diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1111 |
1 files changed, 831 insertions, 280 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 53c49e3ac7..199bc69c03 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -102,6 +102,7 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages ssh) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) @@ -438,14 +439,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.7.1") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "1jn22qv0s6nbfih3n249v9ynl7s4m102wyw1rnkmxjwryz8vr73p")))) + "18i27mmf3z8a3wa49k8jjcs17nd0h4gmmjybbnaihyqm6r7yv8qk")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs @@ -722,6 +723,26 @@ dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.") (license license:agpl3))) +(define-public r-ggfittext + (package + (name "r-ggfittext") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (cran-uri "ggfittext" version)) + (sha256 + (base32 + "06xfv552nhw13wc8dixyqhhmw5zh8hphrabw090nzb33cpfwzin8")))) + (properties `((upstream-name . "ggfittext"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi)) + (native-inputs (list r-knitr)) + (home-page "https://wilkox.org/ggfittext/") + (synopsis "Ggfittext is a ggplot2 extension for fitting text into boxes") + (description + "Ggfittext is a ggplot2 extension for fitting text into boxes.") + (license license:gpl2))) + (define-public r-glmpca (package (name "r-glmpca") @@ -747,14 +768,14 @@ such as counts or binary matrices.") (define-public r-googledrive (package (name "r-googledrive") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "googledrive" version)) (sha256 (base32 - "0x2biilbphh77p7cxp2cvinjx45hnb5xksw775nwksqvpwxkaw0d")))) + "10pv70nvsqh1yc12g5fj7avfihjzpj02m8s9f8sb0c1np9s4z2qb")))) (properties `((upstream-name . "googledrive"))) (build-system r-build-system) (propagated-inputs @@ -982,14 +1003,14 @@ pronounceable identifiers.") (define-public r-googlesheets4 (package (name "r-googlesheets4") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "googlesheets4" version)) (sha256 (base32 - "1jcfih6f62phj7fdvknkkj46s9cvsnhshvkglg6xif7mpr1mbqah")))) + "1kzwhs9zrx1i4kqhdqrkzyhnwx25j8j2pcg7ja2dxfalihs67k65")))) (properties `((upstream-name . "googlesheets4"))) (build-system r-build-system) (propagated-inputs @@ -1419,15 +1440,17 @@ similar rank-based tests for equal probability distributions due to Neuhauser (define-public r-v8 (package (name "r-v8") - (version "4.3.0") + (version "4.3.2") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1l70vdqcagp9cdyxa231gk33z5blsg96j0l28zbaklnhmr7mqfby")))) - (properties `((upstream-name . "V8"))) + "0w5n9dv9bbaqzjcnsgw1bxpbx8yqzsbrkr8j6bfc4f78bac2si0k")))) + (properties + `((upstream-name . "V8") + (updater-extra-inputs . ("libnode")))) (build-system r-build-system) (arguments `(#:phases @@ -2053,13 +2076,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "1zvq580vi1h2afdgxaqabjhfsphvmdchwiaahqvvhljxmpmh82q6")))) + "1j504pvhxvl9cfagsjcsw7rbc94q5ysh1f8qhb7hzpx04fpnm65a")))) (build-system r-build-system) (propagated-inputs (list r-confintr @@ -2144,14 +2167,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gprofiler2 (package (name "r-gprofiler2") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 - "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g")))) + "1zbfvpb4qqj6vipz0ps4pyy14h6rc4jaqfa8q4zrbhi5vvw9805r")))) (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs @@ -2164,7 +2187,7 @@ organisms via the @code{g:Profiler} toolkit.") r-rcurl r-tidyr r-viridislite)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/gprofiler2/") (synopsis "Interface to the g:Profiler toolset") (description @@ -2262,16 +2285,37 @@ provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) +(define-public r-swagger + (package + (name "r-swagger") + (version "3.33.1") + (source (origin + (method url-fetch) + (uri (cran-uri "swagger" version)) + (sha256 + (base32 + "1ldgmy5vjzd11z5yl5a518wkw6y0l469b2zf0lp12hk19jq6k0sj")))) + (properties `((upstream-name . "swagger"))) + (build-system r-build-system) + (home-page "https://github.com/rstudio/swagger") + (synopsis + "Dynamically generate documentation from a Swagger-compliant API") + (description + "This package provides a collection of HTML, JavaScript, and CSS assets +that dynamically generate beautiful documentation from a Swagger compliant +API.") + (license license:asl2.0))) + (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")))) + (method url-fetch) + (uri (cran-uri "pacman" version)) + (sha256 + (base32 + "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) (build-system r-build-system) (propagated-inputs (list r-remotes)) @@ -2387,6 +2431,54 @@ extends the signature of the @code{dist} function and uses the same parameter naming conventions as distance methods of existing R packages.") (license license:gpl2+))) +(define-public r-paramhelpers + (package + (name "r-paramhelpers") + (version "1.14.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ParamHelpers" version)) + (sha256 + (base32 + "088sl3az4ysq8cyw82brdn9xm5yy7rqskxih462d1m5hi62gyl04")))) + (properties `((upstream-name . "ParamHelpers"))) + (build-system r-build-system) + (propagated-inputs (list r-backports r-bbmisc r-checkmate r-fastmatch)) + (home-page "https://paramhelpers.mlr-org.com") + (synopsis + "Helpers for parameters in black-box optimization, tuning, and machine learning") + (description + "This is a package for parameter description and operations in +optimization, tuning and machine learning. Parameters can be described (type, +constraints, defaults, etc.), combined to parameter sets and can in general be +programmed on. A useful @code{OptPath} object (archive) to log function +evaluations is also provided.") + (license license:bsd-2))) + +(define-public r-parallelmap + (package + (name "r-parallelmap") + (version "1.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "parallelMap" version)) + (sha256 + (base32 + "1qg7zpz5sd9jp8wzjqahkhipwj1jn192llwg06q4gv9mlcsac261")))) + (properties `((upstream-name . "parallelMap"))) + (build-system r-build-system) + (propagated-inputs (list r-bbmisc r-checkmate)) + (home-page "https://parallelmap.mlr-org.com") + (synopsis "Unified interface to parallelization backends") + (description + "This package provides a unified parallelization framework for multiple +backends. This package is designed for internal package and interactive +usage. The main operation is parallel mapping over lists. It supports local, +multicore, mpi and BatchJobs mode. It allows tagging of the parallel +operation with a level name that can be later selected by the user to switch +on parallel execution for exactly this operation.") + (license license:bsd-2))) + (define-public r-pheatmap (package (name "r-pheatmap") @@ -2484,6 +2576,40 @@ does not use formula input or special syntax, but can be used in combination with default R plot functions.") (license license:gpl2+))) +(define-public r-plumber + (package + (name "r-plumber") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "plumber" version)) + (sha256 + (base32 + "1k0y7ylc8bld16imn86g0i0dmxmr3kmh9ax4ys0yrxqzrvji7z3g")))) + (properties `((upstream-name . "plumber"))) + (build-system r-build-system) + (propagated-inputs (list r-crayon + r-ellipsis + r-httpuv + r-jsonlite + r-lifecycle + r-magrittr + r-mime + r-promises + r-r6 + r-rlang + r-sodium + r-stringi + r-swagger + r-webutils)) + (home-page "https://www.rplumber.io") + (synopsis "API generator for R") + (description + "This package gives you the ability to automatically generate and serve +an HTTP API from R functions using the annotations in the R documentation +around your functions.") + (license license:expat))) + (define-public r-polychrome (package (name "r-polychrome") @@ -2577,13 +2703,13 @@ conventions.") (define-public r-ecp (package (name "r-ecp") - (version "3.1.4") + (version "3.1.5") (source (origin (method url-fetch) (uri (cran-uri "ecp" version)) (sha256 (base32 - "0kf0kkawds86kqx3p2ahyzw9xvaz5bz51ffik3f1g5b5lwjvz60v")))) + "17m2m3nz7kqzjw2bkkp6c1a3zhwjq2c5mw9pk5g0ma274iiqj8wy")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -2903,6 +3029,28 @@ dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.") (license license:gpl2+))) +(define-public r-tidyft + (package + (name "r-tidyft") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (cran-uri "tidyft" version)) + (sha256 + (base32 + "00qcsr2sx8fwyil384vgppx0q72qjrkj7h5nv4mdxdi8f9h6ph2r")))) + (properties `((upstream-name . "tidyft"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-fst r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hope-data-science/tidyft") + (synopsis "Fast and memory efficient data operations in tidy syntax") + (description "Tidyft is an extension of @code{data.table}. It uses +modifification by reference whenever possible. This toolkit is designed for +big data analysis in high-performance desktop or laptop computers. The syntax +of the package is similar or identical to tidyverse.") + (license license:expat))) + (define-public r-tidyverse (package (name "r-tidyverse") @@ -3135,14 +3283,14 @@ mixture models.") (define-public r-readxl (package (name "r-readxl") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "04dsia2sx958ybw1ga8ccqmqih9cv7q340pcc54cl3dyqpi08wrq")))) + "0j2rkb012h0kvcm8n3817lgfir52dvmkwaxn7mij71gbxz6vpzky")))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cpp11 r-progress r-tibble)) @@ -3433,16 +3581,16 @@ Notation (JSON) using the rapidjsonr library.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.8.4") + (version "1.8.7") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "0y0jzf74c3q1sghgarvwmrkvxs7yahywd342m8c0jsr28bhapskr")))) + "07301wdpf014m8pfr7x3zwaj07pmin0rfax0irljimvj9dwbfhkx")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-r-rsp)) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description @@ -3581,13 +3729,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "5.0.0") + (version "5.0.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "1cn9b6xcc6xp2q66pkla6xrq4v6rbpxfcr3gizx4z48knp4wmwyp")))) + "19lkvy5hngdsh59slvvlrzf0iz432fv88daq0nan93zsqyf8y1dp")))) (build-system r-build-system) (arguments `(#:phases @@ -3663,13 +3811,13 @@ and vice-versa.") (define-public r-fastdummies (package (name "r-fastdummies") - (version "1.6.3") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "fastDummies" version)) (sha256 (base32 - "1pw1bpp69sbs8yc1s5ffz11q249ljfwbgfrq6irg5pyp37z38fdx")))) + "0sm02pxbabckxpi3mn36h5bz2wx5pyx7a1dhc2abc4c7fwpihsng")))) (properties `((upstream-name . "fastDummies"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-stringr r-tibble)) @@ -3911,51 +4059,66 @@ expression estimates for all genes.") (define-public r-bslib (package (name "r-bslib") - (version "0.4.2") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "069ghbzp0bsmbw2nzw28cmbym65i3a90v50y7qksy2g4pfhvfh4s")) + "05fi1cbb33hvrxx3vibbai7bzlx60jxd3iaqpc86x0224b3gpim2")) (snippet '(for-each delete-file - '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" + '("inst/components/accordion.min.js" + "inst/components/card.min.js" + "inst/components/sidebar.min.js" + "inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) (properties `((upstream-name . "bslib"))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) + (list + #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'process-javascript - (lambda* (#:key inputs #:allow-other-keys) - (with-directory-excursion "inst/lib/" - (call-with-values - (lambda () - (unzip2 - `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js" - "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") - ("bs-colorpicker/js/bootstrap-colorpicker.js" - "bs-colorpicker/js/bootstrap-colorpicker.min.js") - ("bs3/assets/javascripts/bootstrap.js" - "bs3/assets/javascripts/bootstrap.min.js") - (,(assoc-ref inputs "js-bootstrap4-bundle") - "bs4/dist/js/bootstrap.bundle.min.js") - (,(assoc-ref inputs "js-bootstrap5-bundle") - "bs5/dist/js/bootstrap.bundle.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets))))))))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + ;; See srcts/build/index.ts + (for-each (lambda (component) + (invoke "esbuild" + "--bundle" "--minify" "--sourcemap" + "--target=es6" ;"--external=:bootstrap" + (string-append + #$(this-package-native-input "typescript-components") + "/srcts/src/components/" component ".ts") + (string-append "--outfile=inst/components/" + component ".min.js"))) + '("accordion" "sidebar" "card")) + (with-directory-excursion "inst/lib/" + (call-with-values + (lambda () + (unzip2 + `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js" + "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") + ("bs-colorpicker/js/bootstrap-colorpicker.js" + "bs-colorpicker/js/bootstrap-colorpicker.min.js") + ("bs3/assets/javascripts/bootstrap.js" + "bs3/assets/javascripts/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap4-bundle") + "bs4/dist/js/bootstrap.bundle.min.js") + (,(assoc-ref inputs "js-bootstrap5-bundle") + "bs5/dist/js/bootstrap.bundle.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) (propagated-inputs (list r-base64enc r-cachem @@ -3981,7 +4144,17 @@ expression estimates for all genes.") (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.2.2/dist/js/bootstrap.bundle.js") (sha256 (base32 - "1ibfb1lwwm50did0b4fvxaqc7xyljmp20f3qb1ybdlvcy22mk8bg")))))) + "1ibfb1lwwm50did0b4fvxaqc7xyljmp20f3qb1ybdlvcy22mk8bg")))) + ("typescript-components" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rstudio/bslib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1krmavvbnpikiyxgv36vf70p8qzy1rymh1l41pjc7z74hk526p7c")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description @@ -4534,13 +4707,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.4.1") + (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "0w0kg6755kfpczqpaly251fgqv31js9gdzr17x734l2adycji3yr")))) + (base32 "1xmh0gi81xrzkgjlbxb3jl9mrj407q7ykm4wpdbmd4gdswv20y61")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs @@ -4937,19 +5110,21 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.5.2") + (version "2.5.3") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "07an4d8638m27765l6l4p6vfjxm8nfwbxx2bwpxfy6xffw1znc91")) + "1qxp0hp7clmd70383lsbiijq1i5037zv4haja60czw09mnprjncs")) (modules '((guix build utils))) (snippet ;; unvendor readstat '(delete-file-recursively "src/readstat")))) (build-system r-build-system) + (properties + '((updater-extra-inputs . ("readstat")))) (arguments '(#:phases (modify-phases %standard-phases @@ -4965,15 +5140,15 @@ including functions for geolocation and routing.") (inputs (list readstat zlib)) (native-inputs - (list r-knitr)) + (list pkg-config r-knitr)) (propagated-inputs (list r-cli r-cpp11 r-forcats r-hms r-lifecycle - r-rlang r-readr + r-rlang r-tibble r-tidyselect r-vctrs)) @@ -5298,13 +5473,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "1mjyln5njbvi0k97w8az2v5klmas6pqiz68mlylfll4nr503qzrm")))) + (base32 "1ic2zjcz29jbfwmsqsja4jjalzsz9ayac5zjz6nv482lsx2s4d13")))) (build-system r-build-system) (propagated-inputs (list r-callr @@ -5314,8 +5489,7 @@ processes. Most of its code is based on the @code{psutil} Python package.") r-prettyunits r-processx r-r6 - r-rprojroot - r-withr)) + r-rprojroot)) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description @@ -5327,14 +5501,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.3.2") + (version "1.3.2.1") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0bvbnj98b1yaiksdmfi017g2w3229a5pcsnpjamzrvpy5c1rml9m")))) + "1ckl6cqjk93n91p1i42hza6dciygsc25mibdif89vnyb7w97p651")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -5376,13 +5550,13 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.10") + (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "0inmnmi0pqmbqnl00d5yal1bmd7awigxd7sgzjsil9c1k55f4r8y")))) + (base32 "0pzssba79z90rax2v02r5m1a6ysljfnvq03r6q2nr72rd0q7qxfz")))) (build-system r-build-system) (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -5442,13 +5616,13 @@ factorization and divisive clustering for large sparse and dense matrices.") (define-public r-rcppspdlog (package (name "r-rcppspdlog") - (version "0.0.12") + (version "0.0.13") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 - (base32 "1nan0hm49xdl2l1lskm1jf01clfh7aw2v6h57j35qysvg8219fcx")))) + (base32 "1149kh047301hrp15479ikcmrix968pwqw3jza7mp7bsxhrjrp3k")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -5466,16 +5640,17 @@ functions and compiled functions callable by other packages.") (define-public r-rcppthread (package (name "r-rcppthread") - (version "2.1.3") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "RcppThread" version)) (sha256 (base32 - "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj")))) + "0rra7qqbq2y4bj54x76559p5ghpj3r03c4vlpg96phwafwnc2y8m")))) (properties `((upstream-name . "RcppThread"))) (build-system r-build-system) + (native-inputs (list r-r-rsp)) (home-page "https://github.com/tnagler/RcppThread") (synopsis "R threading in C++") @@ -5706,13 +5881,13 @@ graphics packages that comes with the base installation.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "1n38bwcr26vmiwc8jwl0mw15vwbvvkd9gi0mvsr1arzp846lkcyw")))) + "15vs8b2jxap5ya59n6pdby1p89hd0y0b4say72q6icxsjzzj979z")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs @@ -6203,13 +6378,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.6-1") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "09d3jhk7iwjfhzyq0cwws1p5gspj9nxww5x7xvngh8hr9gan5wkn")))) + (base32 "1wc8bwfqalpbsicgdrfkvmg3lm65nghf35m2g8fh4q9hr5gxpy09")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -6669,14 +6844,14 @@ classes in the @code{stats4} package.") (define-public r-emdbook (package (name "r-emdbook") - (version "1.3.12") + (version "1.3.13") (source (origin (method url-fetch) (uri (cran-uri "emdbook" version)) (sha256 (base32 - "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) + "069w10i1590bcyzv4kfsg7wsr1yl9nlsyj6yvys088xll5z4n116")))) (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) @@ -6835,6 +7010,37 @@ non-parametric analysis of structured data, and other energy statistics/methods are implemented.") (license license:gpl2+))) +(define-public r-envstats + (package + (name "r-envstats") + (version "2.8.0") + (source (origin + (method url-fetch) + (uri (cran-uri "EnvStats" version)) + (sha256 + (base32 + "17fgwa5rdjpsxk95p1j48bkpbmm01vy25vzbgggj31a1k2i4i85p")))) + (properties `((upstream-name . "EnvStats"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-mass r-nortest)) + (home-page "https://github.com/alexkowa/EnvStats") + (synopsis + "Package for environmental statistics, including US EPA guidance") + (description + "This is a package for graphical and statistical analyses of +environmental data, with a focus on analyzing chemical concentrations and +physical parameters, usually in the context of mandated environmental +monitoring. It provides major environmental statistical methods found in the +literature and regulatory guidance documents, with extensive help that +explains what these methods do, how to use them, and where to find them in the +literature. It comes with numerous built-in data sets from regulatory +guidance documents and environmental statistics literature. It includes +scripts reproducing analyses presented in the book \"EnvStats: An R Package +for Environmental Statistics\" (Millard, 2013, Springer, ISBN +978-1-4614-8455-4, +@url{https://link.springer.com/book/10.1007/978-1-4614-8456-1}).") + (license license:gpl3+))) + (define-public r-suppdists (package (name "r-suppdists") @@ -7472,14 +7678,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.3.3") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0vzvdrajkd2z4bqfr1lzh2z1vqb8h3mqk6vha8vmfhw2kz1z7acl")))) + "1z5h2hs56fw54dsvpi3sl463l31yn0qjvk779wdb7w175gwmr6db")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) @@ -7525,14 +7731,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1mhavmma0d075bbcnis9jkr4ar2dw91p44yxzx2qlskq16si2pqx")))) + "14fr17cvpy6jzdffzrf46xah70xcq2nkbjyxmkyzwbz3kvpdsxwx")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -7906,14 +8112,14 @@ impute compatibly with the substantive model.") (define-public r-pan (package (name "r-pan") - (version "1.6") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "pan" version)) (sha256 (base32 - "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) + "1vhk65j10gp9wgjj7j9nyq7wny7hkh0xa91hj47a392qq417m9yi")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") @@ -7951,23 +8157,27 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.15.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0yz88b40mpn24z40yfpxrkwrsxk362gwks3v5x69rkix1qkdsr1x")))) + "0h20lirk2257y3i1ww5y2pqp9lc21ilmf8yykmz36h55hm8jiw19")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cpp11 r-dplyr r-generics + r-glmnet r-lattice + r-mitml + r-nnet r-rcpp r-rlang + r-rpart r-tidyr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") @@ -8081,6 +8291,33 @@ University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) +(define-public r-smoof + (package + (name "r-smoof") + (version "1.6.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "smoof" version)) + (sha256 + (base32 + "1cazhnd0m5jjzixaqgqh2h3rsa2sw3k8slj5cmgm8v47aaqn91mg")))) + (properties `((upstream-name . "smoof"))) + (build-system r-build-system) + (propagated-inputs (list r-bbmisc + r-checkmate + r-ggplot2 + r-paramhelpers + r-rcpp + r-rcpparmadillo)) + (home-page "https://jakobbossek.github.io/smoof/") + (synopsis "Single and multi-objective optimization test functions") + (description + "This tool generates high number of both single- and multi-objective test +functions. These functions are frequently used for the benchmarking of +(numerical) optimization algorithms. Moreover, it offers a set of convenient +functions to generate, plot and work with objective functions.") + (license license:bsd-2))) + (define-public r-smurf (package (name "r-smurf") @@ -8479,13 +8716,13 @@ plots in @code{ggplot2}.") (define-public r-gss (package (name "r-gss") - (version "2.2-4") + (version "2.2-5") (source (origin (method url-fetch) (uri (cran-uri "gss" version)) (sha256 (base32 - "0hbl1i687cgx9rn714s3dvbnljfiyidk5rgk3p2wmsdywggqjglm")))) + "0f9sqmcb46ilwq4cdqd1j0vhclchb69fc6kj9c56l1ivvi75dl32")))) (properties `((upstream-name . "gss"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -8608,13 +8845,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.8.1") + (version "3.8.2") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "0g79k7zfjhqdhk4crj245smrckwlbs7dazdslhvimjnlh4mlf270")))) + (base32 "1kbyhpzcfiqqx9csn0869zbiza6w97vq1j1y01qlph93bfpqf6z9")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) @@ -8717,14 +8954,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.4") + (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "094ggb6yby5irf3hj45p6vp5wdy6rjwpc0h6xbgf2mbqxyxbkhix")))) + "04xrrf72323sgzsdkbl05p2fdsi486i9avrrxvw0l3n8r8y92xfn")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) @@ -8859,14 +9096,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "117fh63r96i811y8dbrawmphlzqq8acaavykfx1y0mbc3zhspv7y")))) + "1hm5rw85ln0mk1mfmhgygnhjgs2lyc74cq12ddc41d78rl6j5p4k")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) @@ -9577,14 +9814,14 @@ Fisher's method), and Sidak correction.