diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 362 |
1 files changed, 362 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f0d819df7..3bd0d664da 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -118,6 +118,51 @@ experiment that allows a generic to warn if any arguments passed in @code{...} are not used.") (license license:gpl3))) +(define-public r-grr + (package + (name "r-grr") + (version "0.9.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "grr" version)) + (sha256 + (base32 + "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/grr") + (synopsis "Alternative implementations of base R functions") + (description + "This package provides alternative implementations of some base R +functions, including @code{sort}, @code{order}, and @code{match}. The +functions are simplified but can be faster or have other advantages.") + (license license:gpl3))) + +(define-public r-matrix-utils + (package + (name "r-matrix-utils") + (version "0.9.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "Matrix.utils" version)) + (sha256 + (base32 + "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va")))) + (properties `((upstream-name . "Matrix.utils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-grr" ,r-grr) + ("r-matrix" ,r-matrix))) + (home-page "https://github.com/cvarrichio/Matrix.utils") + (synopsis + "Data.frame-Like Operations on Sparse and Dense Matrix Objects") + (description + "This package implements data manipulation methods such as @code{cast}, +@code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like +objects.") + (license license:gpl3))) + (define-public r-sys (package (name "r-sys") @@ -822,6 +867,121 @@ this gives the user direct access to the file system without the need to well as file saving is available.") (license license:gpl2+))) +;; The package sources include minified variants of d3.js and non-minified +;; source code of d3-jetpack. +(define-public r-d3r + (package + (name "r-d3r") + (version "0.8.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "d3r" version)) + (sha256 + (base32 + "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/www/d3/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "d3.v3.js") + "v3/dist/d3.min.js") + (,(assoc-ref inputs "d3.v4.js") + "v4/dist/d3.min.js") + (,(assoc-ref inputs "d3.v5.js") + "v5/dist/d3.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-htmltools" ,r-htmltools) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("d3.v3.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))) + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) + ("d3.v5.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v5.js") + (sha256 + (base32 + "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) + (home-page "https://github.com/timelyportfolio/d3r") + (synopsis "d3.js utilities for R") + (description + "This package provides a suite of functions to help ease the use of the +d3.js visualization library in R. These helpers include +@code{htmltools::htmlDependency} functions, hierarchy builders, and conversion +tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame} +R objects into the JSON format that the d3.js library expects.") + (license license:bsd-3))) + +;; We use the latest commit here because the last release was in 2016 while +;; the latest commit was in 2018. +(define-public r-sankeyd3 + (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc") + (revision "1")) + (package + (name "r-sankeyd3") + (version (git-version "0.3.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fbreitwieser/sankeyD3.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-d3r" ,r-d3r) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-shiny" ,r-shiny) + ("r-magrittr" ,r-magrittr))) + (home-page "https://github.com/fbreitwieser/sankeyD3") + (synopsis "Sankey network graphs from R") + (description + "This package provides an R library to generate Sankey network graphs +in R and Shiny via the D3 visualization library.") + ;; The R code is licensed under GPLv3+. It includes the non-minified + ;; JavaScript source code of d3-sankey, which is released under the + ;; 3-clause BSD license. + (license (list license:gpl3+ license:bsd-3))))) + (define-public r-crosstalk (package (name "r-crosstalk") @@ -8675,6 +8835,29 @@ package provides a minimal R interface by relying on the Rcpp package.") ;; hnswlib is released under Version 2.0 of the Apache License. (license (list license:gpl3 license:asl2.0)))) +(define-public r-rcppparallel + (package + (name "r-rcppparallel") + (version "4.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppParallel" version)) + (sha256 + (base32 + "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s")))) + (properties `((upstream-name . "RcppParallel"))) + (build-system r-build-system) + (home-page "http://rcppcore.github.io/RcppParallel") + (synopsis "Parallel programming tools for Rcpp") + (description + "This package provides high level functions for parallel programming with +Rcpp. For example, the @code{parallelFor()} function can be used to convert +the work of a standard serial @code{for} loop into a parallel one and the +@code{parallelReduce()} function can be used for accumulating aggregates or +other values.") + (license license:gpl2))) + (define-public r-ncdf4 (package (name "r-ncdf4") @@ -9279,6 +9462,29 @@ only sparse real matrices in Matrix package format are supported.") ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) +(define-public r-speedglm + (package + (name "r-speedglm") + (version "0.3-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "speedglm" version)) + (sha256 + (base32 + "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/speedglm") + (synopsis "Fit linear and generalized linear models to large data sets") + (description + "This package provides tools for fitting linear models and generalized +linear models to large data sets by updating algorithms.") + ;; Any version of the GPL + (license license:gpl2+))) + (define-public r-densityclust (package (name "r-densityclust") @@ -14199,6 +14405,25 @@ Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of the functions can also be applied to other types of categorical data.") (license license:gpl2))) +(define-public r-pbmcapply + (package + (name "r-pbmcapply") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbmcapply" version)) + (sha256 + (base32 + "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz")))) + (build-system r-build-system) + (home-page "https://github.com/kvnkuang/pbmcapply") + (synopsis "Track the progress of apply procedures with a progress bar") + (description + "This light-weight package helps you track and visualize the progress of +parallel versions of vectorized R functions of the @code{mc*apply} family.") + (license license:expat))) + (define-public r-blme (package (name "r-blme") @@ -14530,3 +14755,140 @@ including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) + +(define-public r-umap + (package + (name "r-umap") + (version "0.2.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "umap" version)) + (sha256 + (base32 + "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-reticulate" ,r-reticulate) + ("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/tkonopka/umap") + (synopsis "Uniform manifold approximation and projection") + (description + "Uniform manifold approximation and projection is a technique for +dimension reduction. This package provides an interface to the UMAP algorithm +in R, including a translation of the original algorithm into R.") + (license license:expat))) + +(define-public r-uwot + (package + (name "r-uwot") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "uwot" version)) + (sha256 + (base32 + "1mq6qi8q9xslh1b99srj480s2a08pfv4bs9m2ykyijj44j9fcdj9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dqrng" ,r-dqrng) + ("r-fnn" ,r-fnn) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rcppprogress" ,r-rcppprogress) + ("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/jlmelville/uwot") + (synopsis "Uniform manifold approximation and projection") + (description + "This package provides an implementation of the Uniform Manifold +Approximation and Projection dimensionality reduction by McInnes et +al. (2018). It also provides means to transform new data and to carry out +supervised dimensionality reduction. An implementation of the related +LargeVis method of Tang et al. (2016) is also provided.") + (license license:gpl3))) + +(define-public r-kableextra + (package + (name "r-kableextra") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kableExtra" version)) + (sha256 + (base32 + "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) + (properties `((upstream-name . "kableExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-readr" ,r-readr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-rvest" ,r-rvest) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-viridislite" ,r-viridislite) + ("r-webshot" ,r-webshot) + ("r-xml2" ,r-xml2))) + (home-page "https://haozhu233.github.io/kableExtra/") + (synopsis "Construct complex tables with pipe syntax") + (description + "Build complex HTML or LaTeX tables using @code{kable()} from +@code{knitr} and the piping syntax from @code{magrittr}. The function +@code{kable()} is a light weight table generator coming from @code{knitr}. +This package simplifies the way to manipulate the HTML or LaTeX codes +generated by @code{kable()} and allows users to construct complex tables and +customize styles using a readable syntax.") + (license license:expat))) + +(define-public r-glasso + (package + (name "r-glasso") + (version "1.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "glasso" version)) + (sha256 + (base32 + "0nshpx14v2yny7lr8ll6nnz71n0f02sddh2c2dglfprbk89p9yp6")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://www-stat.stanford.edu/~tibs/glasso") + (synopsis "Graphical Lasso: estimation of Gaussian graphical models") + (description + "This is a package for estimation of a sparse inverse covariance matrix +using a lasso (L1) penalty. Facilities are provided for estimates along a +path of values for the regularization parameter.") + (license license:gpl2))) + +(define-public r-rhpcblasctl + (package + (name "r-rhpcblasctl") + (version "0.18-205") + (source + (origin + (method url-fetch) + (uri (cran-uri "RhpcBLASctl" version)) + (sha256 + (base32 + "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp")))) + (properties `((upstream-name . "RhpcBLASctl"))) + (build-system r-build-system) + (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/") + (synopsis "Control the number of threads on BLAS") + (description + "This package allows you to control the number of threads the BLAS +library uses. It is also possible to control the number of threads in +OpenMP.") + (license license:agpl3+))) |