diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 904 |
1 files changed, 797 insertions, 107 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8709cd21fa..2e7e9041c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,7 +33,6 @@ ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> -;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -351,6 +350,54 @@ easier.") for authoring journal articles and conference submissions.") (license license:gpl3))) +(define-public r-benchmarkmedata + (package + (name "r-benchmarkmedata") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkmeData" version)) + (sha256 + (base32 + "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/csgillespie/benchmarkme-data") + (synopsis "Data set for the @code{benchmarkme} package") + (description "This package contains the data set for the crowd-sourced +benchmarks from running the @code{benchmarkme} package.") + (license license:gpl2+))) + +(define-public r-benchmarkme + (package + (name "r-benchmarkme") + (version "1.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkme" version)) + (sha256 + (base32 + "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-benchmarkmedata" ,r-benchmarkmedata) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-tibble" ,r-tibble))) + (home-page "https://csgillespie.github.io/benchmarkme/") + (synopsis "Crowd-sourced system benchmarks") + (description "This package provides functionality to benchmark your CPU +and compare against other CPUs. Also provides functions for obtaining system +specifications, such as RAM, CPU type, and R version.") + (license license:gpl2+))) + (define-public r-bezier (package (name "r-bezier") @@ -671,6 +718,28 @@ provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) +(define-public r-pacman + (package + (name "r-pacman") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pacman" version)) + (sha256 + (base32 + "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-remotes" ,r-remotes))) + (home-page "https://github.com/trinker/pacman") + (synopsis "Package Management Tool") + (description "This package provides tools to more conveniently perform +tasks associated with add-on packages. @code{pacman} conveniently wraps +library and package related functions and names them in an intuitive and +consistent fashion. It seeks to combine functionality from lower level +functions which can speed up workflow.") + (license license:gpl2))) + (define-public r-pheatmap (package (name "r-pheatmap") @@ -1130,6 +1199,29 @@ without affecting the current R process at all. This package does exactly that.") (license license:expat))) +(define-public r-depmixs4 + (package + (name "r-depmixs4") + (version "1.5-0") + (source (origin + (method url-fetch) + (uri (cran-uri "depmixS4" version)) + (sha256 + (base32 + "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) + (propagated-inputs + `(("r-nnet" ,r-nnet) + ("r-nlme" ,r-nlme) + ("r-mass" ,r-mass) + ("r-rsolnp" ,r-rsolnp))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/depmixS4/") + (synopsis "Dependent Mixture Models") + (description "This package fits latent (hidden) Markov models on mixed +categorical and continuous (time series) data, otherwise known as dependent +mixture models.") + (license license:gpl2+))) + (define-public r-readxl (package (name "r-readxl") @@ -1157,6 +1249,36 @@ the embedded @code{RapidXML} C++ library.") ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) +(define-public r-model4you + (package + (name "r-model4you") + (version "0.9-7") + (source (origin + (method url-fetch) + (uri (cran-uri "model4you" version)) + (sha256 + (base32 + "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-partykit" ,r-partykit) + ("r-sandwich" ,r-sandwich) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/model4you/") + (synopsis "Stratified and personalised models based on trees and forests") + (description + "This package provides procedures for model-based trees for subgroup +analyses in clinical trials and model-based forests for the estimation and +prediction of personalised treatment effects. Currently partitioning of linear +models, @code{lm()}, generalised linear models, @code{glm()}, and +Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is +supported for the trees and a test for parameter heterogeneity is provided for +the personalised models.") + (license license:gpl2+))) + (define-public r-modelr (package (name "r-modelr") @@ -1204,6 +1326,28 @@ and make inference with discrete time and discrete space hidden Markov models.") (license license:gpl2+))) +(define-public r-hiddenmarkov + (package + (name "r-hiddenmarkov") + (version "1.8-13") + (source (origin + (method url-fetch) + (uri (cran-uri "HiddenMarkov" version)) + (sha256 + (base32 + "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") + (synopsis "Hidden markov models for R") + (description "This package contains functions for the analysis of Discrete +Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated +Poisson Process. It includes functions for simulation, parameter estimation, +and the Viterbi algorithm. The algorithms are based of those of Walter +Zucchini.") + (license license:gpl2+))) + (define-public r-httpuv (package (name "r-httpuv") @@ -1307,6 +1451,29 @@ documents that can be converted to HTML files (e.g., R Markdown) under a given directory.") (license license:expat))) +(define-public r-howmany + (package + (name "r-howmany") + (version "0.3-1") + (source (origin + (method url-fetch) + (uri (cran-uri "howmany" version)) + (sha256 + (base32 + "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/howmany/") + (synopsis "Lower bound for the number of correct rejections") + (description "When testing multiple hypotheses simultaneously, this package +provides functionality to calculate a lower bound for the number of correct +rejections (as a function of the number of rejected hypotheses), which holds +simultaneously -with high probability- for all possible number of rejections. +As a special case, a lower bound for the total number of false null hypotheses +can be inferred. Dependent test statistics can be handled for multiple tests +of associations. For independent test statistics, it is sufficient to provide +a list of p-values.") + (license license:gpl2+))) + (define-public r-htmltools (package (name "r-htmltools") @@ -2894,6 +3061,26 @@ attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) +(define-public r-pvclust + (package + (name "r-pvclust") + (version "2.2-0") + (source (origin + (method url-fetch) + (uri (cran-uri "pvclust" version)) + (sha256 + (base32 + "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq")))) + (build-system r-build-system) + (home-page "https://github.com/shimo-lab/pvclust") + (synopsis + "Hierarchical clustering with P-values via multiscale bootstrap resampling") + (description "This package provides an implementation of multiscale bootstrap +resampling for assessing the uncertainty in hierarchical cluster analysis. It +provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) +value for each cluster in a dendrogram.") + (license license:gpl2+))) + (define-public r-rcpp (package (name "r-rcpp") @@ -2939,6 +3126,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see safely be interrupted from R.") (license license:expat))) +(define-public r-rcppnumerical + (package + (name "r-rcppnumerical") + (version "0.4-0") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppNumerical" version)) + (sha256 + (base32 + "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/yixuan/RcppNumerical") + (synopsis"Numerical computing libraries integration with @code{Rcpp}") + (description "This package provides a collection of libraries for numerical +computing (numerical integration, optimization, etc.) and their integration +with @code{Rcpp}.") + (license license:gpl2+))) + (define-public r-bindr (package (name "r-bindr") @@ -3288,6 +3496,25 @@ statistical functions and other utilities to ease their usage.") quantities.") (license license:expat))) +(define-public r-princurve + (package + (name "r-princurve") + (version "2.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "princurve" version)) + (sha256 + (base32 + "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rcannood/princurve") + (synopsis "Fit a principal curve in arbitrary dimension") + (description "This package provides procedures for fitting a principal +curve to a data matrix in arbitrary dimensions.") + (license license:gpl2))) + (define-public r-reshape (package (name "r-reshape") @@ -3584,14 +3811,14 @@ which should be seen for details.") (define-public r-extremes (package (name "r-extremes") - (version "2.1") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid")))) + "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs @@ -3653,13 +3880,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.18") + (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0fpcfwbhfg1lhkqc0gdqv2sq64r3ljld7piy34vv0nimq30xi2fc")))) + "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -3843,14 +4070,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-3") + (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp")))) + "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -5058,6 +5285,44 @@ 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))) +(define-public r-vcfr + (package + (name "r-vcfr") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (cran-uri "vcfR" version)) + (sha256 + (base32 + "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-memuse" ,r-memuse) + ("r-pinfsc50" ,r-pinfsc50) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vegan" ,r-vegan) + ("r-viridislite" ,r-viridislite))) + (home-page "https://github.com/knausb/vcfR") + (synopsis "Manipulate and visualize VCF data") + (description "This package facilitates easy manipulation of variant call +format (VCF) data. Functions are provided to rapidly read from and write to +VCF files. Once VCF data is read into R, a parser function extracts matrices +of data. This information can then be used for quality control or other +purposes. Additional functions provide visualization of genomic data. Once +processing is complete data may be written to a VCF file. It also may be +converted into other popular R objects. This package provides a link between +VCF data and familiar R software.") + (license license:gpl3))) + (define-public r-ica (package (name "r-ica") @@ -5535,6 +5800,25 @@ columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) +(define-public r-pinfsc50 + (package + (name "r-pinfsc50") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "pinfsc50" version)) + (sha256 + (base32 + "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pinfsc50/") + (synopsis "Genomic data for the plant pathogen Phytophthora infestans") + (description "This package contains genomic data for the plant pathogen +Phytophthora infestans. It includes a variant file, a sequence file and an +annotation file. This package is intended to be used as example data for +packages that work with genomic data.") + (license license:gpl2+))) + (define-public r-uuid (package (name "r-uuid") @@ -5557,14 +5841,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p")))) + "17y20kb5xgmz77n4rrkqmcm0cnjwfi4mn84h6zabij76b8cjiykh")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -6280,6 +6564,30 @@ fixed values. Other functions include a custom @code{geom}, and helper functions to enforce symmetric scales or add tags to facetted plots.") (license license:gpl3))) +(define-public r-heatmap3 + (package + (name "r-heatmap3") + (version "1.