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4.22") + (version "0.4.23") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "0pknwssha01hjsf3c7lgrabk2c3rzq5wa2m7mf8sz7wsrbqrd57j")))) + "0jjhkcp51j7bfvv9f8sid8vkrf2a8g5hvshplsn0szzc3z6vaz2d")))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite r-ttr r-xts r-zoo)) @@ -9789,14 +10026,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "2.0.4.6") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "0nprx74mcsw4zz89gc3c53nw2iyyqalfyh7xfda83xlvpv19s31k")))) + "0r9n4xpm3ssjn3vywzlgh3naynzp1cxvjsd0pvah04k115b7i0jx")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -10495,13 +10732,13 @@ also be used as an engine for writing package vignettes.") (define-public r-sitar (package (name "r-sitar") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "sitar" version)) (sha256 - (base32 "0lhwbbpq6anqrk3818xw3nrl63bj3vwgsmxad0dpl8y50rkcc4cs")))) + (base32 "14qc5qy21qyj4gml0gwfn8izbsmzwy30ddc7mazhszi487jrcrp0")))) (properties `((upstream-name . "sitar"))) (build-system r-build-system) (propagated-inputs @@ -10960,6 +11197,33 @@ It is a replacement for the @code{zip} function, that does not require any additional external tools on any platform.") (license license:cc0))) +(define-public r-openai + (package + (name "r-openai") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (cran-uri "openai" version)) + (sha256 + (base32 + "1fi1nc9c7kfnig6b5ifpb1v9r3gxszk984rwyq7i1lb6s5jv0b9z")))) + (properties `((upstream-name . "openai"))) + (build-system r-build-system) + (propagated-inputs (list r-assertthat + r-glue + r-httr + r-jsonlite + r-lifecycle + r-magrittr)) + (home-page "https://github.com/irudnyts/openai") + (synopsis "R Wrapper for OpenAI API") + (description + "This package provides an R wrapper of OpenAI API endpoints (see +@url{https://platform.openai.com/docs/introduction} for details). This +package covers Models, Completions, Chat, Edits, Images, Embeddings, Audio, +Files, Fine-tunes, Moderations, and legacy Engines endpoints.") + (license license:expat))) + (define-public r-openxlsx (package (name "r-openxlsx") @@ -11119,6 +11383,26 @@ promises, but with a syntax that is idiomatic R.") using the @code{snow} package.") (license license:gpl2))) +(define-public r-fsa + (package + (name "r-fsa") + (version "0.9.4") + (source (origin + (method url-fetch) + (uri (cran-uri "FSA" version)) + (sha256 + (base32 + "0m63pik6bcqsbzizq8zjzilr2pxjl8b64ivdqzdnz09gmck73r5h")))) + (properties `((upstream-name . "FSA"))) + (build-system r-build-system) + (propagated-inputs (list r-car r-dunn-test r-lmtest r-plotrix r-withr)) + (home-page "https://fishr-core-team.github.io/FSA/") + (synopsis "Simple fisheries stock assessment methods") + (description + "This package provides a variety of simple fish stock assessment +methods.") + (license license:gpl2+))) + (define-public r-fstcore (package (name "r-fstcore") @@ -11512,14 +11796,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.17.3") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "1w7mwk3drf3bzfyhsy6mlnpbhgp8il8is7q95ad567ry4g6jhkqw")))) + "0ssp0mam8zkk0qsgadab0c1lkbqac3cq12s3066xz44h2jzsrfj8")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -11635,14 +11919,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.28") + (version "1.30") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0vsia6rcr4nlvzpnpwy9izhlmrl65g62yx9n97qkzaps33nrk8jq")))) + "1pqpc1bhdkhkzddwfpnwv907x29x20za4if30bwgljgsj0x8m3zf")))) (build-system r-build-system) (arguments (list @@ -11661,6 +11945,7 @@ always locate the files relative to your project root.") r-rappdirs r-rcpp r-rcpptoml + r-rlang r-withr)) (native-inputs (list r-knitr)) @@ -12530,14 +12815,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.19.2") + (version "0.19.3") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0xi9qsaxdsf2g62izh28h4kn5ada6w03znrn1zq9zdxhi5vwbavp")))) + "0zl8in5mvqjq58kprn1slrgc5wfh8vv7wprfc3qp3xl4bsqkj7zz")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12693,14 +12978,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0ic3mny2kgfyckjc77sycq5czhx68i9dgqp7g3lc06h303kcjqm4")))) + "0gcjkw35dlhf71djkvmlz0rp62sy3zd45vm8qhk1v3z5ka8m7kdw")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -12794,13 +13079,13 @@ distribution).") (define-public r-golem (package (name "r-golem") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "golem" version)) (sha256 (base32 - "0qjnrkwyn8im5zfd0fxf7rkz0gxdywnckpzsn0cqb0fxsa0z0xmv")))) + "0pcvp2rmwzvl0wi73fp9pmjq1rrknq2h45sfvbjhmbz8ilvr8zpa")))) (properties `((upstream-name . "golem"))) (build-system r-build-system) (propagated-inputs @@ -13098,14 +13383,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.18.2") + (version "1.18.4") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "01q5qv2g2npfn7xyd62mhfvdb0647r3y1j4sm0fb7p9ncyifm0hz")))) + "0lqar1lbm461in4jb9rkdnpccl8lshrhig2qxr892m91mdxym46m")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -13737,14 +14022,14 @@ data with multiple data types.") (define-public r-qualv (package (name "r-qualv") - (version "0.3-4") + (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "qualV" version)) (sha256 (base32 - "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b")))) + "09qqfx94f46x585iipr9wii8ji6ih31xymbw4p5v3qixmfpja276")))) (properties `((upstream-name . "qualV"))) (build-system r-build-system) (propagated-inputs @@ -13790,14 +14075,14 @@ subsequence} (LCS) using a dynamic programming algorithm.") (define-public r-labelled (package (name "r-labelled") - (version "2.11.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "1pg5l2c3ai8gkrqryq5xzsal85pljmdzc2ln8k1ak3j4racm5p7d")))) + "1f6jh1mrbwb3v1kc49pb65sf5ffqs0h9vizpig4r5rhhv4n3q17y")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs @@ -13874,14 +14159,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-20") + (version "3.6-23") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "04x8b4fhqrl3x44dpjs6j6aknr2n54jinrl77d5c38ip9sgy8nvy")))) + "0ng18sfw9kmhi48j8b5bzgh2ylvf5wi2zidn66k4vqaxl5s6hidz")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -14593,13 +14878,13 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.7.6") + (version "0.7.7") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "06hqwzh5mca7606rq5bwhqk9cbhqsw6vl1pax1y1890fnkzcm1my")))) + "1vqyabk04kpskx1ny7c4knzg90ri99x17vfnwcb6syjbzpcfg444")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest @@ -14630,13 +14915,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.1.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "0m5sdbzyhwmfhv08b0bld4fp8vs1ga6zxy8cjpvm8amlskgxxxdm")))) + "14vm97jjlpy3a0l0lgzgpk96igvzfpxv38xqcwa0lmp0ia7hj2p8")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url @@ -15007,14 +15292,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-23") + (version "1.4-25") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1qfdm0h6sg51cvfy9hmif7aw1jvk6jq9fvniynpxpwnqifjm8la2")))) + "10njzzxdi3jw5f419s7chcynxkzyqmmvzf7jk7ybdrwrlqhpiylx")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) @@ -15052,14 +15337,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.6") + (version "1.8.7") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "11gma8sz3bxy59flyzxqh400a4pm1cg6maaqvxxbms77svhb8vd4")))) + "0gpqgbybxpcpxc2n3pisd4yr1s9dq2m4z8j29f5mq0c5w5axgm68")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) @@ -15346,14 +15631,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1nmlx64g2x3xprhm99axw2n1agmbhwz2ck1wy16a8ach6az7rf4x")))) + "13m9di2q1npsc3mxrzkcznpq25y1brbwjixayy5ag8d9skvfx9hk")))) (build-system r-build-system) (propagated-inputs (list r-insight)) @@ -15683,14 +15968,14 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.1.6") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i")))) + "0imy9izchr9xzc5wrr91ydfr4jifv8lsqx712zkx0vxfi6kw3n6r")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -16318,14 +16603,14 @@ mathematics.