#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system r)
+ #:use-module (gnu packages gcc)
+ #:use-module (gnu packages machine-learning)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages perl)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
(define-public r-glue
(package
(name "r-glue")
- (version "1.1.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "glue" version))
(sha256
(base32
- "01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih"))))
+ "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr"))))
(build-system r-build-system)
(home-page "https://github.com/tidyverse/glue")
(synopsis "Interpreted string literals")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "0.12.12")
+ (version "0.12.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz"))))
+ (base32 "1bm84yc48475plgsnnbvzi6nzkixpnfw8ry86ax63f9g524asw55"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ integration")
(define-public r-shape
(package
(name "r-shape")
- (version "1.4.2")
+ (version "1.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "shape" version))
(sha256
(base32
- "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"))))
+ "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/shape")
(synopsis "Functions for plotting graphical shapes")
(define-public r-circlize
(package
(name "r-circlize")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "circlize" version))
(sha256
(base32
- "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b"))))
+ "1w7i3jgxgq510axglzmw54ma9kq7k4c86i9ccndz10mrwc51fji0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)
(define-public r-powerlaw
(package
(name "r-powerlaw")
- (version "0.70.0")
+ (version "0.70.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "poweRlaw" version))
(sha256
(base32
- "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"))))
+ "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m"))))
(properties `((upstream-name . "poweRlaw")))
(build-system r-build-system)
(propagated-inputs
"This package provides data structures that are stored on disk but
behave (almost) as if they were in RAM by transparently mapping only a section
in main memory.")
+ ;; error Architecture not supported.
+ (supported-systems (delete "aarch64-linux" %supported-systems))
(license license:gpl2)))
(define-public r-ffbase
(define-public r-reshape
(package
(name "r-reshape")
- (version "0.8.6")
+ (version "0.8.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "reshape" version))
(sha256
(base32
- "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq"))))
+ "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig"))))
(build-system r-build-system)
(propagated-inputs
`(("r-plyr" ,r-plyr)
(define-public r-ggally
(package
(name "r-ggally")
- (version "1.3.0")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "GGally" version))
(sha256
(base32
- "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b"))))
+ "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"))))
(properties `((upstream-name . "GGally")))
(build-system r-build-system)
(propagated-inputs
(define-public r-proxy
(package
(name "r-proxy")
- (version "0.4-17")
+ (version "0.4-19")
(source
(origin
(method url-fetch)
(uri (cran-uri "proxy" version))
(sha256
(base32
- "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2"))))
+ "0ladwgi70jw2a3adgg2xadw8hz3mm6llsw428c1fcrl305sy49vb"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/proxy")
(synopsis "Distance and similarity measures")
(define-public r-sp
(package
(name "r-sp")
- (version "1.2-4")
+ (version "1.2-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "sp" version))
(sha256
(base32
- "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2"))))
+ "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
and other distributions related to the eigenvalues of large Wishart
matrices.")
(license license:bsd-3)))
+
+(define-public r-lmoments
+ (package
+ (name "r-lmoments")
+ (version "1.2-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Lmoments" version))
+ (sha256
+ (base32
+ "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
+ (properties `((upstream-name . "Lmoments")))
+ (build-system r-build-system)
+ (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
+ (synopsis "L-moments and quantile mixtures")
+ (description
+ "This package contains functions to estimate L-moments and trimmed
+L-moments from the data. It also contains functions to estimate the
+parameters of the normal polynomial quantile mixture and the Cauchy polynomial
+quantile mixture from L-moments and trimmed L-moments.")
+ (license license:gpl2)))
+
+(define-public r-distillery
+ (package
+ (name "r-distillery")
+ (version "1.0-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "distillery" version))
+ (sha256
+ (base32
+ "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix"))))
+ (build-system r-build-system)
+ (home-page "http://www.ral.ucar.edu/staff/ericg")
+ (synopsis "Functions for confidence intervals and object information")
+ (description
+ "This package provides some very simple method functions for confidence
+interval calculation and to distill pertinent information from a potentially
+complex object; primarily used in common with the packages extRemes and
+SpatialVx.")