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmap3" version)) + (sha256 + (base32 + "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fastcluster" ,r-fastcluster))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/heatmap3/") + (synopsis "Improved heatmap package") + (description + "This package provides an improved heatmap package. It is completely +compatible with the original R function @code{heatmap}, and provides more +powerful and convenient features.") + (license license:gpl2+))) + (define-public r-heatmaply (package (name "r-heatmaply") @@ -6561,14 +6869,14 @@ and within plot factors interact.") (define-public r-signal (package (name "r-signal") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 - "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) + "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,gfortran))) @@ -6948,14 +7256,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i")))) + "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -7882,14 +8190,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.4.2") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2")))) + "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -8064,14 +8372,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb")))) + "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -8316,14 +8624,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1zkifkj2qg9vdv26z4qvi81qv9l1cqyrq3ihdpacpax80plkgdln")))) + "0af15kqz4kiyi5p4qi748hvdw462vdwigzyykh1k7vj6gacn2xqf")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8913,13 +9221,13 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.10.1") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx")))) + (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) @@ -8931,7 +9239,10 @@ based on index arrays and simple triplet representations, respectively.") ("r-knitr" ,r-knitr) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs) ("r-webshot" ,r-webshot))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description @@ -10261,14 +10572,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "07iw3faprf98mncymbjbmfm2yi294yiwdg30xlql5sfx12qbf6r0")))) + "02sh1q6f2ik56w348pfkg4a8jvdn3a31r7d8mzg7zq3sv7lmvqwl")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -10497,14 +10808,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0msr24ymnazpaz8s9qs5v3xn1i9984p98lr9x4qq9cxgx34rm9h0")))) + "1qr51mag5wf44h4sygkn5arsirpqdanf039cg6fxmyw83k51fi2v")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -10581,14 +10892,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.4-1") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb")))) + "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -10608,13 +10919,13 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.7") + (version "2.8.8") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0")))) + (base32 "050aarycgzy1n8ad67pj09s8k7s7xk6dicg0kjg0ivlkyyq0shqz")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -11187,14 +11498,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.9") + (version "4.1.12") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30")))) + "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -11301,21 +11612,21 @@ al. (2016)).") (define-public r-weights (package (name "r-weights") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 - "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5")))) + "1sq8ls5idspddn8m2c8n2107lgx53kbach8vgjrhqx1mc6xfvrvw")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-hmisc" ,r-hmisc) + ("r-lme4" ,r-lme4) ("r-mice" ,r-mice))) - (home-page - "https://cran.r-project.org/web/packages/weights/") + (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial @@ -11531,13 +11842,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.12.0") + (version "1.13.1") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6")))) + (base32 "0zi7yixz3hvqvb5fxipkxprk5p4irr61csd3k6scsxqyhrb5ffls")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) @@ -11548,7 +11859,8 @@ isosurfaces.") ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm) - ("r-plot3d" ,r-plot3d))) + ("r-plot3d" ,r-plot3d) + ("r-pracma" ,r-pracma))) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description @@ -11997,13 +12309,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6")))) + (base32 "0bqsb0zplkqkx2mp8kpanadkds4kwwvdrc07lp0qzwqqzaxq5xa3")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -12385,6 +12697,89 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) +(define-public r-rncl + (package + (name "r-rncl") + (version "0.8.4") + (source (origin + (method url-fetch) + (uri (cran-uri "rncl" version)) + (sha256 + (base32 + "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-progress" ,r-progress) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/fmichonneau/rncl") + (synopsis "Interface to the Nexus class library") + (description "This package provides an interface to the Nexus class +library which allows parsing of NEXUS, Newick and other phylogenetic tree + file formats. It provides elements of the file that can