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.20") + (version "0.0.21") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "11fgxbx3w36937h22v9pqx0nk5vpxp3hybj7k1b0lk8mj7hcginw")))) + "1xzhax5hmn79h6kmz7inrlaya5mdpzqj6j7n5ridyzc4vcrs412q")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -16425,13 +16710,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.20") + (version "1.30.21") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "1snm2sjr7cakb7hvi5dylrbj5nbar0757jzyd5d7igdbhxv2vrxr")))) + (base32 "025a3sc8r98sl40xqvw3jcf5ngkp0nznn4r4kqv0rj49hs6v6rlq")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs @@ -16449,16 +16734,19 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "1.1.3") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1blasg60x38z57ds6x7yb4rvjx21yf4s99q93sl1w9h6mg14d8jg")) + "16ybdly3cjm6ibvhfad7d5k6bxaxf33l5s1s766hy9kza8skyani")) (snippet '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js")))) + ;; For OpenGL and X11 support + (properties + '((updater-extra-inputs . ("glu" "libx11")))) (build-system r-build-system) (arguments (list @@ -16896,13 +17184,13 @@ Tabelow (2007) <DOI:10.18637/jss.v019.i01>.") (define-public r-admisc (package (name "r-admisc") - (version "0.32") + (version "0.33") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 - (base32 "1dv5n3hg74wp8nazbxl9mbdkdwpk7z0mibcxfpvdyjgmvfix33nk")))) + (base32 "1anvh581jh1mw3yhpbm2dyihs9npi9gd0isgkphw5gr64fivw49r")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") @@ -17188,6 +17476,29 @@ Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).") (license license:bsd-3))) +(define-public r-word2vec + (package + (name "r-word2vec") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (cran-uri "word2vec" version)) + (sha256 + (base32 + "0qj39vms6zgwb8lpmfkppayizdmhakic3pkacglary3ain61vnsk")))) + (properties `((upstream-name . "word2vec"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcppprogress)) + (home-page "https://github.com/bnosac/word2vec") + (synopsis "Distributed representations of words") + (description + "Learn vector representations of words by continuous bag of words and +skip-gram implementations of the word2vec algorithm. The techniques are +detailed in the paper \"Distributed Representations of Words and Phrases and +their Compositionality\" by Mikolov et al. (2013), available at +<arXiv:1310.4546>.") + (license license:asl2.0))) + (define-public r-wordcloud (package (name "r-wordcloud") @@ -17287,6 +17598,38 @@ manipulate tree data.") R packages (on CRAN, Bioconductor or Github).") (license license:artistic2.0))) +(define-public r-doc2vec + (package + (name "r-doc2vec") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "doc2vec" version)) + (sha256 + (base32 + "0249hm0103kxxsi4gks4h20wf6p00gbrk9jf8c148mbja1l56f6v")))) + (properties `((upstream-name . "doc2vec"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "https://github.com/bnosac/doc2vec") + (synopsis "Distributed representations of sentences, documents and topics") + (description + "Learn vector representations of sentences, paragraphs or documents by +using the Paragraph Vector algorithms, namely the distributed bag of +words (PV-DBOW) and the distributed memory (PV-DM) model. Top2vec finds +clusters in text documents by combining techniques to embed documents and +words and density-based clustering. It does this by embedding documents in +the semantic space as defined by the doc2vec algorithm. Next it maps these +document embeddings to a lower-dimensional space using the Uniform Manifold +Approximation and Projection (UMAP) clustering algorithm and finds dense areas +in that space using a Hierarchical Density-Based Clustering +technique (HDBSCAN). These dense areas are the topic clusters which can be +represented by the corresponding topic vector which is an aggregate of the +document embeddings of the documents which are part of that topic cluster. In +the same semantic space similar words can be found which are representative of +the topic.") + (license license:expat))) + (define-public r-docopt (package (name "r-docopt") @@ -17645,6 +17988,48 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) +(define-public r-rnaturalearth + (package + (name "r-rnaturalearth") + (version "0.3.3") + (source (origin + (method url-fetch) + (uri (cran-uri "rnaturalearth" version)) + (sha256 + (base32 + "0cji6hpcpkrsx615627z9dgk0zf78l2nnj3x5kkkpj9lvsm5gj6m")))) + (properties `((upstream-name . "rnaturalearth"))) + (build-system r-build-system) + (propagated-inputs (list r-httr r-jsonlite r-sf r-sp r-terra)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=rnaturalearth") + (synopsis "World map data from Natural Earth") + (description + "This package facilitates mapping by making natural earth map data from +@url{https://www.naturalearthdata.com/} more easily available to R users.") + (license license:expat))) + +(define-public r-rnaturalearthdata + (package + (name "r-rnaturalearthdata") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rnaturalearthdata" version)) + (sha256 + (base32 + "1z32j5lz2lb8xgpkr73majw22k0b49iazj6jjc7j4w9k4zxxa102")))) + (properties `((upstream-name . "rnaturalearthdata"))) + (build-system r-build-system) + (propagated-inputs (list r-sp)) + (home-page "https://github.com/ropenscilabs/rnaturalearthdata") + (synopsis "World vector map data from Natural Earth") + (description + "This package provides vector map data from +@url{https://www.naturalearthdata.com/}. Access functions are provided in the +accompanying package @code{rnaturalearth}.") + (license license:cc0))) + (define-public r-rncl (package (name "r-rncl") @@ -17964,14 +18349,14 @@ be imported and then exported via the @code{gridSVG} package.") (define-public r-kohonen (package (name "r-kohonen") - (version "3.0.11") + (version "3.0.12") (source (origin (method url-fetch) (uri (cran-uri "kohonen" version)) (sha256 (base32 - "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381")))) + "188cxw2fvpfr3dyi8g52igcyc8d5jffyn6rhc84dja52da8lp520")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -18212,14 +18597,14 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "1.4.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "12s980jfw98czzrxdn83b2blj4qcrkqqmycjplkzvm4mapgiw3wf")))) + "19drzhzfivjwgs04rdgap86fv4fjayrscifjr03gxrax82sjgfp3")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -18282,20 +18667,17 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.7-1") + (version "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "1djxhc4v874asmrj8qy054779wsq499f5f2wc6vmr40qab33v1x6")))) + "12rd0j3sawzipfz4xr3ikrxrjabpjp4s3y4ikvk16z8rhjs2i5bw")))) + (properties + '((updater-extra-inputs . ("gmp")))) (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-CC - (lambda _ (setenv "CC" "gcc") #t))))) (inputs (list gmp)) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") @@ -19483,14 +19865,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.32.0") + (version "1.33.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0xigdxcxx0nv0lbbrfqwbgcm02yw95ja706m9lc4b5q65m8p9fym")))) + "0nwk8y3qv2dj41qxrciic6rkpy6lzrhpd5v886zmcjyf6ndyna22")))) (build-system r-build-system) (arguments `(#:phases @@ -20625,22 +21007,23 @@ plotting functions are available for analyzing clustering results.") (define-public r-remacor (package (name "r-remacor") - (version "0.0.11") + (version "0.0.16") (source (origin (method url-fetch) (uri (cran-uri "remaCor" version)) (sha256 (base32 - "0hhk1zrjz6sxg219h9ca7jya0vc8dmrvwaddajkcdns6bv3rj1km")))) + "1xznj2y3qszw8s1fgbs8fiadg7c0gl3ml1blxmwixb32kr2cv5vq")))) (properties `((upstream-name . "remaCor"))) (build-system r-build-system) (propagated-inputs - (list r-clustergeneration + (list r-envstats r-ggplot2 r-mvtnorm + r-rcpp + r-rcpparmadillo r-rdpack - r-reshape2 - r-runit)) + r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://diseaseneurogenomics.github.io/remaCor/") (synopsis "Random effects meta-analysis for correlated test statistics") @@ -21082,14 +21465,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "2.2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "1v8407lkkj0flsphsnqvdr35knkasvjv9v29451mkwkciglmi2l7")))) + "12w4chk71vqy1chij79928ppxdg2cz03hx9bgs5cgwj9f1ciyb2b")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs @@ -21459,13 +21842,13 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.22") + (version "1.1.23") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 - (base32 "0ys5sxr5q55ip49dsc3kbgcr3bn9dj5bblmshwm4jz8d0a7ikwmj")))) + (base32 "1qa9j7s09yzi65fav27zxc1w1wxwsmgjz8a8ghy7hhi5f3gvsqw3")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") @@ -22305,14 +22688,14 @@ package.") (define-public r-ggplotify (package (name "r-ggplotify") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 - "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) + "1x4fnsh66rxdd2k7w1mhs6if8i4qjjkfj5x1hf4zjpqqm8f5sf1k")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridgraphics r-yulab-utils)) @@ -22959,14 +23342,14 @@ function for computing a matrix of correlation p-values.") (define-public r-ggfun (package (name "r-ggfun") - (version "0.0.9") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 - "04kn367mzgrfwnwz97vw5jqp2kig94hmxmhyyic7ddvk3sfhwx2w")))) + "1gypky0ksnwq98w9zqp9nfayhc1fx8wpn82mj2jpv1ydd5hfsicq")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs @@ -23371,14 +23754,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "12.0.0") + (version "12.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "1hv18ksaghifj4jjdy1cf2ic0rrgfi7jbjpzxb7v6r3bbshs9vwi")))) + "0wrx9nvv7vw1ywdh6afk496dljwglnbkhjl5ywrrynfhidj7hnql")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs @@ -23764,14 +24147,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "1zaxwhcgfasrchg2qcrr3i9scyvz57g363q77d39zrz69yk363ic")))) + "0rswg2habyk38hcx0gn9hnvb200bq0dc4fy4k3gqhfhwjq9l7a1b")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments @@ -24357,14 +24740,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.14") + (version "0.1.16") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "1q4z98w3pkc51vrcpmwaibnwmlm17zjcnh0qlx660wky5ccyh5l0")))) + "0j4f7vnb3mwf6p4nhg2limy7i32qrcj2gxbs8wsq9c6xxpcs0qsz")))) (build-system r-build-system) (propagated-inputs (list r-dqrng @@ -24706,14 +25089,16 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (define-public r-leidenalg (package (name "r-leidenalg") - (version "1.0.5") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 - (base32 "1z96zrsms93gspylmficaggb0xj94kq9rg3p2svdbb451jbga9an")))) - (properties `((upstream-name . "leidenAlg"))) + (base32 "1hn5fps5m5am4s82wvhr4fgfw49h0jar4i687czbkab3l9x1dr68")))) + (properties + `((upstream-name . "leidenAlg") + (updater-extra-inputs . ("gmp")))) (build-system r-build-system) (inputs (list glpk gmp libxml2)) @@ -25045,21 +25430,25 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-29") + (version "1.7-39") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "19bwakxccgyn054p7nrf820jq7nwpcjlrgj2ldk137scld9b0f9z")))) + "03kc2m89236qh50qfxl1101ys466ddhgjwp80x6hjpmd9fz5jf5l")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs - (list gdal + (list curl + gdal geos + openssh + openssl + pcre2 proj - sqlite ; needed for proj + sqlite zlib)) (propagated-inputs (list r-rcpp)) @@ -25331,13 +25720,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.35") + (version "1.36") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "126l473wvmy7zsm34alskwigbf85dn657hsnzy24yx8kfx4pzwcn")))) + (base32 "1ygijjvmi7igk3xmm2mzfnbw05kynjdqbwddifg798awk7mfffjw")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs @@ -25360,13 +25749,13 @@ to ODEs by numerical differencing.") (define-public r-pmcmrplus (package (name "r-pmcmrplus") - (version "1.9.6") + (version "1.9.7") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 - (base32 "1mvj3cwrdkl3frk7fvh6l7v7yya5p3xm4z0qhc4fvykxdmb92ivz")))) + (base32 "06i5vsf8hpzv0c8v156072xbqpxk1wf2iami7mnsjfp9xjjjzbhx")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) @@ -25379,7 +25768,7 @@ to ODEs by numerical differencing.") r-mvtnorm r-rmpfr r-suppdists)) - (native-inputs (list gfortran r-knitr)) + (native-inputs (list gfortran r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/package=PMCMRplus") (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") (description @@ -25899,6 +26288,25 @@ been created, it no longer relies on the font files. No external software such as Ghostscript is needed to use this package.") (license license:asl2.0))) +(define-public r-emoa + (package + (name "r-emoa") + (version "0.5-0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "emoa" version)) + (sha256 + (base32 + "0fr4ia3hkv8c7wkl64a51s6ynldppc812ynwldvbwy25dhlbvs6r")))) + (properties `((upstream-name . "emoa"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/emoa/") + (synopsis "Evolutionary multiobjective optimization algorithms") + (description + "This package provides building blocks for the design and analysis of +multiobjective optimization algorithms.") + (license license:gpl2))) + (define-public r-emojifont (package (name "r-emojifont") @@ -26187,14 +26595,14 @@ data.") (define-public r-mda (package (name "r-mda") - (version "0.5-3") + (version "0.5-4") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 - "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx")))) + "0nd7p3yz7qdzka7jizymv5vhbhzb4v8bjpmmn5wa83vxh0l7ypzj")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs (list r-class)) @@ -26725,14 +27133,14 @@ settings.") (define-public r-r-huge (package (name "r-r-huge") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "R.huge" version)) (sha256 (base32 - "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) + "1wjcssvn76fblpivwkapdwcw08pygbkj7qskcl0wn8mda9w5f72b")))) (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs @@ -27041,6 +27449,31 @@ forest) is fit on the kernel matrix of a subset of the training data.") classes into dummy/indicator variables.") (license license:gpl2+))) +(define-public r-dunn-test + (package + (name "r-dunn-test") + (version "1.3.5") + (source (origin + (method url-fetch) + (uri (cran-uri "dunn.test" version)) + (sha256 + (base32 + "0lqwvyl3pyygfc73nf81gzw3zl3w43r7ki0yw2dgrzhkpb2iji4a")))) + (properties `((upstream-name . "dunn.test"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dunn.test") + (synopsis "Dunn's test of multiple comparisons using rank sums") + (description + "Dunn's test computes stochastic dominance & reports pairwise comparisons. +This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952). It +employs Dunn's z-test-statistic approximations for rank statistics, conducting +k(k-1)/2 comparisons. The null hypothesis assumes that the probability of a +randomly selected value from the first group being larger than one from the +second group is one half, similar to the Wilcoxon-Mann-Whitney test. Dunn's +test serves as a test for median difference and takes into account tied +ranks.") + (license license:gpl2))) + (define-public r-acrm (package (name "r-acrm") @@ -27310,14 +27743,14 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.9.3") + (version "2.9.4") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "0bwg9sfsqs5nsqwhjnbb631fbhj0mx2dc4c185qkym9cjb5lfkm9")))) + "10bbwr4q6cp36dnwhddviqg7f00h92gdmvblw0lxn72v4869vhn1")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs @@ -28066,13 +28499,13 @@ Visualizations are also available for most of these settings.") (define-public r-torch (package (name "r-torch") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "torch" version)) (sha256 - (base32 "1ydazl7v10vm69573y871rq1dvbgdvlvhcs6di7xw7i4z4kg2gxm")))) + (base32 "04hvr3f4rgnxxc42fiv58kpyld4aagj6ambhw769v3bfz7s2v879")))) (properties `((upstream-name . "torch"))) (build-system r-build-system) (arguments @@ -29597,14 +30030,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.26") + (version "2.26.27") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1jr5sflqhg70jkgz3x0q9nrk2xjzm1l4zmyc7j89m755b209sq4k")))) + "1cf9hc7z3d8b70jck37j3lc2ml040di91dylfb18yi6wx936bq3h")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) @@ -29697,14 +30130,14 @@ estimate parameters given observed data.") (define-public r-kutils (package (name "r-kutils") - (version "1.70") + (version "1.72") (source (origin (method url-fetch) (uri (cran-uri "kutils" version)) (sha256 (base32 - "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37")))) + "0mnrh1bfpwssw9j5lspvwfawqx9s4fxy2gh3n60knjzbzrzqckp4")))) (properties `((upstream-name . "kutils"))) (build-system r-build-system) (propagated-inputs @@ -31022,14 +31455,14 @@ is also implemented here.") (define-public r-aws (package (name "r-aws") - (version "2.5-1") + (version "2.5-3") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 - "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8")))) + "022igrvxlyi0ckl3c6chcm459kv213jxy5hrvc14m36yhn3xckhm")))) (properties `((upstream-name . "aws"))) (build-system r-build-system) @@ -31517,18 +31950,23 @@ multi-state models.") (define-public r-scatterpie (package (name "r-scatterpie") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "scatterpie" version)) (sha256 (base32 - "06crdylakwig8ryi1w5a6mmfy67gakmk6gp0xbrg749da1asd7a9")))) + "0wfrckyvy4zw34qdvgg1gwqfdi1xhs63v3gfwa4akm7ifd1canlb")))) (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs - (list r-dplyr r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr)) + (list r-dplyr + r-ggforce + r-ggfun + r-ggplot2 + r-rlang + r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/scatterpie/") @@ -31973,25 +32411,20 @@ Kemeny distance and correlation coefficient.") (define-public r-fastshap (package (name "r-fastshap") - (version "0.0.7") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "fastshap" version)) (sha256 (base32 - "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv")))) + "112hc585aryzc5pgvr3qaa7arlx2h2sj9jlq9xha3nncyzqkh7c6")))) (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs - (list r-abind - r-ggplot2 - r-gridextra - r-matrixstats - r-plyr - r-rcpp - r-rcpparmadillo - r-tibble)) + (list r-foreach r-rcpp r-rcpparmadillo)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/bgreenwell/fastshap") (synopsis "Fast approximate Shapley values") (description @@ -32266,14 +32699,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "070ddmi73ly2lv23z556adgn7vc7xyhl2cnh1cis8sinmpfz071c")))) + "1gnlgz11dv66b41kdyyzm8nhkhhi4yajlcr2g52h2lfxlryb5g2h")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) @@ -32312,14 +32745,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.2-1") + (version "3.2-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "1yrms8jwk5svggm73y0nk4j1k85rd92fvgvd4ia6nina63pmvbph")))) + "1hvk61j8xxkj8n5g0fdbpa3h8j2km1q689l9l87jzzdsz95jgk9f")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -32483,14 +32916,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "1wcq4lq7xa62xn6zsg6r8nf6vdlvnlwxgfqndb7vnvd8f54hx9pi")))) + "10c6i5daw3xy4w0f1pjc09x5iykv0fjdp2a33qjl0yrivmmdamkj")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -32555,14 +32988,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.7") + (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "13yzvvl49sibf2py990fb60nyjby5h10pbli3i7159v08yd1b1lg")))) + "1c64j8hg6id4ri3m32aa1r0qyn09kl3dvl865dzf43qdb3qcichv")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -33178,13 +33611,13 @@ value.") (define-public r-confintr (package (name "r-confintr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "confintr" version)) (sha256 (base32 - "0p2k1bflyb82grp6ikh7dw3dacvsch8zfwxwwr4v325q0yk98iiz")))) + "0gi9cnk2cd67vmywrkb19g6f9gr8k999kg0k03khad7lgqp4l43s")))) (properties `((upstream-name . "confintr"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -33284,21 +33717,26 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.4.3") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "08b0q5fb9wrnzq32izylq8fxyagibrng5yb80acsbmnfdkxb7g86")))) + "01kkzl0akq5ygz2mvn29myhnfx4b74xkpmn592ih1vnh1zzph1yq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) (inputs - (list gmp glpk libxml2 zlib)) + (list glpk gmp libxml2 zlib)) (propagated-inputs - (list r-cpp11 r-magrittr r-matrix r-pkgconfig r-rlang)) + (list r-cli + r-cpp11 + r-magrittr + r-matrix + r-pkgconfig + r-rlang)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -33588,6 +34026,24 @@ different types of resampling objects (e.g. bootstrap, cross-validation).") Design} (SFD) and to test their quality.") (license license:gpl3))) +(define-public r-dicekriging + (package + (name "r-dicekriging") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (cran-uri "DiceKriging" version)) + (sha256 + (base32 + "0jfb2li6b93fkwgjkr4jwxnvv7zb0aqk9lkf2mnv2awzh0r16pdb")))) + (properties `((upstream-name . "DiceKriging"))) + (build-system r-build-system) + (home-page "https://dicekrigingclub.github.io/www/") + (synopsis "Kriging methods for computer experiments") + (description "This is a package for the estimation, validation and +prediction of kriging models.") + (license license:gpl2+))) + (define-public r-dials (package (name "r-dials") @@ -34395,14 +34851,14 @@ as allowing spectra with different resolutions.") (define-public r-scattermore (package (name "r-scattermore") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "scattermore" version)) (sha256 (base32 - "1iairy18k1k66863f5avxs5mq1a42477w1kcl6w465is1awc1sb3")))) + "1l820rc4ncmqd5sacdc420xf6r5dh34sbhgzzgq7a4yx1dxshd2m")))) (properties `((upstream-name . "scattermore"))) (build-system r-build-system) (propagated-inputs @@ -34481,13 +34937,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.3.0") + (version "4.3.0.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0z7rzxi1gli56k50s6w1363ndw18wykgk5xmc3g7jhpphqxwpfky")))) + "04lbwk8mcv7gsi70sij264mz80frx1pr60ihv9dqg63sgr234ax4")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -34994,6 +35450,96 @@ well as email and push notifications.") \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") (license license:gpl2))) +(define-public r-mlr + (package + (name "r-mlr") + (version "2.19.1") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr" version)) + (sha256 + (base32 + "00jjhvaqifj6glqsyzixlp56bvlch5smck8kk3klcmwx9pasyllx")))) + (properties `((upstream-name . "mlr"))) + (build-system r-build-system) + (inputs (list gdal + geos + glu + gmp + gsl + jags + mpfr + openmpi + proj + udunits)) + (propagated-inputs (list r-backports + r-bbmisc + r-checkmate + r-data-table + r-ggplot2 + r-parallelmap + r-paramhelpers + r-stringi + r-survival + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://mlr.mlr-org.com") + (synopsis "Machine learning in R") + (description + "This package provides an interface to a large number of classification +and regression techniques. These techniques include machine-readable +parameter descriptions. There is also an experimental extension for survival +analysis, clustering and general, example-specific cost-sensitive learning. +Also included: + +@itemize + +@item Generic resampling, including cross-validation, bootstrapping and + subsampling; +@item Hyperparameter tuning with modern optimization techniques, for single- + and multi-objective problems; +@item Filter and wrapper methods for feature selection; +@item Extension of basic learners with additional operations common in machine + learning, also allowing for easy nested resampling. +@end itemize + +Most operations can be parallelized.") + (license license:bsd-2))) + +(define-public r-mlrmbo + (package + (name "r-mlrmbo") + (version "1.1.