+ (license license:gpl2+)))
+
+(define-public r-extremes
+ (package
+ (name "r-extremes")
+ (version "2.0-8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "extRemes" version))
+ (sha256
+ (base32
+ "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
+ (properties `((upstream-name . "extRemes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-car" ,r-car)
+ ("r-distillery" ,r-distillery)
+ ("r-lmoments" ,r-lmoments)))
+ (home-page "http://www.assessment.ucar.edu/toolkit/")
+ (synopsis "Extreme value analysis")
+ (description
+ "ExtRemes is a suite of functions for carrying out analyses on the
+extreme values of a process of interest; be they block maxima over long blocks
+or excesses over a high threshold.")
+ (license license:gpl2+)))
+
+(define-public r-lmtest
+ (package
+ (name "r-lmtest")
+ (version "0.9-35")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lmtest" version))
+ (sha256
+ (base32
+ "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-zoo" ,r-zoo)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://cran.r-project.org/web/packages/lmtest")
+ (synopsis "Testing linear regression models")
+ (description
+ "This package provides a collection of tests, data sets, and examples for
+diagnostic checking in linear regression models. Furthermore, some generic
+tools for inference in parametric models are provided.")
+ ;; Either version is okay
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-inline
+ (package
+ (name "r-inline")
+ (version "0.3.14")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "inline" version))
+ (sha256
+ (base32
+ "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/inline")
+ (synopsis "Functions to inline C, C++, Fortran function calls from R")
+ (description
+ "This package provides functionality to dynamically define R functions
+and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
+@code{.Call} calling conventions.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
+(define-public r-bbmle
+ (package
+ (name "r-bbmle")
+ (version "1.0.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bbmle" version))
+ (sha256
+ (base32
+ "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-numderiv" ,r-numderiv)))
+ (home-page "http://cran.r-project.org/web/packages/bbmle")
+ (synopsis "Tools for General Maximum Likelihood Estimation")
+ (description
+ "Methods and functions for fitting maximum likelihood models in R. This
+package modifies and extends the @code{mle} classes in the @code{stats4}
+package.")
+ ;; Any version of the GPL
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-emdbook
+ (package
+ (name "r-emdbook")
+ (version "1.3.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "emdbook" version))
+ (sha256
+ (base32
+ "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmle" ,r-bbmle)
+ ("r-coda" ,r-coda)
+ ("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
+ (synopsis "Support functions and data for \"Ecological Models and Data\"")
+ (description
+ "This package provides auxiliary functions and data sets for \"Ecological
+Models and Data\", a book presenting maximum likelihood estimation and related
+topics for ecologists (ISBN 978-0-691-12522-0).")
+ ;; Any GPL version
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-lpsolve
+ (package
+ (name "r-lpsolve")
+ (version "5.6.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lpSolve" version))
+ (sha256
+ (base32
+ "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
+ (properties `((upstream-name . "lpSolve")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/lpSolve")
+ (synopsis "R interface to Lp_solve to solve linear/integer programs")
+ (description
+ "Lp_solve is software for solving linear, integer and mixed integer
+programs. This implementation supplies a \"wrapper\" function in C and some R
+functions that solve general linear/integer problems, assignment problems, and
+transportation problems.")
+ (license license:lgpl2.0)))
+
+(define-public r-limsolve
+ (package
+ (name "r-limsolve")
+ (version "1.5.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "limSolve" version))
+ (sha256
+ (base32
+ "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
+ (properties `((upstream-name . "limSolve")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lpsolve" ,r-lpsolve)
+ ("r-mass" ,r-mass)
+ ("r-quadprog" ,r-quadprog)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "http://cran.r-project.org/web/packages/limSolve")
+ (synopsis "Solving linear inverse models")
+ (description
+ "This package provides functions that:
+
+@enumerate
+@item find the minimum/maximum of a linear or quadratic function,
+@item sample an underdetermined or overdetermined system,
+@item solve a linear system Ax=B for the unknown x.
+@end enumerate
+
+It includes banded and tridiagonal linear systems. The package calls Fortran
+functions from LINPACK.")