be used to build + phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s +@code{phylo4(d)}. This functionality is demonstrated with +@code{read_newick_phylo()} and @code{read_nexus_phylo()}.") + (license license:bsd-2))) + +(define-public r-phylobase + (package + (name "r-phylobase") + (version "0.8.10") + (source (origin + (method url-fetch) + (uri (cran-uri "phylobase" version)) + (sha256 + (base32 + "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-rcpp" ,r-rcpp) + ("r-rncl" ,r-rncl) + ("r-rnexml" ,r-rnexml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/fmichonneau/phylobase") + (synopsis "Base package for phylogenetic structures and comparative data") + (description "This package provides a base @code{S4} class for comparative +methods, incorporating one or more trees and trait data.") + (license license:gpl2+))) + +(define-public r-rnexml + (package + (name "r-rnexml") + (version "2.4.5") + (source (origin + (method url-fetch) + (uri (cran-uri "RNeXML" version)) + (sha256 + (base32 + "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-lazyeval" ,r-lazyeval) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr) + ("r-uuid" ,r-uuid) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/RNeXML/") + (synopsis "Semantically rich I/O for the NeXML Format") + (description "This package provides access to phyloinformatic data in +NeXML format. The package should add new functionality to R such as the +possibility to manipulate NeXML objects in more various and refined way +and compatibility with @code{ape} objects.") + (license license:bsd-3))) + (define-public r-rnifti (package (name "r-rnifti") @@ -13504,6 +13899,23 @@ Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) +(define-public r-locfdr + (package + (name "r-locfdr") + (version "1.1-8") + (source (origin + (method url-fetch) + (uri (cran-uri "locfdr" version)) + (sha256 + (base32 + "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/locfdr/") + (synopsis "Computes local false discovery rates") + (description "This package can be used to compute local false +discovery rates.") + (license license:gpl2))) + (define-public r-longitudinal (package (name "r-longitudinal") @@ -15493,14 +15905,26 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-7") - (source - (origin - (method url-fetch) - (uri (cran-uri "spdep" version)) - (sha256 - (base32 - "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1")))) + (version "1.1-8") + (source (origin + (method url-fetch) + (uri (cran-uri "spdep" version)) + (sha256 + (base32 + "1k82vx58kpn0fwgcpxq2jc3qfffl8wzbgr4cdkxihrfk28kkqh7l")) + (snippet + '(for-each delete-file '("inst/doc/nb_igraph.html" + "inst/doc/nb_igraph.R" + "inst/doc/nb_igraph.Rmd" + "inst/doc/sids.html" + "inst/doc/sids.R" + "inst/doc/nb.html" + "inst/doc/nb.R" + "inst/doc/CO69.html" + "inst/doc/CO69.R" + "inst/doc/nb_sf.html" + "inst/doc/nb_sf.R" + "inst/doc/nb_sf.Rmd"))))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -17249,6 +17673,116 @@ making it possible to download files over HTTPS across platforms. The external dependencies. This package has is implemented purely in R.") (license license:gpl2))) +(define-public r-aplot + (package + (name "r-aplot") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "aplot" version)) + (sha256 + (base32 + "08kqrm9r57l8zgij897wpp428l4i50qfhp7y78r3pk5pjz37bsan")))) + (properties `((upstream-name . "aplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-patchwork" ,r-patchwork))) + (home-page "https://github.com/YuLab-SMU/aplot") + (synopsis "Decorate a ggplot with associated information") + (description + "Users may want to align plots with associated information that requires +axes to be exactly matched in subplots, e.g. hierarchical clustering with a +heatmap. This package provides utilities to align associated subplots to a +main plot at different sides (left, right, top and bottom) with axes exactly +matched.") + (license license:artistic2.0))) + +(define-public r-ggnewscale + (package + (name "r-ggnewscale") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggnewscale" version)) + (sha256 + (base32 + "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702")))) + (properties `((upstream-name . "ggnewscale"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://cran.r-project.org/package=ggnewscale") + (synopsis "Multiple fill and color scales in ggplot2") + (description + "This package lets you use multiple fill and color scales in ggplot2.") + (license license:gpl3))) + +(define-public r-ggpointdensity + (package + (name "r-ggpointdensity") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpointdensity" version)) + (sha256 + (base32 + "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy")))) + (properties + `((upstream-name . "ggpointdensity"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/LKremer/ggpointdensity") + (synopsis "Cross between a 2D density plot and a scatter plot") + (description + "This package provides a cross between a 2D density plot and a scatter +plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are +colored by the number of neighboring points. This is useful to visualize the +2D-distribution of points in case of overplotting.") + (license license:gpl3))) + +(define-public r-arrow + (package + (name "r-arrow") + (version "4.