32 + "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6")))) + (build-system r-build-system) + (home-page "https://github.com/jdonaldson/rtsne/") + (synopsis "t-Distributed Stochastic Neighbor Embedding for R") + (description + "This package provides a pure R implementation of the t-SNE algorithm.") + (license license:gpl2+))) |