+ ;; Any GPL version.
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-fitdistrplus
+ (package
+ (name "r-fitdistrplus")
+ (version "1.0-9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fitdistrplus" version))
+ (sha256
+ (base32
+ "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mass" ,r-mass)
+ ("r-survival" ,r-survival)))
+ (home-page "http://riskassessment.r-forge.r-project.org")
+ (synopsis "Fitting a parametric distribution from data")
+ (description
+ "This package extends the @code{fitdistr} function of the MASS package
+with several functions to help the fit of a parametric distribution to
+non-censored or censored data. Censored data may contain left-censored,
+right-censored and interval-censored values, with several lower and upper
+bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
+provides moment matching (MME), quantile matching (QME) and maximum
+goodness-of-fit estimation (MGE) methods (available only for non-censored
+data). Weighted versions of MLE, MME and QME are available.")
+ (license license:gpl2+)))
+
+(define-public r-energy
+ (package
+ (name "r-energy")
+ (version "1.7-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "energy" version))
+ (sha256
+ (base32
+ "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-boot" ,r-boot)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "http://cran.r-project.org/web/packages/energy")
+ (synopsis "Multivariate inference via the energy of data")
+ (description
+ "This package provides e-statistics (energy) tests and statistics for
+multivariate and univariate inference, including distance correlation,
+one-sample, two-sample, and multi-sample tests for comparing multivariate
+distributions, are implemented. Measuring and testing multivariate
+independence based on distance correlation, partial distance correlation,
+multivariate goodness-of-fit tests, clustering based on energy distance,
+testing for multivariate normality, distance components (disco) for
+non-parametric analysis of structured data, and other energy
+statistics/methods are implemented.")
+ (license license:gpl2+)))
+
+(define-public r-suppdists
+ (package
+ (name "r-suppdists")
+ (version "1.1-9.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "SuppDists" version))
+ (sha256
+ (base32
+ "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
+ (properties `((upstream-name . "SuppDists")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/SuppDists")
+ (synopsis "Supplementary distributions")
+ (description
+ "This package provides ten distributions supplementing those built into
+R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
+Spearman's rho, maximum F ratio, the Pearson product moment correlation
+coefficient, Johnson distributions, normal scores and generalized
+hypergeometric distributions. In addition two random number generators of
+George Marsaglia are included.")
+ (license license:gpl2+)))
+
+(define-public r-ksamples
+ (package
+ (name "r-ksamples")
+ (version "1.2-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "kSamples" version))
+ (sha256
+ (base32
+ "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj"))))
+ (properties `((upstream-name . "kSamples")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-suppdists" ,r-suppdists)))
+ (home-page "http://cran.r-project.org/web/packages/kSamples")
+ (synopsis "K-Sample rank tests and their combinations")
+ (description
+ "This package provides tools to compares k samples using the
+Anderson-Darling test, Kruskal-Wallis type tests with different rank score
+criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
+test. It computes asymptotic, simulated or (limited) exact P-values, all
+valid under randomization, with or without ties, or conditionally under random
+sampling from populations, given the observed tie pattern. Except for Steel's
+test and the JT test it also combines these tests across several blocks of
+samples.")
+ (license license:gpl2+)))
+
+(define-public r-cvst
+ (package
+ (name "r-cvst")
+ (version "0.2-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "CVST" version))
+ (sha256
+ (base32
+ "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2"))))
+ (properties `((upstream-name . "CVST")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-kernlab" ,r-kernlab)
+ ("r-matrix" ,r-matrix)))
+ (home-page "http://cran.r-project.org/web/packages/CVST")
+ (synopsis "Fast cross-validation via sequential testing")
+ (description
+ "This package implements the fast cross-validation via sequential
+testing (CVST) procedure. CVST is an improved cross-validation procedure
+which uses non-parametric testing coupled with sequential analysis to
+determine the best parameter set on linearly increasing subsets of the data.