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "mlrMBO" version)) + (sha256 + (base32 + "16fwj7m28g4km7yalqppxmh3lw2jln0z072l6awia38qkdg6xwhc")))) + (properties `((upstream-name . "mlrMBO"))) + (build-system r-build-system) + (propagated-inputs (list r-backports + r-bbmisc + r-checkmate + r-data-table + r-lhs + r-mlr + r-parallelmap + r-paramhelpers + r-smoof)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mlr-org/mlrMBO") + (synopsis "Model-based optimization with mlr") + (description + "This package is a flexible and comprehensive R toolbox for model-based +optimization. It implements Efficient Global Optimization Algorithm for +single- and multi-objective optimization. It supports mixed parameters. The +machine learning toolbox mlr offers regression learners. It provides various +infill criteria and features batch proposal, parallel execution, +visualization, and logging. Its modular implementation allows easy +customization by the user.") + (license license:bsd-2))) + (define-public r-mlr3measures (package (name "r-mlr3measures") @@ -35126,17 +35672,16 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.16.0") + (version "0.16.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "1nzj73qsbb02fcim9826zkxzzpar32pq2r0yfkis1nxaxky4cclr")))) + "09klavihc2j6wsd9m2ycppl2ir85z5cxlxl9h6ay9skacylk559n")))) (build-system r-build-system) (propagated-inputs - (list r-r6 - r-backports + (list r-backports r-checkmate r-data-table r-evaluate @@ -35149,6 +35694,7 @@ implemented as @code{R6} classes.") r-palmerpenguins r-paradox r-parallelly + r-r6 r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") @@ -35220,13 +35766,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "1wvrdg977a2nibgyvccz2mw8043nsvm716mmwkspx4sgacf0sgx7")))) + "1iz7izmkx11jma95305wq8aapi4dmqg20flgxxvdvrfy6hf98k33")))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -35237,6 +35783,8 @@ annealing.") r-mlr3misc r-paradox r-r6)) + (native-inputs + (list r-knitr)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter @@ -35540,14 +36088,14 @@ AGG to use as alternative to the raster devices provided through the (define-public r-downlit (package (name "r-downlit") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 - "0g3yncj3gmaqsc6cw7g9slgvd0kfk2414yz5m1dilk8h15lzdprk")))) + "1gdk6rj3539vnm979spd8py0rpvlaniyiy336abi39g8xjcbw3vc")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs @@ -36163,14 +36711,14 @@ latter.") (define-public r-readtext (package (name "r-readtext") - (version "0.82") + (version "0.90") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 - "13j0avf5443m46lczdznpw1zlc01psk61m5wrxks9inv0684xg1s")))) + "01hscqmjb3fz4iqqgi0l2s1z48a53a25jnsxb0cdd631c97alqrh")))) (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs @@ -36369,14 +36917,14 @@ Application Program Interfaces (API)}.") (define-public r-intervals (package (name "r-intervals") - (version "0.15.3") + (version "0.15.4") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 - "1i6z86dnsb5md4hxaz049azpjpp8m8c9b0q7x1sfi6sbqzvzw0c5")))) + "13wzwg5yc1wr8ww8bhv9x5ha78yajsfmb9phq4nbgrxkmbiy3h2h")))) (properties `((upstream-name . "intervals"))) (build-system r-build-system) (home-page "https://github.com/edzer/intervals") @@ -36445,14 +36993,14 @@ BTM-WWW13.pdf}.") (define-public r-delaporte (package (name "r-delaporte") - (version "8.1.0") + (version "8.1.1") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 - "08si87f6zjsmmzgvhnfjw8l7lcwlfj2qd4zf6ypm197vdhqw0d0r")))) + "0vcz23nm1wb49yp57xhdfjixla0ikyalc55m03hsis91cdnwh28g")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -36917,18 +37465,21 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.9") + (version "2.2.10") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "18vlr1isi92zc9a16ld3fczdw2mcd142k5cbpls3nfxgdjbx3qqk")) + (base32 "0wpr3cgkznrm2ivapi1vdlcm2729v1jkyah5q82nfmnzisdlrc4a")) (snippet '(for-each delete-file '("inst/test/jquery-1.10.2.min.js" "inst/test/bootstrap/js/bootstrap.min.js"))))) - (properties `((upstream-name . "opencpu"))) + (properties + `((upstream-name . "opencpu") + (updater-ignored-inputs . ("apparmor")) + (updater-extra-native-inputs . ("js-jquery")))) (build-system r-build-system) (arguments (list @@ -37518,14 +38069,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.6") + (version "0.5.8") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "0kymia03q6fy9hjlvdfwddizkk5liamhq800m05qmi10qa3sg059")))) + "1vx74lxgzsl1yl4ak5zympkgwza023qbjwskp19nm2dvxhz75cfh")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -37549,14 +38100,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "12viq760wd5b7dl800075hvm8jy19q112m6rlgyz85znwbiam2qj")))) + "18gkr3272jj1pkksm6fy6qz5s5jn0yvb12pz29k204xrzmqwdwgm")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) @@ -37573,14 +38124,14 @@ service, and more.") (define-public r-paws-cost-management (package (name "r-paws-cost-management") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 - "0rpl6dfv6xa7ysqhhskcj7kix4s087yrxav9n33730hk1gjf1g62")))) + "0v0s8wwx2j3a6s0pl9vnvbpgdyhn3jlxri0b2fl3gc3zx6qh07dl")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) @@ -37597,13 +38148,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "0d1j9wilwx2harvslg9vs6k8w7631pqgr1c8346wzjk5387fpsac")))) + (base32 "1b661gpg7rsdkgpriwczj4cvqg9rh1ajz9ma457bw4p3lv7n53x2")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs @@ -37619,13 +38170,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "0709jwrihggqsp3p99sqldsfk7bww3pgl9x0akrnm60daqxhhyqv")))) + (base32 "0as9ix46rsa7sg8k96v6l3ibxqc95pf7swrij31ljmwfy82z2rq3")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs @@ -37641,14 +38192,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "0m79k4q3yalzym4alv4h1mggr9sf8sc1vk1islx5j63s2p6m4j3g")))) + "19lz1vcvb1bn405saxx4zjsmm1q4zaw77z08iw4xbyny5xhkgyvi")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) @@ -37665,14 +38216,14 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "0rnws1d8wy3nhg2fyidpa21sfbz3r7jalrklnx6l8s92jyycmhbd")))) + "02k15skswd58icafydrbjrp7br5x8l93lwi5z1pwqak6xasi0vqh")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) @@ -37690,14 +38241,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "1ixgrcfixx7h17wryml63n28ldgxi2srqw3bqglws54h5acgqza9")))) + "0qjk1gn4p41l4ryqf9xppiphfakypl0xdjk23c9c8xdhqkbw0lcw")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) @@ -37714,14 +38265,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "0nmxb53x0vsd2g69qnxxs4hapcbg53r9b26cdkhpmj6ijj7v1hh3")))) + "092n5p5hjwaqkdnw4r7n71znabfazc2pg19raja69jgk6zh6csvy")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) @@ -37738,14 +38289,14 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "1hdjgbrfrhrh9ss3lhnsjd2qpz22mrb95qvdcfngz2i8aa73hmpg")))) + "0hdmc07i75hbk2fh580p7q7p3pk8ykr5m1jibnfk8azc4flikwv6")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) @@ -37762,14 +38313,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "1fyr236pk6pyc6qck8i8mn855wxlbcmb40mnwmhaqjfxy503jjh7")))) + "0pf1vvwmgsz65bq5diabybnsgyxfbjq1f64srf3qk49ycfh2sc7h")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) @@ -37786,14 +38337,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "0fg1z87rk24iaci44xp005sbsx48qxgw4hccds17znys7da868bx")))) + "08ak299kyr6dr8idcna7i433aab1bis2b9zqmwm1yma3m3xk4n8i")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs @@ -37810,14 +38361,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "1yqd1a1c0m978x1ngk39x7sb0glmcy855nw7m1wbgn2mxma0q3li")))) + "0z693wawgm975lw54xkbg9hwsf1lz69a4dsg85ywjpjcfvl1g1b7")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs @@ -37832,14 +38383,14 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.2.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "10bfcwsriyl73mp3wi9kvn6msy1g4ci71jmpv61bcqngp9qmv4wg")))) + "17xzc1ngir4v043xclw6c1qs092aicj83qmn8sydn9apmlzcps1r")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs @@ -37855,14 +38406,14 @@ functions-as-a-service, containers, batch processing, and more.") (define-public r-paws (package (name "r-paws") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 - "0pwm4pnrjcbsp396fc7r2b8p3cfnrdnk0zcdbw6b92bgv9hpbp14")))) + "1s4nya5xghjj1a2w8bqcmnpnpdw7li22asssm2ihv68zvlxavzdk")))) (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs |