diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 2419 |
1 files changed, 2057 insertions, 362 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1db2e1c27a..5617383cbc 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 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2020, 2021 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> @@ -26,7 +26,7 @@ ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es> -;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org> +;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org> ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> @@ -68,6 +68,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) + #:use-module (gnu packages fribidi) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) @@ -90,6 +91,7 @@ #:use-module (gnu packages networking) #:use-module (gnu packages node) #:use-module (gnu packages pcre) + #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile @@ -98,6 +100,7 @@ #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages web) @@ -107,14 +110,14 @@ (define-public r-brio (package (name "r-brio") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 - "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb")))) + "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") @@ -125,6 +128,30 @@ functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.") (license license:expat))) +(define-public r-cachem + (package + (name "r-cachem") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "cachem" version)) + (sha256 + (base32 + "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh")))) + (properties `((upstream-name . "cachem"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fastmap" ,r-fastmap) + ("r-rlang" ,r-rlang))) + (home-page "https://cachem.r-lib.org/") + (synopsis "Cache R objects with automatic pruning") + (description + "This package provides key-value stores with automatic pruning. Caches +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-diffobj (package (name "r-diffobj") @@ -150,14 +177,14 @@ visualization of their differences.") (define-public r-waldo (package (name "r-waldo") - (version "0.2.3") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 - "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz")))) + "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr")))) (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs @@ -180,14 +207,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.18") + (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1srczjy9dqw06glrv95798xsg462kfbbwm3yk1fv1zhpz9jhakwv")))) + "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -316,13 +343,13 @@ the system clipboards.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-8") + (version "1.8-9") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) + "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -365,17 +392,17 @@ variables.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.7") + (version "0.3.8-1") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn")))) + "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) + `(("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) @@ -846,18 +873,21 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "0.3.6") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka")))) + (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) ("r-selectr" ,r-selectr) + ("r-tibble" ,r-tibble) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -896,23 +926,27 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "0.3.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10")))) + "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) ("r-clipr" ,r-clipr) ("r-fs" ,r-fs) + ("r-glue" ,r-glue) + ("r-knitr" ,r-knitr) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) - ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description @@ -1130,13 +1164,13 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.1") + (version "0.5.1.1") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "01v33zcs9rv16r6v8ckqh92k5axj6skmk9hyakmqqmgra522xj3a")))) + "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -1294,14 +1328,14 @@ and vice-versa.") (define-public r-fastmap (package (name "r-fastmap") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "fastmap" version)) (sha256 (base32 - "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) + "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) (home-page "https://r-lib.github.io/fastmap/") @@ -1315,10 +1349,230 @@ are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") (license license:expat))) +(define-public r-fastghquad + (package + (name "r-fastghquad") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastGHQuad" version)) + (sha256 + (base32 + "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj")))) + (properties `((upstream-name . "fastGHQuad"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/awblocker/fastGHQuad") + (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature") + (description + "This package implements numerically-stable Gauss-Hermite quadrature +rules and utility functions for adaptive GH quadrature.") + (license license:expat))) + +(define-public r-rstpm2 + (package + (name "r-rstpm2") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rstpm2" version)) + (sha256 + (base32 + "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4")))) + (properties `((upstream-name . "rstpm2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmle" ,r-bbmle) + ("r-bh" ,r-bh) + ("r-desolve" ,r-desolve) + ("r-fastghquad" ,r-fastghquad) + ("r-mgcv" ,r-mgcv) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://github.com/mclements/rstpm2") + (synopsis "Link-based survival models") + (description + "This package provides R implementations of @dfn{generalized survival +models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov +multi-state models.") + ;; One of these licenses + (license (list license:gpl2 license:gpl3)))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-jquerylib + (package + (name "r-jquerylib") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "jquerylib" version)) + (sha256 + (base32 + "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq")) + (snippet + '(for-each delete-file + '("inst/lib/jquery-1.12.4.min.js" + "inst/lib/jquery-2.2.4.min.js" + "inst/lib/jquery-3.5.1.min.js"))))) + (properties `((upstream-name . "jquerylib"))) + (build-system r-build-system) + (arguments + `(#: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 + `(("jquery-1.12.4.js" + "jquery-1.12.4.min.js") + ("jquery-2.2.4.js" + "jquery-2.2.4.min.js") + ("jquery-3.5.1.js" + "jquery-3.5.1.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 + `(("r-htmltools" ,r-htmltools))) + (native-inputs + `(("esbuild" ,esbuild))) + (home-page "https://cran.r-project.org/package=jquerylib") + (synopsis "Obtain jQuery as an HTML dependency object") + (description + "Obtain any major version of jQuery and use it in any webpage generated +by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't +need to use this package directly, but other R packages (e.g. shiny, +rmarkdown, etc.) depend on this package to avoid bundling redundant copies of +jQuery.") + (license license:expat))) + +(define-public r-sass + (package + (name "r-sass") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sass" version)) + (sha256 + (base32 + "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s")))) + (properties `((upstream-name . "sass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-fs" ,r-fs) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-rappdirs" ,r-rappdirs) + ("r-rlang" ,r-rlang))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rstudio/sass") + (synopsis "Syntactically Awesome Style Sheets (SASS)") + (description + "This package provides an SCSS compiler, powered by the libsass library. +With this, R developers can use variables, inheritance, and functions to +generate dynamic style sheets. The package uses the Sass CSS extension +language, which is stable, powerful, and CSS compatible.") + (license license:expat))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-bslib + (package + (name "r-bslib") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "bslib" version)) + (sha256 + (base32 + "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac")) + (snippet + '(for-each delete-file + '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" + "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" + "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js" + "inst/lib/bs/dist/js/bootstrap.bundle.min.js"))))) + (properties `((upstream-name . "bslib"))) + (build-system r-build-system) + (arguments + `(#: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") + ("bs-sass/assets/javascripts/bootstrap.js" + "bs-sass/assets/javascripts/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap-bundle") + "bs/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 + `(("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-jquerylib" ,r-jquerylib) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-sass" ,r-sass))) + (native-inputs + `(("esbuild" ,esbuild) + ("js-bootstrap-bundle" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js") + (sha256 + (base32 + "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak")))))) + (home-page "https://rstudio.github.io/bslib/") + (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") + (description + "This package simplifies custom CSS styling of both shiny and rmarkdown +via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their +various Bootswatch themes. An interactive widget is also provided for +previewing themes in real time.") + (license license:expat))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. (define-public r-shiny (package (name "r-shiny") - (version "1.4.0.2") + (version "1.6.0") (source (origin (method git-fetch) @@ -1328,7 +1582,23 @@ data structures in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs")))) + "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9")) + (snippet + '(for-each delete-file + '("inst/www/shared/bootstrap/js/bootstrap.min.js" + "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO + "inst/www/shared/datatables/js/jquery.dataTables.min.js" + "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js" + "inst/www/shared/highlight/highlight.pack.js" + "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js" + "inst/www/shared/jquery.min.js" + "inst/www/shared/jqueryui/jquery-ui.min.js" + "inst/www/shared/legacy/jquery.min.js" + "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js" + "inst/www/shared/selectize/js/selectize.min.js" + "inst/www/shared/shiny.min.js" + "inst/www/shared/showdown/compressed/showdown.js" + "inst/www/shared/strftime/strftime-min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -1343,21 +1613,11 @@ data structures in C++.") (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) (format #t "replacing ~a with ~a\n" old new) - (delete-file old) (symlink new old)))) ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ ;; contain just data. They are not minified code, so we don't ;; replace them. (with-directory-excursion "inst/www/shared" - (replace-file "bootstrap/shim/respond.min.js" - (string-append (assoc-ref inputs "js-respond") - "/share/javascript/respond.min.js")) - (replace-file "bootstrap/shim/html5shiv.min.js" - (string-append (assoc-ref inputs "js-html5shiv") - "/share/javascript/html5shiv.min.js")) - (replace-file "json2-min.js" - (string-append (assoc-ref inputs "js-json2") - "/share/javascript/json2-min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) @@ -1370,14 +1630,10 @@ data structures in C++.") (replace-file "selectize/js/selectize.min.js" (string-append (assoc-ref inputs "js-selectize") "/share/javascript/selectize.min.js")) - (replace-file "selectize/js/es5-shim.min.js" - (string-append (assoc-ref inputs "js-es5-shim") - "/share/javascript/es5-shim.min.js")) (for-each (match-lambda ((source . target) - (delete-file target) (minify source #:target target))) - '(("jqueryui/jquery-ui.js" . + `(("jqueryui/jquery-ui.