+Additionally to the CVST the package contains an implementation of the
+ordinary k-fold cross-validation with a flexible and powerful set of helper
+objects and methods to handle the overall model selection process. The
+implementations of the Cochran's Q test with permutations and the sequential
+testing framework of Wald are generic and can therefore also be used in other
+contexts.")
+ (license license:gpl2+)))
+
+(define-public r-lava
+ (package
+ (name "r-lava")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lava" version))
+ (sha256
+ (base32
+ "1vcm04h9i39gmf2prl5d4j4il4gs6skzr6y2fvl1vn4hklna87f4"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-numderiv" ,r-numderiv)
+ ("r-survival" ,r-survival)))
+ (home-page "https://github.com/kkholst/lava")
+ (synopsis "Latent variable models")
+ (description
+ "This package provides tools for the estimation and simulation of latent
+variable models.")
+ (license license:gpl3)))
+
+(define-public r-drr
+ (package
+ (name "r-drr")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "DRR" version))
+ (sha256
+ (base32
+ "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2"))))
+ (properties `((upstream-name . "DRR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cvst" ,r-cvst)
+ ("r-kernlab" ,r-kernlab)
+ ("r-matrix" ,r-matrix)))
+ (home-page "http://cran.r-project.org/web/packages/DRR")
+ (synopsis "Dimensionality reduction via regression")
+ (description
+ "This package provides an implementation of dimensionality reduction via
+regression using Kernel Ridge Regression.")
+ (license license:gpl3)))
+
+(define-public r-prodlim
+ (package
+ (name "r-prodlim")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "prodlim" version))
+ (sha256
+ (base32
+ "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-kernsmooth" ,r-kernsmooth)
+ ("r-lava" ,r-lava)
+ ("r-rcpp" ,r-rcpp)
+ ("r-survival" ,r-survival)))
+ (home-page "http://cran.r-project.org/web/packages/prodlim")
+ (synopsis "Product-limit estimation for censored event history analysis")
+ (description
+ "This package provides a fast and user-friendly implementation of
+nonparametric estimators for censored event history (survival) analysis with
+the Kaplan-Meier and Aalen-Johansen methods.")
+ (license license:gpl2+)))
+
+(define-public r-dimred
+ (package
+ (name "r-dimred")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dimRed" version))
+ (sha256
+ (base32
+ "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v"))))
+ (properties `((upstream-name . "dimRed")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-drr" ,r-drr)))
+ (home-page "https://github.com/gdkrmr/dimRed")
+ (synopsis "Framework for dimensionality reduction")
+ (description
+ "This package provides a collection of dimensionality reduction
+techniques from R packages and provides a common interface for calling the
+methods.")
+ (license license:gpl3)))
+
+(define-public r-timedate
+ (package
+ (name "r-timedate")
+ (version "3012.100")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "timeDate" version))
+ (sha256
+ (base32
+ "0cn4h23y2y2bbg62qgm79xx4cvfla5xbpmi9hbdvkvpmm5yfyqk2"))))
+ (properties `((upstream-name . "timeDate")))
+ (build-system r-build-system)
+ (home-page "https://www.rmetrics.org")
+ (synopsis "Chronological and calendar objects")
+ (description
+ "This package provides an environment for teaching \"Financial
+Engineering and Computational Finance\" and for managing chronological and
+calendar objects.")
+ (license license:gpl2+)))
+
+(define-public r-ddalpha
+ (package
+ (name "r-ddalpha")
+ (version "1.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ddalpha" version))
+ (sha256
+ (base32
+ "0pczw9543y7f92m7gyk7rxcjn8vsjaldc5vl0r56ywip9i374zbh"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-class" ,r-class)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)
+ ("r-robustbase" ,r-robustbase)
+ ("r-sfsmisc" ,r-sfsmisc)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://cran.r-project.org/web/packages/ddalpha")
+ (synopsis "Depth-Based classification and calculation of data depth")
+ (description
+ "This package contains procedures for depth-based supervised learning,
+which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
+Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
+statistical depth function to a compact low-dimensional space, where the final
+classification is done. It also offers an extension to functional data and
+routines for calculating certain notions of statistical depth functions. 50
+multivariate and 5 functional classification problems are included.")
+ (license license:gpl2)))
+
+(define-public r-gower
+ (package
+ (name "r-gower")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gower" version))
+ (sha256
+ (base32
+ "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/markvanderloo/gower")
+ (synopsis "Gower's distance")
+ (description
+ "This package provides tools to compute Gower's distance (or similarity)
+coefficient between records, and to compute the top-n matches between records.
+Core algorithms are executed in parallel on systems supporting OpenMP.")
+ (license license:gpl3)))
+
+(define-public r-rcpproll
+ (package
+ (name "r-rcpproll")
+ (version "0.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RcppRoll" version))
+ (sha256
+ (base32
+ "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi"))))
+ (properties `((upstream-name . "RcppRoll")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://cran.r-project.org/web/packages/RcppRoll")
+ (synopsis "Efficient rolling and windowed operations")
+ (description
+ "This package provides fast and efficient routines for common rolling /
+windowed operations. Routines for the efficient computation of windowed mean,
+median, sum, product, minimum, maximum, standard deviation and variance are
+provided.")
+ (license license:gpl2+)))
+
+(define-public r-ipred
+ (package
+ (name "r-ipred")
+ (version "0.9-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ipred" version))
+ (sha256
+ (base32
+ "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-class" ,r-class)
+ ("r-mass" ,r-mass)
+ ("r-nnet" ,r-nnet)
+ ("r-prodlim" ,r-prodlim)
+ ("r-rpart" ,r-rpart)
+ ("r-survival" ,r-survival)))
+ (home-page "http://cran.r-project.org/web/packages/ipred")
+ (synopsis "Improved predictors")
+ (description
+ "This package provides improved predictive models by indirect
+classification and bagging for classification, regression and survival
+problems as well as resampling based estimators of prediction error.")
+ (license license:gpl2+)))
+
+(define-public r-recipes
+ (package
+ (name "r-recipes")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "recipes" version))
+ (sha256
+ (base32
+ "0rydk403qihxmcv3zz323r3ywk4g1v7ibvj452rxhm0z22sqk9kb"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ddalpha" ,r-ddalpha)
+ ("r-dimred" ,r-dimred)
+ ("r-dplyr" ,r-dplyr)
+ ("r-gower" ,r-gower)
+ ("r-ipred" ,r-ipred)
+ ("r-lubridate" ,r-lubridate)
+ ("r-magrittr" ,r-magrittr)
+ ("r-purrr" ,r-purrr)
+ ("r-rcpproll" ,r-rcpproll)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-timedate" ,r-timedate)))
+ (home-page "https://github.com/topepo/recipes")
+ (synopsis "Preprocessing tools to create design matrices")
+ (description
+ "Recipes is an extensible framework to create and preprocess design
+matrices. Recipes consist of one or more data manipulation and analysis
+\"steps\". Statistical parameters for the steps can be estimated from an
+initial data set and then applied to other data sets. The resulting design
+matrices can then be used as inputs into statistical or machine learning
+models.")
+ (license license:gpl2)))
+
+(define-public r-pdist
+ (package
+ (name "r-pdist")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pdist" version))
+ (sha256
+ (base32
+ "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/jeffwong/pdist")
+ (synopsis "Partitioned distance function")
+ (description
+ "Pdist computes the euclidean distance between rows of a matrix X and
+rows of another matrix Y. Previously, this could be done by binding the two
+matrices together and calling @code{dist}, but this creates unnecessary
+computation by computing the distances between a row of X and another row of
+X, and likewise for Y. Pdist strictly computes distances across the two
+matrices, not within the same matrix, making computations significantly faster
+for certain use cases.")
+ (license license:gpl3+)))
+
+(define-public r-ggrepel
+ (package
+ (name "r-ggrepel")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggrepel" version))
+ (sha256
+ (base32
+ "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-rcpp" ,r-rcpp)
+ ("r-scales" ,r-scales)))
+ (home-page "http://github.com/slowkow/ggrepel")
+ (synopsis "Repulsive text and label geometries for ggplot2")
+ (description
+ "This package provides text and label geometries for ggplot2 that help to
+avoid overlapping text labels. Labels repel away from each other and away
+from the data points.")
