diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 209 |
1 files changed, 206 insertions, 3 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 32ae4140ae..7ca7ab0f9a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> -;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> @@ -31,11 +31,11 @@ ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> -;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> -;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de> ;;; Copyright © 2022 Greg Hogan <code@greghogan.com> ;;; ;;; This file is part of GNU Guix. @@ -256,6 +256,33 @@ can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.") (license license:expat))) +(define-public r-castor + (package + (name "r-castor") + (version "1.7.6") + (source (origin + (method url-fetch) + (uri (cran-uri "castor" version)) + (sha256 + (base32 + "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36")))) + (properties `((upstream-name . "castor"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) + (home-page "https://cran.r-project.org/package=castor") + (synopsis "Efficient phylogenetics on large trees") + (description + "This tool supports analyses on massive phylogenies comprising up to +millions of tips. Functions include pruning, rerooting, calculation of +most-recent common ancestors, calculating distances from the tree root and +calculating pairwise distances. In addition, this tool takes care of +calculation of phylogenetic signal and mean trait depth (trait conservatism), +ancestral state reconstruction and hidden character prediction of discrete +characters, simulating and fitting models of trait evolution, fitting and +simulating diversification models, dating trees, comparing trees, and +reading/writing trees in Newick format.") + (license license:gpl2+))) + (define-public r-collections (package (name "r-collections") @@ -717,6 +744,57 @@ differential abundance analysis of zero-inflated high-dimensional compositional data.") (license license:gpl3))) +(define-public r-gwidgets2 + (package + (name "r-gwidgets2") + (version "1.0-9") + (source (origin + (method url-fetch) + (uri (cran-uri "gWidgets2" version)) + (sha256 + (base32 + "1ifljpdazzmwf3mgkg9g76365n2cmw8dd3da161fpvw84xxyznfl")))) + (properties `((upstream-name . "gWidgets2"))) + (build-system r-build-system) + (propagated-inputs (list r-digest)) + (home-page "https://github.com/gWidgets3/gWidgets2") + (synopsis "Rewrite of gWidgets API for simplified GUI construction") + (description + "This package provides a re-implementation of the @code{gWidgets} API. +The API is defined in this package. A second, toolkit-specific package is +required to use it.") + (license license:gpl3+))) + +(define-public r-gwidgets2tcltk + (package + (name "r-gwidgets2tcltk") + (version "1.0-8") + (source (origin + (method url-fetch) + (uri (cran-uri "gWidgets2tcltk" version)) + (sha256 + (base32 + "02ic4avpa33dnqsnm1mzg7ci1psngk1p169pqf259szf6v39qf8h")))) + (properties `((upstream-name . "gWidgets2tcltk"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'start-x-server + (lambda _ + ;; Tests require a running X server. + (system "Xvfb :1 +extension GLX &") + (setenv "DISPLAY" ":1")))))) + (propagated-inputs (list r-digest r-gwidgets2 r-memoise)) + (native-inputs + (list xorg-server-for-tests)) + (home-page "https://github.com/jverzani/gWidgets2tcltk") + (synopsis "Toolkit implementation of gWidgets2 for tcltk") + (description "This package is a port of the @code{gWidgets2} API for the +@code{tcltk} package.") + (license license:gpl2+))) + (define-public r-ids (package (name "r-ids") @@ -3202,6 +3280,30 @@ rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.") (license license:expat))) +(define-public r-jqr + (package + (name "r-jqr") + (version "1.