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") @@ -1385,23 +1641,32 @@ data structures in C++.") "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap-accessibility") . + "bootstrap/accessibility/js/bootstrap-accessibility.min.js") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js") ("legacy/jquery.js" . "legacy/jquery.min.js") + ("selectize/accessibility/js/selectize-plugin-a11y.js" . + "selectize/accessibility/js/selectize-plugin-a11y.min.js") ("showdown/src/showdown.js" . - "showdown/compressed/showdown.js"))))) - #t))))) + "showdown/compressed/showdown.js")))))))))) (propagated-inputs - `(("r-crayon" ,r-crayon) + `(("r-bslib" ,r-bslib) + ("r-cachem" ,r-cachem) + ("r-commonmark" ,r-commonmark) + ("r-crayon" ,r-crayon) ("r-digest" ,r-digest) + ("r-ellipsis" ,r-ellipsis) ("r-fastmap" ,r-fastmap) + ("r-glue" ,r-glue) ("r-htmltools" ,r-htmltools) ("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-later" ,r-later) + ("r-lifecycle" ,r-lifecycle) ("r-mime" ,r-mime) ("r-promises" ,r-promises) ("r-r6" ,r-r6) @@ -1411,17 +1676,21 @@ data structures in C++.") ("r-xtable" ,r-xtable))) (inputs `(("js-datatables" ,js-datatables) - ("js-html5shiv" ,js-html5shiv) - ("js-json2" ,js-json2) - ("js-respond" ,js-respond) ("js-selectize" ,js-selectize) ("js-strftime" ,js-strftime) - ("js-highlight" ,js-highlight) - ("js-es5-shim" ,js-es5-shim))) + ("js-highlight" ,js-highlight))) (native-inputs `(("uglify-js" ,uglify-js) - ("gfortran" ,gfortran))) - (home-page "http://shiny.rstudio.com") + ("gfortran" ,gfortran) + ("js-bootstrap-accessibility" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\ +v1.0.7/_site/plugins/js/bootstrap-accessibility.js") + (sha256 + (base32 + "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) + (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications @@ -1581,14 +1850,14 @@ well as file saving is available.") (define-public r-shinythemes (package (name "r-shinythemes") - (version "1.1.2") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "shinythemes" version)) (sha256 (base32 - "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf")))) + "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny))) @@ -1745,6 +2014,29 @@ in R and Shiny via the D3 visualization library.") from Wes Anderson movies.") (license license:expat))) +(define-public r-gg-gap + (package + (name "r-gg-gap") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "gg.gap" version)) + (sha256 + (base32 + "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h")))) + (properties `((upstream-name . "gg.gap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") + (synopsis "Define segments on the y-axis for ggplot2") + (description + "The @code{gg.gap} function enables you to define segments for the y-axis +in a ggplot2 plot.") + (license license:gpl3))) + (define-public r-tablerdash (package (name "r-tablerdash") @@ -2100,10 +2392,25 @@ including functions for geolocation and routing.") (uri (cran-uri "haven" version)) (sha256 (base32 - "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")))) + "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor readstat + (delete-file-recursively "src/readstat") + #t)))) (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unbundle-readstat + (lambda _ + ;; Not required, since we’re not building readstat. + (substitute* "src/Makevars" + (("-lz") "-lreadstat")) + #t))))) (inputs - `(("zlib" ,zlib))) + `(("readstat" ,readstat))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs @@ -2244,6 +2551,30 @@ inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) +(define-public r-palmerpenguins + (package + (name "r-palmerpenguins") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "palmerpenguins" version)) + (sha256 + (base32 + "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x")))) + (properties + `((upstream-name . "palmerpenguins"))) + (build-system r-build-system) + (home-page "https://allisonhorst.github.io/palmerpenguins/") + (synopsis "Palmer Archipelago (Antarctica) penguin data") + (description + "This package includes size measurements, clutch observations, and blood +isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins +observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. +Data were collected and made available by Dr. Kristen Gorman and the Palmer +Station Long Term Ecological Research (LTER) Program.") + (license license:cc0))) + (define-public r-pastecs (package (name "r-pastecs") @@ -2257,7 +2588,7 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot))) - (home-page "http://www.sciviews.org/pastecs") + (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description "This package provides functions for regulation, decomposition and analysis @@ -2268,13 +2599,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-11") + (version "1.2-13") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "00n6a74x257m2jk7jadjfxaclihxqpqwh356bgxmq8rag0nk70rs")))) + "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4")))) (build-system r-build-system) (propagated-inputs `(("r-formula" ,r-formula) @@ -2348,13 +2679,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl")))) + (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -2394,14 +2725,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q")))) + "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2444,6 +2775,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppthread + (package + (name "r-rcppthread") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppThread" version)) + (sha256 + (base32 + "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl")))) + (properties `((upstream-name . "RcppThread"))) + (build-system r-build-system) + (home-page + "https://github.com/tnagler/RcppThread") + (synopsis "R threading in C++") + (description + "This package provides a C++11-style thread class and thread pool that can +safely be interrupted from R.") + (license license:expat))) + (define-public r-bindr (package (name "r-bindr") @@ -2779,14 +3131,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.13.1") + (version "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x")))) + "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) @@ -2899,14 +3251,14 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "0lvcvlc8p2cii7rqx7m81f7cv3kk9mlf7cbbgv7l75g7ljw8dyvz")))) + "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs @@ -2938,14 +3290,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-24") + (version "0.4-25") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc")))) + "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -3021,13 +3373,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-9") + (version "0.6-9.1") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) + "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments @@ -3203,13 +3555,13 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (define-public r-inum (package (name "r-inum") - (version "1.0-1") + (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 - "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw")))) + "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin))) @@ -3403,17 +3755,18 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-7") + (version "1.7-8") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37")))) + "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) + ("r-gsl" ,r-gsl) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") @@ -3538,14 +3891,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.8.1") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d")))) + "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -3866,14 +4219,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-9") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) + "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -3946,14 +4299,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.3") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0bxwmqj37m06ci378xqlf7kar7pg5g903i1vnrv4i256dkj50mny")))) + "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4251,19 +4604,21 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.3-7") + (version "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) + "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) ("r-jomo" ,r-jomo) ("r-pan" ,r-pan))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description @@ -4276,14 +4631,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.12.0") + (version "3.13.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap")))) + "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -4717,19 +5072,17 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.2.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr")))) + "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-fansi" ,r-fansi) ("r-glue" ,r-glue))) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") @@ -4741,14 +5094,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (define-public r-argparser (package (name "r-argparser") - (version "0.6") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 - "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) + "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") @@ -4929,13 +5282,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.20") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "043wv9qihs3r29810mf8ajpn2iks1bxq44wbxz8sfpix5b8kjhi8")))) + (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4951,15 +5304,17 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.1.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) + "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -5031,14 +5386,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.7") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd")))) + "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -5049,6 +5404,8 @@ to variables on the left-hand side of the assignment.") ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8) ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description @@ -5079,14 +5436,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.28") + (version "0.30") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "11pa1q7gl17ala74lz10qbghk2yqanl9pylwvi9b4kmhx856b83n")))) + "0dk6mpszwh1m65b0wfwjlcvpzywmasf6p31niqiq53wnd92my0gw")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -5160,27 +5517,29 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-stabs (package - (name "r-stabs") - (version "0.6-3") - (source - (origin - (method url-fetch) - (uri (cran-uri "stabs" version)) - (sha256 + (name "r-stabs") + (version "0.6-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "stabs" version)) + (sha256 (base32 - "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9")))) - (build-system r-build-system) - (home-page "https://github.com/hofnerb/stabs") - (synopsis "Stability selection with error control") - (description - "This package provides resampling procedures to assess the stability of + "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/hofnerb/stabs") + (synopsis "Stability selection with error control") + (description + "This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013) are implemented. The package can be combined with arbitrary user specified variable selection approaches.") - (license license:gpl2))) + (license license:gpl2))) (define-public r-rle (package @@ -5350,17 +5709,16 @@ exhaustive search.") (define-public r-splus2r (package (name "r-splus2r") - (version "1.2-2") + (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "splus2R" version)) (sha256 (base32 - "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) + "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x")))) (properties `((upstream-name . "splus2R"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/splus2R/") (synopsis "Supplemental S-PLUS functionality in R") (description @@ -5804,14 +6162,14 @@ functions to enforce symmetric scales or add tags to facetted plots.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "1.1.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr")))) + "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6296,15 +6654,19 @@ are included.") (define-public r-riverplot (package (name "r-riverplot") - (version "0.6") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "riverplot" version)) (sha256 (base32 - "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z")))) + "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj")))) (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description @@ -6513,14 +6875,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.16") + (version "0.5.26") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) + "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -6530,6 +6892,8 @@ dependency on Java.") ("r-openxlsx" ,r-openxlsx) ("r-readxl" ,r-readxl) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description @@ -6547,14 +6911,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.0-2") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s")))) + "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -6600,14 +6964,14 @@ time after the current time, after the R execution stack has emptied.") (define-public r-promises (package (name "r-promises") - (version "1.1.1") + (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "promises" version)) (sha256 (base32 - "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p")))) + "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld")))) (build-system r-build-system) (propagated-inputs `(("r-later" ,r-later) @@ -6807,7 +7171,7 @@ JavaScript library) and interact with the igraph package.") ("r-stringi" ,r-stringi))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://github.com/gluc/data.tree") + (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description "Create tree structures from hierarchical data, and traverse the tree in @@ -6871,14 +7235,14 @@ the source data frame.") (define-public r-rappdirs (package (name "r-rappdirs") - (version "0.3.1") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rappdirs" version)) (sha256 (base32 - "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g")))) + "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") @@ -6891,14 +7255,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.49") + (version "0.50") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk")))) + "0m7fjd53apxim0d0rjnyzc28vmfcg4spcrn0zbnk8llillxji1hi")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs @@ -6908,6 +7272,7 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") ("r-raster" ,r-raster) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-sp" ,r-sp) + ("r-terra" ,r-terra) ("r-viridislite" ,r-viridislite) ("r-zoo" ,r-zoo))) (home-page "https://oscarperpinan.github.io/rastervis/") @@ -6949,14 +7314,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.12.5") + (version "0.13.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh")))) + "16n2dz9jibc03f7q1wrzxss6l5jmaks7m2lnli9dz9anvcmxbdia")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -7139,14 +7504,14 @@ movies, and TV shows.") (define-public r-ggsignif (package (name "r-ggsignif") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 - "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) + "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7166,14 +7531,14 @@ and adds the annotation to the plot.") (define-public r-rstatix (package (name "r-rstatix") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 - "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb")))) + "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs @@ -7542,19 +7907,18 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16")))) + "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs - `(("r-rbibutils" ,r-rbibutils) - ("r-gbrd" ,r-gbrd))) + `(("r-rbibutils" ,r-rbibutils))) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description @@ -7569,14 +7933,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.16") + (version "0.3.17") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj")))) + "1apg0dh1zfhrqcbbmm8318l40gyjbqc2l9sdvwxx7qi8mzc1mqvw")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -7830,14 +8194,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.12.0") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s")))) + "1la4yxzfl9fnknamnaziil6gvpdzl78z16lfzis9jgzg8r9q0y5l")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7966,14 +8330,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.1") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li")))) + "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -8098,14 +8462,14 @@ support for default values, positional argument support, etc.") (define-public r-findpython (package (name "r-findpython") - (version "1.0.5") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 - "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy")))) + "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") @@ -8192,14 +8556,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "4.1.2") + (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64")))) + "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") @@ -8214,14 +8578,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.8") + (version "4.6.9") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg")))) + "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -8236,7 +8600,7 @@ the work.") ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") + (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description "This package contains: @@ -8300,14 +8664,14 @@ procedures to speed up calculations in R.") (define-public r-blockfest (package (name "r-blockfest") - (version "1.8") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 - "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5")))) + "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) @@ -8648,22 +9012,22 @@ and coverage methods to tune the choice of threshold.") (define-public r-labelled (package (name "r-labelled") - (version "2.7.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi")))) + "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-haven" ,r-haven) ("r-lifecycle" ,r-lifecycle) - ("r-pillar" ,r-pillar) ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) ("r-tidyr" ,r-tidyr) ("r-vctrs" ,r-vctrs))) (native-inputs @@ -8934,14 +9298,14 @@ genotypes as \"graphical genotypes\".") (define-public r-furrr (package (name "r-furrr") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 - "16s6sgfgh1ayzhf3kvpy9vhsd5h6p57waj1xgbksgdmf4j1wkcq7")))) + "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -9186,13 +9550,13 @@ singular or ill-conditioned Jacobian.") (define-public r-physicalactivity (package (name "r-physicalactivity") - (version "0.2-2") + (version "0.2-4") (source (origin (method url-fetch) (uri (cran-uri "PhysicalActivity" version)) (sha256 - (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) + (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40")))) (properties `((upstream-name . "PhysicalActivity"))) (build-system r-build-system) @@ -9327,14 +9691,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36")))) + "0m1kij6pp7dmsrhl80h60iyccjqmbbb3zdnqdc9sgy1kj1x3pscp")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -9741,14 +10105,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-15") + (version "1.4-16") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr")))) + "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) @@ -9769,14 +10133,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.3") + (version "1.5.4") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "11x7bn260v91gb7qri1pq54l339zm4msa5frc8saqb9ykbg4dby5")))) + "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -9820,13 +10184,13 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-7") + (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 - (base32 "1vb21pw3vpv2pdnfcddw2bax13v0dg656r28j0p8njcyhwk89xln")))) + (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") @@ -9839,14 +10203,14 @@ and permutation inference in the framework of Strasser and Weber (1999).") (define-public r-coin (package (name "r-coin") - (version "1.4-0") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 - "1n2ad4m3zw8px6yc0h750k59pci3fqpnr742hhvsqirrwcdzp6zv")))) + "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) @@ -9902,14 +10266,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.18") + (version "1.7.19") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y")))) + "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -10005,14 +10369,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw")))) + "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -10032,14 +10396,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0wz2zc98r99pg6r4l09qxxzv1fwxwp1md6wmhay401568kd8h5zn")))) + "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -10089,14 +10453,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2")))) + "0mgkq12ym72ncakkjpkzkjglhksyhj3iw8v4a8fjgpf7prvn191g")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -10317,14 +10681,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.0.2") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1lq4hgv2727lwcv8vha5af26nslj99rjxjrgflshmmcihawpls1n")))) + "0ag2ia6cfb5drf3517lg5nhik1w0nv09a75wdy5jdciws1qra3d6")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -10335,6 +10699,7 @@ user credentials.") ("r-credentials" ,r-credentials) ("r-openssl" ,r-openssl) ("r-rstudioapi" ,r-rstudioapi) + ("r-sys" ,r-sys) ("r-zip" ,r-zip))) (native-inputs `(("pkg-config" ,pkg-config) @@ -10352,14 +10717,14 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "0m4qnnkdiizsdvq33x502zwkn98hw2qcfm45cjj031vaydcjpai2")))) + "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -10645,14 +11010,14 @@ algorithms, clusterings, and individual clusters.") (define-public r-tweedie (package (name "r-tweedie") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "tweedie" version)) (sha256 (base32 - "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) + "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/tweedie/") @@ -10694,14 +11059,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.6") + (version "4.1.9") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f")))) + "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -10883,14 +11248,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.0.2") + (version "5.0.3") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc")))) + "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -10952,14 +11317,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.104.16") + (version "0.105.22") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq")))) + "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -11036,13 +11401,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.11.7") + (version "1.12.0") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba")))) + (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) @@ -11052,8 +11417,9 @@ isosurfaces.") ("r-mclust" ,r-mclust) ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) - ("r-mvtnorm" ,r-mvtnorm))) - (home-page "http://www.mvstat.net/tduong/") + ("r-mvtnorm" ,r-mvtnorm) + ("r-plot3d" ,r-plot3d))) + (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate @@ -11066,20 +11432,21 @@ hypothesis testing.") (define-public r-feature (package (name "r-feature") - (version "1.2.14") + (version "1.2.15") (source (origin (method url-fetch) (uri (cran-uri "feature" version)) (sha256 (base32 - "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1")))) + "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs - `(("r-ks" ,r-ks))) + `(("r-ks" ,r-ks) + ("r-plot3d" ,r-plot3d))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://www.mvstat.net/tduong/") + (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel @@ -11145,14 +11512,14 @@ Scientific.") (define-public r-activity (package (name "r-activity") - (version "1.3") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 - "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) + "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5")))) (build-system r-build-system) (propagated-inputs `(("r-circular" ,r-circular) @@ -11171,14 +11538,14 @@ circular variables).") (define-public r-ouch (package (name "r-ouch") - (version "2.14-1") + (version "2.15-1") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 - "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) + "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) (home-page "https://kingaa.github.io/ouch/") @@ -11329,16 +11696,18 @@ components).") (define-public r-fftwtools (package (name "r-fftwtools") - (version "0.9-9") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 - "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9")))) + "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs `(("fftw" ,fftw))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description @@ -11354,14 +11723,14 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-6") + (version "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2")))) + "101n6x70fr1dhcwx53g3s8q1j4wh93y0388v1s1316f8558rxqxh")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) @@ -12208,14 +12577,14 @@ Emphasis is always given to methods for visualizing the data.") (define-public r-pixmap (package (name "r-pixmap") - (version "0.4-11") + (version "0.4-12") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 - "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) + "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") @@ -12246,16 +12615,18 @@ library.") (define-public r-ontologyindex (package (name "r-ontologyindex") - (version "2.5") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 - "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) + "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") (synopsis "Functions for processing ontologies in R") (description @@ -12266,14 +12637,14 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "0.5.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n")))) + "0hsqn4hf935wn6vk2pwym7la4sdvy271y4cashp38pg4hkpg9zph")))) (build-system r-build-system) (propagated-inputs `(("r-fs" ,r-fs) @@ -12384,14 +12755,14 @@ Precision Floating-Point Reliable} (MPFR) library.") (define-public r-assertive-base (package (name "r-assertive-base") - (version "0.0-7") + (version "0.0-9") (source (origin (method url-fetch) (uri (cran-uri "assertive.base" version)) (sha256 (base32 - "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) + "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b")))) (properties `((upstream-name . "assertive.base"))) (build-system r-build-system) @@ -12800,14 +13171,14 @@ to throw errors if they aren't in the right form.") (define-public r-dotcall64 (package (name "r-dotcall64") - (version "1.0-0") + (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 - "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) + "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -13146,14 +13517,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.42") + (version "2.44") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl")))) + "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -13166,6 +13537,7 @@ model with finite state space using the Aalen-Johansen estimator.") ("r-mgcv" ,r-mgcv) ("r-numderiv" ,r-numderiv) ("r-plyr" ,r-plyr) + ("r-purrr" ,r-purrr) ("r-survival" ,r-survival) ("r-zoo" ,r-zoo))) (home-page "https://BendixCarstensen.com/Epi/") @@ -13329,14 +13701,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.23.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p")))) + "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -13603,14 +13975,14 @@ several common set, element and attribute related tasks.") (define-public r-shinyjqui (package (name "r-shinyjqui") - (version "0.3.3") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjqui" version)) (sha256 (base32 - "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x")) + "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah")) (snippet '(begin (delete-file "inst/www/shinyjqui.min.js"))))) @@ -13820,13 +14192,13 @@ such software by imputing dropout events.") (define-public r-gamlss-dist (package (name "r-gamlss-dist") - (version "5.1-7") + (version "5.3-2") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 - (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq")))) + (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -14077,21 +14449,21 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-7") + (version "0.6-8") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk")))) + "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-mnormt" ,r-mnormt) ("r-numderiv" ,r-numderiv) ("r-pbivnorm" ,r-pbivnorm))) - (home-page "http://lavaan.ugent.be") + (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description "This package provides tools to fit a variety of latent variable models, @@ -14228,14 +14600,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-4") + (version "0.3-5") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "0adiac53yq305ymhrds1gas4jm0rn1ddv7c7df5ky2cfhpb4ny87")))) + "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs @@ -14256,14 +14628,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.1.0") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl")))) + "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -14280,14 +14652,14 @@ several formats and MIME types.") (define-public r-irdisplay (package (name "r-irdisplay") - (version "0.7.0") + (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 - "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) + "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs @@ -14779,14 +15151,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.6-7") + (version "0.7-0") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz")))) + "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) @@ -14804,6 +15176,27 @@ is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} classes.") (license license:gpl2))) +(define-public r-udunits2 + (package + (name "r-udunits2") + (version "0.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "udunits2" version)) + (sha256 + (base32 + "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi")))) + (properties `((upstream-name . "udunits2"))) + (build-system r-build-system) + (inputs + `(("udunits" ,udunits))) + (home-page "https://cran.r-project.org/package=udunits2") + (synopsis "Udunits-2 bindings for R") + (description + "This package provides simple bindings to Unidata's udunits library.") + (license license:gpl2))) + (define-public r-classint (package (name "r-classint") @@ -14887,14 +15280,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.2-9") + (version "0.2-10") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm")))) + "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -15076,14 +15469,14 @@ genetics of complex population dynamics.") (define-public r-genetics (package (name "r-genetics") - (version "1.3.8.1.2") + (version "1.3.8.1.3") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 - "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) + "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs `(("r-combinat" ,r-combinat) @@ -15151,13 +15544,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.1-0") + (version "6.1-1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq")))) + (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -15197,14 +15590,14 @@ generalized linear models, and quantile regression.") (define-public r-arsenal (package (name "r-arsenal") - (version "3.5.0") + (version "3.6.2") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 - "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0")))) + "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr))) @@ -15820,14 +16213,14 @@ consists of @code{grid} grobs and viewports that can then be manipulated with (define-public r-farver (package (name "r-farver") - (version "2.0.3") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 - "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f")))) + "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") @@ -15973,14 +16366,14 @@ sets of URLs.") (define-public r-ggforce (package (name "r-ggforce") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 - "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc")))) + "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -16046,14 +16439,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.") (define-public r-ggraph (package (name "r-ggraph") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 - "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w")))) + "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -16083,6 +16476,32 @@ visualizations and provides the same flexible approach to building up plots layer by layer.") (license license:gpl3))) +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.81.