+ (license license:gpl3)))
+
+(define-public r-corrplot
+ (package
+ (name "r-corrplot")
+ (version "0.84")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "corrplot" version))
+ (sha256
+ (base32
+ "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/taiyun/corrplot")
+ (synopsis "Visualization of a correlation matrix")
+ (description
+ "This package provides a graphical display of a correlation matrix or
+general matrix. It also contains some algorithms to do matrix reordering. In
+addition, corrplot is good at details, including choosing color, text labels,
+color labels, layout, etc.")
+ ;; Any version of the GPL
+ (license license:gpl2+)))
+
+(define-public r-stringdist
+ (package
+ (name "r-stringdist")
+ (version "0.9.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "stringdist" version))
+ (sha256
+ (base32
+ "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/markvanderloo/stringdist")
+ (synopsis "Approximate string matching and string distance functions")
+ (description
+ "This package implements an approximate string matching version of R's
+native @code{match} function. It 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.")
+ (license license:gpl3+)))
+
+(define-public r-mice
+ (package
+ (name "r-mice")
+ (version "2.46.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mice" version))
+ (sha256
+ (base32
+ "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-nnet" ,r-nnet)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rpart" ,r-rpart)
+ ("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/mice/")
+ (synopsis "Multivariate imputation by chained equations")
+ (description
+ "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
+implemented by the MICE algorithm as described in @url{Van Buuren and
+Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
+variable has its own imputation model. 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). MICE can also
+impute continuous two-level data (normal model, pan, second-level variables).
+Passive imputation can be used to maintain consistency between variables.
+Various diagnostic plots are available to inspect the quality of the
+imputations.")
+ ;; Any of these two versions.
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-hardyweinberg
+ (package
+ (name "r-hardyweinberg")
+ (version "1.5.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "HardyWeinberg" version))
+ (sha256
+ (base32
+ "0xbcchmzii0jv0ygr91n72r39j1axraxd2i607b56v4yd5d8sy4k"))))
+ (properties `((upstream-name . "HardyWeinberg")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mice" ,r-mice)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://cran.r-project.org/package=HardyWeinberg")
+ (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
+ (description
+ "This package contains tools for exploring Hardy-Weinberg equilibrium for
+diallelic genetic marker data. All classical tests (chi-square, exact,
+likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
+included in the package, as well as functions for power computation and for
+the simulation of marker data under equilibrium and disequilibrium. Routines
+for dealing with markers on the X-chromosome are included. Functions for
+testing equilibrium in the presence of missing data by using multiple
+imputation are also provided. Implements several graphics for exploring the
+equilibrium status of a large set of diallelic markers: ternary plots with
+acceptance regions, log-ratio plots and Q-Q plots.")
+ (license license:gpl2+)))
+
+(define-public r-sm
+ (package
+ (name "r-sm")
+ (version "2.2-5.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sm" version))
+ (sha256
+ (base32
+ "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9"))))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
+ (synopsis "Smoothing methods for nonparametric regression and density estimation")
+ (description
+ "This is software accompanying the book 'Applied Smoothing Techniques for
+Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
+University Press. It provides smoothing methods for nonparametric regression
+and density estimation")
+ (license license:gpl2+)))
+
+(define-public r-vioplot
+ (package
+ (name "r-vioplot")
+ (version "0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "vioplot" version))
+ (sha256
+ (base32
+ "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-sm" ,r-sm)))
+ (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
+ (synopsis "Violin plot")
+ (description
+ "This package provides a violin plot, which is a combination of a box
+plot and a kernel density plot.")
+ (license license:bsd-3)))
+
+(define-public r-rsofia
+ (package
+ (name "r-rsofia")
+ (version "1.1")
+ (source (origin
+ (method url-fetch)
+ ;; This package has been removed from CRAN, so we can
+ ;; only fetch it from the archives.