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "jqr" version)) + (sha256 + (base32 + "1a91zcjxdilhqdyr2lipnwc35f90h0wyqlbg0vw9ay7sq6llxgs9")))) + (properties `((upstream-name . "jqr"))) + (build-system r-build-system) + (inputs (list jq)) + (propagated-inputs (list r-lazyeval r-magrittr)) + (native-inputs (list pkg-config)) + (home-page "https://docs.ropensci.org/jqr/") + (synopsis "R client for jq, a JSON Processor") + (description + "This package provides an R client for @command{jq}, a JSON processor. +@command{jq} allows the following with JSON data: index into, parse, do +calculations, cut up and filter, change key names and values, perform +conditionals and comparisons, and more.") + (license license:expat))) + (define-public r-sass (package (name "r-sass") @@ -9190,6 +9292,27 @@ facilitate data exploration.") experimental designs and random samples for common sampling designs.") (license license:expat))) +(define-public r-roptim + (package + (name "r-roptim") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "roptim" version)) + (sha256 + (base32 + "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) + (properties `((upstream-name . "roptim"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (home-page "https://github.com/ypan1988/roptim/") + (synopsis "General purpose optimization in R using C++") + (description + "This package performs optimization in R using C++. A unified wrapper +interface is provided to call C functions of the five optimization algorithms +(Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.") + (license license:gpl2+))) + (define-public r-base64url (package (name "r-base64url") @@ -9217,6 +9340,34 @@ with a simple base32 encoder/decoder suited for case insensitive file systems.") (license license:gpl3))) +(define-public r-baseline + (package + (name "r-baseline") + (version "1.3-4") + (source (origin + (method url-fetch) + (uri (cran-uri "baseline" version)) + (sha256 + (base32 + "1kl68zvyi2zd73jy3axrvrymwn4y6l4pd62nz0fciwbgkjhz3yyx")))) + (properties `((upstream-name . "baseline"))) + (build-system r-build-system) + (propagated-inputs + (list r-gwidgets2tcltk ;for GUI + r-limsolve + r-sparsem)) + (home-page "https://github.com/khliland/baseline/") + (synopsis "Baseline correction of spectra") + (description + "This package is a collection of baseline correction algorithms. Beside +those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline +algorithm parameters. Typical use is the removal of the background effects from +spectra, which are originating from various types of spectroscopy and spectrometry. +Also, there is a possibility of optimizing this with regard to regression or +classification results. Correction methods include polynomial fitting, weighted +local smoothers and many more.") + (license license:gpl2))) + (define-public r-radiant-data (package (name "r-radiant-data") @@ -10228,6 +10379,28 @@ Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.") (license license:gpl3+))) +(define-public r-rapiclient + (package + (name "r-rapiclient") + (version "0.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "rapiclient" version)) + (sha256 + (base32 + "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) + (properties `((upstream-name . "rapiclient"))) + (build-system r-build-system) + (propagated-inputs + (list r-httr r-jsonlite r-yaml)) + (home-page "https://github.com/bergant/rapiclient") + (synopsis "Dynamic OpenAPI/Swagger client") + (description + "This package lets you access services specified in OpenAPI (formerly +Swagger) format. It is not a code generator. The client is generated +dynamically as a list of R functions.") + (license license:expat))) + (define-public r-rappdirs (package (name "r-rappdirs") @@ -15178,6 +15351,36 @@ isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) +(define-public r-missforest + (package + (name "r-missforest") + (version "1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "missForest" version)) + (sha256 + (base32 + "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21")))) + (properties `((upstream-name . "missForest"))) + (build-system r-build-system) + (propagated-inputs + (list r-dorng + r-foreach + r-iterators + r-itertools + r-randomforest)) + (home-page "https://github.com/stekhoven/missForest") + (synopsis "Nonparametric missing value imputation using Random Forest") + (description + "The function @code{missForest} in this package is used to impute missing +values, particularly in the case of mixed-type data. It uses a random forest +trained on the observed values of a data matrix to predict the missing values. +It can be used to impute continuous and/or categorical data, including complex +interactions and non-linear relations. It yields an @acronym{OOB, out-of-bag} +imputation error estimate without the need of a test set or elaborate cross- +validation. It can be run in parallel to save computation time.") + (license license:gpl2+))) + (define-public r-ks (package (name "r-ks") |