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-seqinr" ,r-seqinr))) + (home-page "https://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) + (define-public r-varselrf (package (name "r-varselrf") @@ -16280,14 +16699,14 @@ using the three.js visualization library.") (define-public r-mlbench (package (name "r-mlbench") - (version "2.1-1") + (version "2.1-3") (source (origin (method url-fetch) (uri (cran-uri "mlbench" version)) (sha256 (base32 - "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) + "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mlbench/") (synopsis "Machine learning benchmark problems") @@ -16368,6 +16787,64 @@ matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.") (license license:gpl2))) +(define-public r-gridtext + (package + (name "r-gridtext") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gridtext" version)) + (sha256 + (base32 + "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61")))) + (properties `((upstream-name . "gridtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-jpeg" ,r-jpeg) + ("r-markdown" ,r-markdown) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-xml2" ,r-xml2))) + (home-page "https://wilkelab.org/gridtext/") + (synopsis "Improved text rendering support for Grid graphics") + (description + "This package provides support for rendering of formatted text using Grid +graphics. Text can be formatted via a minimal subset of Markdown, HTML, and +inline CSS directives, and it can be rendered both with and without word +wrap.") + (license license:expat))) + +(define-public r-ggtext + (package + (name "r-ggtext") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggtext" version)) + (sha256 + (base32 + "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b")))) + (properties `((upstream-name . "ggtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridtext" ,r-gridtext) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://wilkelab.org/ggtext/") + (synopsis "Improved text rendering support for ggplot2") + (description + "This package provides a ggplot2 extension that enables the rendering of +complex formatted plot labels (titles, subtitles, facet labels, axis labels, +etc.). Text boxes with automatic word wrap are also supported.") + (license license:gpl2))) + ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-flexdashboard @@ -16610,14 +17087,14 @@ regular expressions from human readable expressions") (define-public r-xmlparsedata (package (name "r-xmlparsedata") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "xmlparsedata" version)) (sha256 (base32 - "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq")))) + "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n")))) (properties `((upstream-name . "xmlparsedata"))) (build-system r-build-system) (home-page "https://github.com/r-lib/xmlparsedata#readme") @@ -16933,14 +17410,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "2.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w")))) + "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -17038,14 +17515,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.0.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98")))) + "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -17067,19 +17544,22 @@ and model output.") (define-public r-enrichr (package (name "r-enrichr") - (version "2.1") + (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 - "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1")))) + "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) + `(("r-ggplot2" ,r-ggplot2) + ("r-httr" ,r-httr) ("r-rjson" ,r-rjson))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description @@ -17299,14 +17779,14 @@ LargeVis method of Tang et al. (2016) is also provided.") (define-public r-kableextra (package (name "r-kableextra") - (version "1.3.1") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 - "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf")))) + "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs @@ -17320,6 +17800,7 @@ LargeVis method of Tang et al. (2016) is also provided.") ("r-rvest" ,r-rvest) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) + ("r-svglite" ,r-svglite) ("r-viridislite" ,r-viridislite) ("r-webshot" ,r-webshot) ("r-xml2" ,r-xml2))) @@ -17427,14 +17908,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7")))) + "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs @@ -17632,14 +18113,14 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "0.3.2") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "12hdvv66kkd3b4rs82blc3c4ifz2dw1048sqpkbz6vkk1zqpc53x")))) + "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs @@ -17687,6 +18168,41 @@ stress majorization by Gansner et al. (2004) emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) +(define-public r-terra + (package + (name "r-terra") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "terra" version)) + (sha256 + (base32 + "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg")))) + (properties `((upstream-name . "terra"))) + (build-system r-build-system) + (inputs + `(("gdal" ,gdal) + ("geos" ,geos) + ("proj" ,proj) + ("sqlite" ,sqlite) ; needed for proj + ("zlib" ,zlib))) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://rspatial.org/terra") + (synopsis "Spatial data analysis") + (description + "This package provides methods for spatial data analysis, especially +raster data. The included methods allow for low-level data manipulation as +well as high-level global, local, zonal, and focal computation. The predict +and interpolate methods facilitate the use of regression type (interpolation, +machine learning) models for spatial prediction. Processing of very large +files is supported.") + (license license:gpl3+))) + (define-public r-tidygraph (package (name "r-tidygraph") @@ -17753,14 +18269,14 @@ cell RNA-seq experiments.") (define-public r-assertr (package (name "r-assertr") - (version "2.7") + (version "2.8") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 - "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb")))) + "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -17780,14 +18296,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc")))) + "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -17809,13 +18325,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-19") + (version "1.5-23") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg")))) + (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -17838,14 +18354,14 @@ PROJ.4 library.") (define-public r-insol (package (name "r-insol") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 - "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1")))) + "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs @@ -17865,14 +18381,14 @@ atmospheric physics.") (define-public r-lifecycle (package (name "r-lifecycle") - (version "0.2.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 - "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19")))) + "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs @@ -17895,17 +18411,19 @@ signalled with increasing levels of non-invasive verbosity.") (define-public r-assertable (package (name "r-assertable") - (version "0.2.7") + (version "0.2.8") (source (origin (method url-fetch) (uri (cran-uri "assertable" version)) (sha256 (base32 - "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk")))) + "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on @@ -17971,12 +18489,12 @@ to ODEs by numerical differencing.") (define-public r-pracma (package (name "r-pracma") - (version "2.2.9") + (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc")))) + (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -19098,14 +19616,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.2-0") + (version "5.3-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk")))) + "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -20309,14 +20827,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k")))) + "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -20386,14 +20904,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.3") + (version "0.42.7") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg")))) + "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -21202,14 +21720,14 @@ both exclusive and shared locking.") (define-public r-archivist (package (name "r-archivist") - (version "2.3.4") + (version "2.3.5") (source (origin (method url-fetch) (uri (cran-uri "archivist" version)) (sha256 (base32 - "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7")))) + "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k")))) (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs @@ -21221,6 +21739,8 @@ both exclusive and shared locking.") ("r-magrittr" ,r-magrittr) ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://pbiecek.github.io/archivist/") (synopsis "Tools for storing, restoring and searching for R objects") (description @@ -21372,14 +21892,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.13") + (version "8.14") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9")))) + "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -21458,14 +21978,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2020.12.04") + (version "2021.02.24") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx")))) + "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -21480,20 +22000,18 @@ character codes as well as the UN M.49 area codes.") (define-public r-stopwords (package (name "r-stopwords") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 - "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8")))) + "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs - `(("r-desc" ,r-desc) - ("r-isocodes" ,r-isocodes) - ("r-usethis" ,r-usethis))) + `(("r-isocodes" ,r-isocodes))) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description @@ -21598,17 +22116,17 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-11") + (version "0.2-12") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw")))) + "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g")))) (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) - (native-inputs + (inputs `(("gsl" ,gsl))) (propagated-inputs `(("r-modeltools" ,r-modeltools) @@ -21936,14 +22454,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.18.1") + (version "2.19.1") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm")))) + "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -22097,30 +22615,26 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.6.5") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592")))) + "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-bdgraph" ,r-bdgraph) ("r-colorspace" ,r-colorspace) ("r-corpcor" ,r-corpcor) - ("r-d3network" ,r-d3network) ("r-dplyr" ,r-dplyr) ("r-fdrtool" ,r-fdrtool) ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) ("r-glasso" ,r-glasso) ("r-gtools" ,r-gtools) ("r-hmisc" ,r-hmisc) - ("r-huge" ,r-huge) ("r-igraph" ,r-igraph) ("r-jpeg" ,r-jpeg) ("r-lavaan" ,r-lavaan) @@ -22130,8 +22644,7 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") ("r-png" ,r-png) ("r-psych" ,r-psych) ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-tidygraph" ,r-tidygraph))) + ("r-reshape2" ,r-reshape2))) (home-page "http://sachaepskamp.com/qgraph/") (synopsis "Weighted network visualization and analysis") (description @@ -22247,14 +22760,14 @@ Latent regression models and plausible value imputation are also supported.") (define-public r-erm (package (name "r-erm") - (version "1.0-1") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "eRm" version)) (sha256 (base32 - "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9")))) + "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk")))) (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs @@ -22885,18 +23398,16 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr")))) + "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) - (propagated-inputs - `(("r-testthat" ,r-testthat))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/wilkelab/isoband") @@ -22997,7 +23508,7 @@ as possible (with tests to prove it).") "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp")))) (properties `((upstream-name . "boa"))) (build-system r-build-system) - (home-page "http://www.jstatsoft.org/v21/i11") + (home-page "https://www.jstatsoft.org/v21/i11") (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC") (description "This package provides a menu-driven program and library of functions for @@ -23477,6 +23988,17 @@ download images.") (base32 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'install-server-binary + ;; Makevars tries to install to R's store directory. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (substitute* "src/Makevars.in" + (("\\$\\(R_HOME\\)") out)) + (mkdir-p bin))))))) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-mime" ,r-mime) @@ -23596,14 +24118,14 @@ vignette for more information and examples.") (define-public r-brms (package (name "r-brms") - (version "2.14.4") + (version "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j")))) + "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -24274,14 +24796,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "1.20-2") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2")))) + "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -24292,17 +24814,44 @@ diagonals. This package allows you to compute the tensor product of arrays.") which may also be useful for other purposes.") (license license:gpl2+))) +(define-public r-spatstat-sparse + (package + (name "r-spatstat-sparse") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.sparse" version)) + (sha256 + (base32 + "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2")))) + (properties + `((upstream-name . "spatstat.sparse"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-matrix" ,r-matrix) + ("r-spatstat-utils" ,r-spatstat-utils) + ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Sparse three-dimensional arrays and linear algebra utilities") + (description + "This package defines sparse three-dimensional arrays and supports +standard operations on them. The package also includes utility functions for +matrix calculations that are common in statistics, such as quadratic forms.") + (license license:gpl2+))) + (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "1.7-0") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv")))) + "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -24315,31 +24864,111 @@ which may also be useful for other purposes.") package.") (license license:gpl2+))) -(define-public r-spatstat +(define-public r-spatstat-geom (package - (name "r-spatstat") - (version "1.64-1") + (name "r-spatstat-geom") + (version "1.65-5") (source (origin (method url-fetch) - (uri (cran-uri "spatstat" version)) + (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya")))) - (properties `((upstream-name . "spatstat"))) + "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk")))) + (properties `((upstream-name . "spatstat.geom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-deldir" ,r-deldir) + ("r-polyclip" ,r-polyclip) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-sparse" ,r-spatstat-sparse) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Geometrical functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing the +user-level code from spatstat which performs geometrical operations, except +for the geometry of linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-core + (package + (name "r-spatstat-core") + (version "1.65-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.core" version)) + (sha256 + (base32 + "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3")))) + (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-deldir" ,r-deldir) ("r-goftest" ,r-goftest) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-nlme" ,r-nlme) - ("r-polyclip" ,r-polyclip) ("r-rpart" ,r-rpart) ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-sparse" ,r-spatstat-sparse) ("r-spatstat-utils" ,r-spatstat-utils) ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Core functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing all of the +user-level code from spatstat, except for the code for linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-linnet + (package + (name "r-spatstat-linnet") + (version "1.65-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.linnet" version)) + (sha256 + (base32 + "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv")))) + (properties + `((upstream-name . "spatstat.linnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Linear networks functionality of the spatstat package") + (description + "This is a subset of the spatstat package, containing its functionality +for spatial data on a linear network.") + (license license:gpl2+))) + +(define-public r-spatstat + (package + (name "r-spatstat") + (version "2.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat" version)) + (sha256 + (base32 + "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw")))) + (properties `((upstream-name . "spatstat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-linnet" ,r-spatstat-linnet) + ("r-spatstat-utils" ,r-spatstat-utils))) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -24385,14 +25014,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.5") + (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg")))) + "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -24595,26 +25224,36 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "1.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr")))) + "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs - `(("r-desolve" ,r-desolve) + `(("r-assertthat" ,r-assertthat) + ("r-desolve" ,r-desolve) + ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) ("r-mstate" ,r-mstate) ("r-muhaz" ,r-muhaz) ("r-mvtnorm" ,r-mvtnorm) + ("r-numderiv" ,r-numderiv) + ("r-purrr" ,r-purrr) ("r-quadprog" ,r-quadprog) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) + ("r-rstpm2" ,r-rstpm2) ("r-survival" ,r-survival) ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/chjackson/flexsurv-dev") @@ -24780,14 +25419,14 @@ p-value approximations.") (define-public r-survminer (package (name "r-survminer") - (version "0.4.8") + (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "survminer" version)) (sha256 (base32 - "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff")))) + "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz")))) (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs @@ -24795,6 +25434,7 @@ p-value approximations.") ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) + ("r-ggtext" ,r-ggtext) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) ("r-maxstat" ,r-maxstat) @@ -24963,14 +25603,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9")))) + "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -24981,7 +25621,8 @@ more.") ("r-hardhat" ,r-hardhat) ("r-parsnip" ,r-parsnip) ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidymodels/workflows") @@ -25112,14 +25753,14 @@ sliding windows are to be created.") (define-public r-rsample (package (name "r-rsample") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i")))) + "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs @@ -25127,7 +25768,6 @@ sliding windows are to be created.") ("r-ellipsis" ,r-ellipsis) ("r-furrr" ,r-furrr) ("r-generics" ,r-generics) - ("r-modeldata" ,r-modeldata) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-slider" ,r-slider) @@ -25147,14 +25787,14 @@ different types of resampling objects (e.g. bootstrap, cross-validation).") (define-public r-dicedesign (package (name "r-dicedesign") - (version "1.8-1") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "DiceDesign" version)) (sha256 (base32 - "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp")))) + "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk")))) (properties `((upstream-name . "DiceDesign"))) (build-system r-build-system) (home-page "http://dice.emse.fr/") @@ -25199,14 +25839,14 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37")))) + "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs @@ -25218,7 +25858,6 @@ for creating, simulating, or validating values for such parameters.") ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-gpfit" ,r-gpfit) - ("r-hardhat" ,r-hardhat) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) ("r-recipes" ,r-recipes) @@ -25811,18 +26450,59 @@ as allowing spectra with different resolutions.") data to rasters. It speeds up plotting of data with millions of points.") (license license:gpl3+))) +(define-public r-seuratobject + (package + (name "r-seuratobject") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "SeuratObject" version)) + (sha256 + (base32 + "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii")))) + (properties `((upstream-name . "SeuratObject"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rlang" ,r-rlang) + ("r-sctransform" ,r-sctransform))) + (home-page "https://satijalab.org/seurat") + (synopsis "Data structures for single cell data") + (description + "This package defines S4 classes for single-cell genomic data and +associated information, such as dimensionality reduction embeddings, +nearest-neighbor graphs, and spatially-resolved coordinates. It provides data +access methods and R-native hooks to ensure the Seurat object is familiar to +other R users.") + (license license:gpl3))) + (define-public r-seurat (package (name "r-seurat") - (version "3.2.3") + (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3")))) + "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) + ;; This is needed because r-spatstat has been split up and there has + ;; been no new release of Seurat since then. + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-spatstat-import + (lambda _ + (substitute* "NAMESPACE" + (("importFrom\\(spatstat,markvario\\)") + "importFrom(spatstat.core,markvario)") + (("importFrom\\(spatstat,ppp\\)") + "importFrom(spatstat.geom,ppp)"))))))) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) @@ -25857,11 +26537,11 @@ data to rasters. It speeds up plotting of data with millions of points.") ("r-reticulate" ,r-reticulate) ("r-rlang" ,r-rlang) ("r-rocr" ,r-rocr) - ("r-rsvd" ,r-rsvd) ("r-rtsne" ,r-rtsne) ("r-scales" ,r-scales) ("r-scattermore" ,r-scattermore) ("r-sctransform" ,r-sctransform) + ("r-seuratobject" ,r-seuratobject) ("r-shiny" ,r-shiny) ("r-spatstat" ,r-spatstat) ("r-tibble" ,r-tibble) @@ -26208,13 +26888,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-paradox (package (name "r-paradox") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 - "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3")))) + "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -26233,13 +26913,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.9.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb")))) + "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -26252,7 +26932,9 @@ implemented as @code{R6} classes.") ("r-mlbench" ,r-mlbench) ("r-mlr3measures" ,r-mlr3measures) ("r-mlr3misc" ,r-mlr3misc) + ("r-palmerpenguins" ,r-palmerpenguins) ("r-paradox" ,r-paradox) + ("r-parallelly" ,r-parallelly) ("r-uuid" ,r-uuid))) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") @@ -26293,14 +26975,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.2.2") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv")))) + "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -26310,6 +26992,8 @@ vector machines, and gradient boosting.") ("r-mlr3misc" ,r-mlr3misc) ("r-paradox" ,r-paradox) ("r-r6" ,r-r6))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of @@ -26321,13 +27005,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.5.