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "arrow" version)) + (sha256 + (base32 + "19kzfjxp90ybi1px3r93mfx59nqmnagxr4g73y7iby5blwl1bblc")))) + (properties `((upstream-name . "arrow"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-bit64" ,r-bit64) + ("r-cpp11" ,r-cpp11) + ("r-purrr" ,r-purrr) + ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/apache/arrow/") + (synopsis "R integration to Apache Arrow") + (description + "Apache Arrow is a cross-language development platform for in-memory +data. It specifies a standardized language-independent columnar memory format +for flat and hierarchical data, organized for efficient analytic operations on +modern hardware. This package provides an R interface to the Arrow C++ +library.") + (license license:asl2.0))) + (define-public r-rex (package (name "r-rex") @@ -17709,14 +18243,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn")))) + "184mzby1giismhx4brvrdfl5n5kialyvv8ik18blhchvpy145cwf")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -17765,14 +18299,14 @@ annotated biological functions.") (define-public r-plot3d (package (name "r-plot3d") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 - "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) + "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,r-misc3d))) @@ -18103,14 +18637,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp")))) + "0sv0j4sgpz8z65vhbpmaglg878jhq52srzf5rpw4vbsbys2807w1")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs @@ -18491,14 +19025,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.13.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "17dlwx9hrl6z2il14nxji0snwsf4sfbp3mv33jbpcw13sani1q81")))) + "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -19645,6 +20179,31 @@ introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) +(define-public r-rnmf + (package + (name "r-rnmf") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rNMF" version)) + (sha256 + (base32 + "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) + (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/rNMF/") + (synopsis "Robust nonnegative matrix factorization") + (description + "This package provides an implementation of robust nonnegative matrix +factorization (rNMF). The rNMF algorithm decomposes a nonnegative high +dimension data matrix into the product of two low rank nonnegative matrices, +while detecting and trimming outliers. The main function is @code{rnmf()}. +The package also includes a visualization tool, @code{see()}, that arranges +and prints vectorized images.") + (license license:gpl2+))) + (define-public r-randtoolbox (package (name "r-randtoolbox") @@ -20353,6 +20912,23 @@ modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) +(define-public r-tree + (package + (name "r-tree") + (version "1.0-40") + (source (origin + (method url-fetch) + (uri (cran-uri "tree" version)) + (sha256 + (base32 + "1rr6ws62j9h36f3nl713f8h3ndkh95mv46l055jvgmby5lw1dazz")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/tree/") + (synopsis "Classification and regression trees") + (description "This package provides procedures to work with classification +and regression trees.") + (license license:gpl2+))) + (define-public r-treeclust (package (name "r-treeclust") @@ -20563,14 +21139,14 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.8.0") + (version "2.8.7") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7")))) + "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs @@ -21026,14 +21602,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-2") + (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y")))) + "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -21360,14 +21936,14 @@ cluster stability.") (define-public r-biclust (package (name "r-biclust") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "biclust" version)) (sha256 (base32 - "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b")))) + "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp")))) (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs @@ -21922,14 +22498,14 @@ both exclusive and shared locking.") (define-public r-archivist (package (name "r-archivist") - (version "2.3.5") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "archivist" version)) (sha256 (base32 - "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k")))) + "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9")))) (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs @@ -22094,14 +22670,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.14") + (version "8.15") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) + "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -23076,14 +23652,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.17") + (version "0.8.18") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "0cd2bpc22jam1qxn6yg7yr7xdhsm0jgnm5bm2f3vg5b3c96plxk4")))) + "01bj16iggj5fggfa7n312458p8xg30zx2vzfkd8jqcchnbrphfvl")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs @@ -24880,6 +25456,26 @@ theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) +(define-public r-memuse + (package + (name "r-memuse") + (version "4.1-0") + (source (origin + (method url-fetch) + (uri (cran-uri "memuse" version)) + (sha256 + (base32 + "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq")))) + (properties `((upstream-name . "memuse"))) + (build-system r-build-system) + (home-page "https://github.com/shinra-dev/memuse") + (synopsis "Memory Estimation Utilities") + (description + "This package provides procedures to answer the following questions: +How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is +your current R session using? How much ram do you even have?") + (license license:bsd-2))) + (define-public r-metrics (package (name "r-metrics") @@ -25286,17 +25882,41 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.") (license license:gpl2+))) +(define-public r-rffc + (package + (name "r-rffc") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.r-forge.r-project.org/src/contrib/" + "rfFC_" version ".tar.gz")) + (sha256 + (base32 + "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-randomforest",r-randomforest))) + (home-page "https://r-forge.r-project.org/projects/rffc/") + (synopsis "Random Forest Feature Contributions") + (description "This package provides functions for extracting feature +contributions from a random forest model from package @code{randomForest}. +Feature contributions provide detailed information about the relationship +between data variables and the predicted value returned by random forest +model.") + (license license:gpl2))) + (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.4") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "01vgr1mpm7l1lyhril5hm1l72aicqc4iwb0b15ypijb6hwkv7g47")))) + "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs @@ -25412,6 +26032,35 @@ so that natural sort function arranges a character vector by their numbers, not digit characters.") (license license:bsd-3))) +(define-public r-visdat + (package + (name "r-visdat") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (cran-uri "visdat" version)) + (sha256 + (base32 + "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://visdat.njtierney.com/") + (synopsis "Preliminary Visualisation of Data") + (description "This package provides procedures to create preliminary exploratory +data visualisations of an entire dataset to identify problems or unexpected features +using @code{ggplot2}.") + (license license:expat))) + (define-public r-muhaz (package (name "r-muhaz") @@ -26336,14 +26985,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06")))) + "0qhdh2xdswqy94f4gkdxi1iqm0k794p9y8sdh6mgbd1a86c8ngfs")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -26351,6 +27000,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") ("r-generics" ,r-generics) ("r-globals" ,r-globals) ("r-glue" ,r-glue) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) ("r-prettyunits" ,r-prettyunits) ("r-purrr" ,r-purrr) @@ -26795,13 +27445,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p")))) + "1b1wyj4dxjn0hfg09l8z282grdgwgah0czs7pn2ian455x0dphng")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -26923,14 +27573,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj")))) + "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs @@ -27837,14 +28487,14 @@ in same length matches).") (define-public r-textshape (package (name "r-textshape") - (version "1.7.1") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 - "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa")))) + "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs @@ -28629,35 +29279,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr - (package - (name "r-samr") - (version "3.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "samr" version)) - (sha256 - (base32 - "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) - (properties `((upstream-name . "samr"))) - (build-system r-build-system) - (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://statweb.stanford.edu/~tibs/SAM/") - (synopsis "Significance analysis of Microarrays") - (description - "This is a package for significance analysis of Microarrays for -differential expression analysis, RNAseq data and related problems.") - ;; Any version of the LGPL - (license license:lgpl3+))) - (define-public r-randomforestsrc (package (name "r-randomforestsrc") @@ -28683,3 +29304,72 @@ quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) + +(define-public r-contfrac + (package + (name "r-contfrac") + (version "1.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "contfrac" version)) + (sha256 + (base32 + "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) + (properties `((upstream-name . "contfrac"))) + (build-system r-build-system) + (home-page + "https://github.com/RobinHankin/contfrac") + (synopsis "Continued Fractions") + (description + "Various utilities for evaluating continued fractions.") + (license license:gpl2))) + +(define-public r-elliptic + (package + (name "r-elliptic") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "elliptic" version)) + (sha256 + (base32 + "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) + (properties `((upstream-name . "elliptic"))) + (build-system r-build-system) + (inputs `(("pari-gp" ,pari-gp))) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page + "https://github.com/RobinHankin/elliptic") + (synopsis + "Weierstrass and Jacobi Elliptic Functions") + (description + "A suite of elliptic and related functions including Weierstrass and +Jacobi forms. Also includes various tools for manipulating and visualizing +complex functions.") + (license license:gpl2))) + +(define-public r-hypergeo + (package + (name "r-hypergeo") + (version "1.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "hypergeo" version)) + (sha256 + (base32 + "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd")))) + (properties `((upstream-name . "hypergeo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-contfrac" ,r-contfrac) + ("r-desolve" ,r-desolve) + ("r-elliptic" ,r-elliptic))) + (home-page + "https://cran.r-project.org/web/packages/hypergeo/") + (synopsis "The Gauss Hypergeometric Function") + (description + "The Gaussian hypergeometric function for complex numbers.") + (license license:gpl2))) |