+ (uri (string-append "https://cran.r-project.org/src/"
+ "contrib/Archive/RSofia/RSofia_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
+ (properties `((upstream-name . "RSofia")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
+ (synopsis "Port of sofia-ml to R")
+ (description "This package is a port of sofia-ml to R. Sofia-ml is a
+suite of fast incremental algorithms for machine learning that can be used for
+training models for classification or ranking.")
+ (license license:asl2.0)))
+
+(define-public r-bbmle
+ (package
+ (name "r-bbmle")
+ (version "1.0.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bbmle" version))
+ (sha256
+ (base32
+ "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-numderiv" ,r-numderiv)))
+ (home-page "http://cran.r-project.org/web/packages/bbmle/")
+ (synopsis "Tools for General Maximum Likelihood Estimation")
+ (description
+ "This package provides methods and functions for fitting maximum
+likelihood models in R. This package modifies and extends the @code{mle}
+classes in the @code{stats4} package.")
+ ;; Any version of the GPL
+ (license license:gpl2+)))
+
+(define-public r-xts
+ (package
+ (name "r-xts")
+ (version "0.10-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "xts" version))
+ (sha256
+ (base32
+ "1w7lxy3hbf005fvpzbwiznj8jbxi07s4189vbgxisd35l9a4v6q4"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-zoo" ,r-zoo)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://github.com/joshuaulrich/xts")
+ (synopsis "Extensible time series")
+ (description
+ "This package provides for uniform handling of R's different time-based
+data classes by extending @code{zoo}, maximizing native format information
+preservation and allowing for user-level customization and extension, while
+simplifying cross-class interoperability.")
+ (license license:gpl2+)))
+
+(define-public r-performanceanalytics
+ (package
+ (name "r-performanceanalytics")
+ (version "1.4.3541")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "PerformanceAnalytics" version))
+ (sha256
+ (base32
+ "1czchsccsbdfjw743j6rm101q2q01pggyl8zmlva213pwm86zb3v"))))
+ (properties
+ `((upstream-name . "PerformanceAnalytics")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-xts" ,r-xts)
+ ("r-zoo" ,r-zoo)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "http://r-forge.r-project.org/projects/returnanalytics/")
+ (synopsis "Econometric tools for performance and risk analysis")
+ (description "This is a collection of econometric functions for
+performance and risk analysis. This package aims to aid practitioners and
+researchers in utilizing the latest research in analysis of non-normal return
+streams. In general, it is most tested on return (rather than price) data on
+a regular scale, but most functions will work with irregular return data as
+well, and increasing numbers of functions will work with P&L or price data
+where possible.")
+ ;; Either version may be picked.
+ (license (list license:gpl2 license:gpl3))))
+
+(define-public r-laeken
+ (package
+ (name "r-laeken")
+ (version "0.4.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "laeken" version))
+ (sha256
+ (base32
+ "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-boot" ,r-boot)
+ ("r-mass" ,r-mass)))
+ (home-page "http://cran.r-project.org/web/packages/laeken/")
+ (synopsis "Estimation of indicators on social exclusion and poverty")
+ (description "This package provides tools for the estimation of indicators
+on social exclusion and poverty, as well as an implementation of Pareto tail
+modeling for empirical income distributions.")
+ (license license:gpl2+)))
+
+(define-public r-vcd
+ (package
+ (name "r-vcd")
+ (version "1.4-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "vcd" version))
+ (sha256
+ (base32
+ "05azric2w8mrsdk7y0484cjygcgcmbp96q2v500wvn91fj98kkhp"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-colorspace" ,r-colorspace)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)))
+ (home-page "http://cran.r-project.org/web/packages/vcd/")
+ (synopsis "Visualizing categorical data")
+ (description "This package provides visualization techniques, data sets,
+summary and inference procedures aimed particularly at categorical data.
+Special emphasis is given to highly extensible grid graphics. The package was
+originally inspired by the book \"Visualizing Categorical Data\" by Michael
+Friendly and is now the main support package for a new book, \"Discrete Data
+Analysis with R\" by Michael Friendly and David Meyer (2015).")
+ (license license:gpl2)))
HCoop / jackhill / guix / guix.git / blobdiff