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m")))) + "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv")))) (build-system r-build-system) (propagated-inputs `(("r-bbotk" ,r-bbotk) @@ -26559,3 +27243,1014 @@ unit tests of graphics).") to add graphical unit tests. It provides a Shiny application to manage the test cases.") (license license:gpl3))) + +(define-public r-highlight + (package + (name "r-highlight") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "highlight" version)) + (sha256 + (base32 + "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf")))) + (properties `((upstream-name . "highlight"))) + (build-system r-build-system) + (home-page "https://github.com/hadley/highlight") + (synopsis "Syntax highlighter for R code") + (description + "This package provides a syntax highlighter for R code based on the +results of the R parser. It supports rendering in HTML and LaTeX markup. It +includes a custom Sweave driver performing syntax highlighting of R code +chunks.") + (license license:gpl3+))) + +(define-public r-clustree + (package + (name "r-clustree") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "clustree" version)) + (sha256 + (base32 + "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz")))) + (properties `((upstream-name . "clustree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggraph" ,r-ggraph) + ("r-ggrepel" ,r-ggrepel) + ("r-igraph" ,r-igraph) + ("r-rlang" ,r-rlang) + ("r-tidygraph" ,r-tidygraph) + ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lazappi/clustree") + (synopsis "Visualize clusterings at different resolutions") + (description + "Deciding what resolution to use can be a difficult question when +approaching a clustering analysis. One way to approach this problem is to +look at how samples move as the number of clusters increases. This package +allows you to produce clustering trees, a visualization for interrogating +clusterings as resolution increases.") + (license license:gpl3))) + +(define-public r-textshaping + (package + (name "r-textshaping") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "textshaping" version)) + (sha256 + (base32 + "0fqh4z505b2qriqcj70g2hhdgiawd3w2rs9rqxdwizz5vk8jjygx")))) + (properties `((upstream-name . "textshaping"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("fribidi" ,fribidi) + ("harfbuzz" ,harfbuzz) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-cpp11" ,r-cpp11) + ("r-systemfonts" ,r-systemfonts))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/r-lib/textshaping") + (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") + (description + "This package provides access to the text shaping functionality in the +HarfBuzz library and the bidirectional algorithm in the Fribidi library. This +is a low-level utility package mainly for graphic devices that expands upon +the font tool-set provided by the @code{systemfonts} package.") + (license license:expat))) + +(define-public r-ragg + (package + (name "r-ragg") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ragg" version)) + (sha256 + (base32 + "0nh1xxrxgdbq9anzkc6k3n519czp9hqyiizakm3m2gl4l4w0vp0q")))) + (properties `((upstream-name . "ragg"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libjpeg" ,libjpeg-turbo) + ("libpng" ,libpng) + ("libtiff" ,libtiff) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-systemfonts" ,r-systemfonts) + ("r-textshaping" ,r-textshaping))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://ragg.r-lib.org") + (synopsis "Graphic devices based on AGG") + (description + "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D +drawing library. The ragg package provides a set of graphic devices based on +AGG to use as alternative to the raster devices provided through the +@code{grDevices} package.") + (license license:expat))) + +(define-public r-downlit + (package + (name "r-downlit") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "downlit" version)) + (sha256 + (base32 + "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6")))) + (properties `((upstream-name . "downlit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-brio" ,r-brio) + ("r-digest" ,r-digest) + ("r-evaluate" ,r-evaluate) + ("r-fansi" ,r-fansi) + ("r-rlang" ,r-rlang) + ("r-vctrs" ,r-vctrs) + ("r-yaml" ,r-yaml))) + (home-page "https://downlit.r-lib.org/") + (synopsis "Syntax highlighting and automatic linking") + (description + "This package provides syntax highlighting of R code, specifically +designed for the needs of RMarkdown packages like @code{pkgdown}, +@code{hugodown}, and @code{bookdown}. It includes linking of function calls +to their documentation on the web, and automatic translation of ANSI escapes +in output to the equivalent HTML.") + (license license:expat))) + +(define-public r-pkgdown + (package + (name "r-pkgdown") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgdown" version)) + (sha256 + (base32 + "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4")))) + (properties `((upstream-name . "pkgdown"))) + (build-system r-build-system) + (inputs `(("pandoc" ,pandoc))) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) + ("r-digest" ,r-digest) + ("r-downlit" ,r-downlit) + ("r-fs" ,r-fs) + ("r-httr" ,r-httr) + ("r-magrittr" ,r-magrittr) + ("r-memoise" ,r-memoise) + ("r-openssl" ,r-openssl) + ("r-purrr" ,r-purrr) + ("r-ragg" ,r-ragg) + ("r-rematch2" ,r-rematch2) + ("r-rlang" ,r-rlang) + ("r-rmarkdown" ,r-rmarkdown) + ("r-tibble" ,r-tibble) + ("r-whisker" ,r-whisker) + ("r-withr" ,r-withr) + ("r-xml2" ,r-xml2) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://pkgdown.r-lib.org") + (synopsis "Make static HTML documentation for an R package") + (description + "The goal of this package is to generate an attractive and useful website +from a source package. @code{pkgdown} converts your documentation, vignettes, +README file, and more to HTML making it easy to share information about your +package online.") + (license license:expat))) + +(define-public r-prereg + (package + (name "r-prereg") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "prereg" version)) + (sha256 + (base32 + "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi")))) + (properties `((upstream-name . "prereg"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rmarkdown" ,r-rmarkdown))) + (home-page "https://github.com/crsh/prereg") + (synopsis + "R Markdown Templates to preregister Scientific Studies") + (description + "This package provides a collection of templates to author +preregistration documents for scientific studies in PDF format.") + (license license:gpl3))) + +(define-public r-ez + (package + (name "r-ez") + (version "4.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ez" version)) + (sha256 + (base32 + "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) + (properties `((upstream-name . "ez"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/mike-lawrence/ez") + (synopsis "Easy Analysis and Visualization of Factorial Experiments") + (description + "Facilitates easy analysis of factorial experiments, including purely +within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs, +and mixed within-and-between-Ss designs. The functions in this package aim to +provide simple, intuitive and consistent specification of data analysis and +visualization. Visualization functions also include design visualization for +pre-analysis data auditing, and correlation matrix visualization. Finally, +this package includes functions for non-parametric analysis, including +permutation tests and bootstrap resampling. The bootstrap function obtains +predictions either by cell means or by more advanced/powerful mixed effects +models, yielding predictions and confidence intervals that may be easily +visualized at any level of the experiment's design.") + (license license:gpl2+))) + +(define-public r-qdapregex + (package + (name "r-qdapregex") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "qdapRegex" version)) + (sha256 + (base32 + "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p")))) + (properties `((upstream-name . "qdapRegex"))) + (build-system r-build-system) + (propagated-inputs `(("r-stringi" ,r-stringi))) + (home-page + "https://trinker.github.com/qdapRegex/") + (synopsis + "Regular Expression Removal, Extraction, and Replacement Tools") + (description + "This package provides a collection of regular expression tools +associated with the @code{qdap} package that may be useful outside of the +context of discourse analysis. Tools include removal/extraction/replacement of +abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, +percentages, citations, person tags, phone numbers, times, and zip codes.") + (license license:gpl2))) + +(define-public r-mgsub + (package + (name "r-mgsub") + (version "1.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "mgsub" version)) + (sha256 + (base32 + "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr")))) + (properties `((upstream-name . "mgsub"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=mgsub") + (synopsis + "Safe, Multiple, Simultaneous String Substitution") + (description + "Designed to enable simultaneous substitution in strings in a safe +fashion. Safe means it does not rely on placeholders (which can cause errors +in same length matches).") + (license license:expat))) + +(define-public r-textshape + (package + (name "r-textshape") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "textshape" version)) + (sha256 + (base32 + "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa")))) + (properties `((upstream-name . "textshape"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-slam" ,r-slam) + ("r-stringi" ,r-stringi))) + (home-page "http://github.com/trinker/textshape") + (synopsis "Tools for Reshaping Text") + (description + "Tools that can be used to reshape and restructure text data.") + (license license:gpl2))) + +(define-public r-syuzhet + (package + (name "r-syuzhet") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "syuzhet" version)) + (sha256 + (base32 + "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv")))) + (properties `((upstream-name . "syuzhet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-dtt" ,r-dtt) + ("r-nlp" ,r-nlp) + ("r-rlang" ,r-rlang) + ("r-textshape" ,r-textshape) + ("r-tidyr" ,r-tidyr) + ("r-zoo" ,r-zoo))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mjockers/syuzhet") + (synopsis + "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") + (description + "Extracts sentiment and sentiment-derived plot arcs from text using a +variety of sentiment dictionaries conveniently packaged for consumption by R +users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the +Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing} +developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif +M. and Turney, Peter D. Applicable references are available in +@file{README.md} and in the documentation for the @code{get_sentiment} +function. The package also provides a hack for implementing Stanford's coreNLP +sentiment parser. The package provides several methods for plot arc +normalization.") + (license license:gpl3))) + +(define-public r-lexicon + (package + (name "r-lexicon") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lexicon" version)) + (sha256 + (base32 + "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c")))) + (properties `((upstream-name . "lexicon"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-syuzhet" ,r-syuzhet))) + (home-page "https://github.com/trinker/lexicon") + (synopsis "Lexicons for Text Analysis") + (description + "This package provides a collection of lexical hash tables, dictionaries, +and word lists.") + (license license:gpl3))) + +(define-public r-english + (package + (name "r-english") + (version "1.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "english" version)) + (sha256 + (base32 + "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1")))) + (properties `((upstream-name . "english"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=english") + (synopsis "Translate Integers into English") + (description + "Allow numbers to be presented in an English language version, one, two, +three, ... Ordinals are also available, first, second, third, ... and +indefinite article choice, \"a\" or \"an\".") + (license license:gpl2))) + +(define-public r-textclean + (package + (name "r-textclean") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "textclean" version)) + (sha256 + (base32 + "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz")))) + (properties `((upstream-name . "textclean"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-english" ,r-english) + ("r-glue" ,r-glue) + ("r-lexicon" ,r-lexicon) + ("r-mgsub" ,r-mgsub) + ("r-qdapregex" ,r-qdapregex) + ("r-stringi" ,r-stringi) + ("r-textshape" ,r-textshape))) + (home-page + "https://github.com/trinker/textclean") + (synopsis "Text Cleaning Tools") + (description + "Tools to clean and process text. Tools are geared at checking for +substrings that are not optimal for analysis and replacing or removing them +(normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, +Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or +extracting them into new variables. For example, emoticons are often used in +text but not always easily handled by analysis algorithms. The +@code{replace_emoticon()} function replaces emoticons with word equivalents.") + (license license:gpl2))) + +(define-public r-striprtf + (package + (name "r-striprtf") + (version "0.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "striprtf" version)) + (sha256 + (base32 + "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd")))) + (properties `((upstream-name . "striprtf"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/kota7/striprtf") + (synopsis "Extract Text from RTF File") + (description + "Extracts plain text from @dfn{Rich Text Format} (RTF) file.") + (license license:expat))) + +(define-public r-ndjson + (package + (name "r-ndjson") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ndjson" version)) + (sha256 + (base32 + "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor gzstream + (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h")) + #t)))) + (properties `((upstream-name . "ndjson"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-gzstream + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makevars" + (("PKG_LIBS = " all) + (string-append all "-lgzstream "))) + #t))))) + (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream))) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://gitlab.com/hrbrmstr/ndjson") + (synopsis + "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") + (description + "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many +modern ndjson files contain large numbers of records. These constructs may not +be columnar in nature, but it is often useful to read in these files and +\"flatten\" the structure out to enable working with the data in an R +@code{data.frame}-like context. Functions are provided that make it possible +to read in plain ndjson files or compressed (@code{gz}) ndjson files and either +validate the format of the records or create \"flat\" @code{data.table} +structures from them.") + (license license:expat))) + +(define-public r-streamr + (package + (name "r-streamr") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "streamR" version)) + (sha256 + (base32 + "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix")))) + (properties `((upstream-name . "streamR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ndjson" ,r-ndjson) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson))) + (home-page + "https://cran.r-project.org/package=streamR") + (synopsis + "Access to Twitter Streaming API via R") + (description + "This package provides functions to access Twitter's filter, sample, and +user streams, and to parse the output into data frames.") + (license license:gpl2))) + +(define-public r-readods + (package + (name "r-readods") + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "readODS" version)) + (sha256 + (base32 + "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n")))) + (properties `((upstream-name . "readODS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cellranger" ,r-cellranger) + ("r-readr" ,r-readr) + ("r-stringi" ,r-stringi) + ("r-xml2" ,r-xml2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=readODS") + (synopsis "Read and Write ODS Files") + (description + "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. +Also support writing data frame into ODS file.") + (license license:gpl3))) + +(define-public r-qpdf + (package + (name "r-qpdf") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qpdf" version)) + (sha256 + (base32 + "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor libqpdf + (delete-file-recursively "src/libqpdf") + (delete-file-recursively "src/include/qpdf") + #t)))) + (properties `((upstream-name . "qpdf"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure + (lambda _ + (setenv "EXTERNAL_QPDF" "1") + #t))))) + (inputs + `(("zlib" ,zlib) + ("qpdf" ,qpdf))) + (propagated-inputs + `(("r-askpass" ,r-askpass) + ("r-curl" ,r-curl) + ("r-rcpp" ,r-rcpp))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/ropensci/qpdf") + (synopsis + "Split, Combine and Compress PDF Files") + (description + "Content-preserving transformations transformations of PDF files such as +split, combine, and compress. This package interfaces directly to the +@code{qpdf} C++ API and does not require any command line utilities. Note that +@code{qpdf} does not read actual content from PDF files: to extract text and +data you need the @code{pdftools} package.") + (license license:asl2.0))) + +(define-public r-pdftools + (package + (name "r-pdftools") + (version "2.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "pdftools" version)) + (sha256 + (base32 + "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx")))) + (properties `((upstream-name . "pdftools"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib) + ("poppler" ,poppler))) + (propagated-inputs + `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page + "https://docs.ropensci.org/pdftools/") + (synopsis + "Text Extraction, Rendering and Converting of PDF Documents") + (description + "Utilities based on @code{libpoppler} for extracting text, fonts, +attachments and metadata from a PDF file. Also supports high quality rendering +of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for +further processing in R.") + (license license:expat))) + +(define-public r-antiword + (package + (name "r-antiword") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "antiword" version)) + (sha256 + (base32 + "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor libantiword + (delete-file-recursively "src") + #t)))) + (properties `((upstream-name . "antiword"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-antiword + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "R/antiword.R" + (("system.file\\(\"bin\", package = \"antiword\"\\)") + (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) + #t))))) + (inputs `(("antiword" ,antiword))) + (propagated-inputs `(("r-sys" ,r-sys))) + (home-page + "https://github.com/ropensci/antiword#readme") + (synopsis + "Extract Text from Microsoft Word Documents") + (description + "Wraps the @code{AntiWord} utility to extract text from Microsoft Word +documents. The utility only supports the old @code{doc} format, not the new +xml based @code{docx} format. Use the @code{xml2} package to read the +latter.") + (license license:gpl2))) + +(define-public r-readtext + (package + (name "r-readtext") + (version "0.80") + (source + (origin + (method url-fetch) + (uri (cran-uri "readtext" version)) + (sha256 + (base32 + "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y")))) + (properties `((upstream-name . "readtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-antiword" ,r-antiword) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-pdftools" ,r-pdftools) + ("r-readods" ,r-readods) + ("r-readxl" ,r-readxl) + ("r-streamr" ,r-streamr) + ("r-stringi" ,r-stringi) + ("r-striprtf" ,r-striprtf) + ("r-tibble" ,r-tibble) + ("r-xml2" ,r-xml2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/quanteda/readtext") + (synopsis + "Import and Handling for Plain and Formatted Text Files") + (description + "This package provides functions for importing and handling text files +and formatted text files with additional meta-data, such including @code{.csv}, +@code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc}, +@code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.") + (license license:gpl3))) + +(define-public r-packcircles + (package + (name "r-packcircles") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "packcircles" version)) + (sha256 + (base32 + "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) + (properties `((upstream-name . "packcircles"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/mbedward/packcircles") + (synopsis "Circle Packing") + (description + "Algorithms to find arrangements of non-overlapping circles.") + (license license:expat))) + +;; Cannot unbundle liblwgeom, because PostGIS does not support building it on +;; its own. +(define-public r-lwgeom + (package + (name "r-lwgeom") + (version "0.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "lwgeom" version)) + (sha256 + (base32 + "0byhjqa2acns8mznl1ngnfygxxxyszvnq66qfg0smhhhdkwr67aa")))) + (properties `((upstream-name . "lwgeom"))) + (build-system r-build-system) + (inputs `(("geos" ,geos) ("proj" ,proj) ("sqlite" ,sqlite))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-sf" ,r-sf) + ("r-units" ,r-units))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page + "https://github.com/r-spatial/lwgeom/") + (synopsis + "Bindings to Selected 'liblwgeom' Functions for Simple Features") + (description + "Access to selected functions found in +@url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the +light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") + (license license:gpl2))) + +(define-public r-stars + (package + (name "r-stars") + (version "0.5-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "stars" version)) + (sha256 + (base32 + "0ybk899rc0rpf2cv5kwk78fvis5xnr255hfcy5khdxsxdqgl0m9j")))) + (properties `((upstream-name . "stars"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-classint" ,r-classint) + ("r-lwgeom" ,r-lwgeom) + ("r-rlang" ,r-rlang) + ("r-sf" ,r-sf) + ("r-units" ,r-units))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://r-spatial.github.io/stars/") + (synopsis + "Spatiotemporal Arrays, Raster and Vector Data Cubes") + (description + "Reading, manipulating, writing and plotting spatiotemporal arrays +(raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided +by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") + (license license:asl2.0))) + +(define-public r-tmaptools + (package + (name "r-tmaptools") + (version "3.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tmaptools" version)) + (sha256 + (base32 + "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx")))) + (properties `((upstream-name . "tmaptools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dichromat" ,r-dichromat) + ("r-lwgeom" ,r-lwgeom) + ("r-magrittr" ,r-magrittr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-sf" ,r-sf) + ("r-stars" ,r-stars) + ("r-units" ,r-units) + ("r-viridislite" ,r-viridislite) + ("r-xml" ,r-xml))) + (home-page + "https://github.com/mtennekes/tmaptools") + (synopsis "Thematic Map Tools") + (description + "Set of tools for reading and processing spatial data. The aim is to +supply the workflow to create thematic maps. This package also facilitates +@code{tmap}, the package for visualizing thematic maps.") + (license license:gpl3))) + +(define-public r-rworldmap + (package + (name "r-rworldmap") + (version "1.3-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "rworldmap" version)) + (sha256 + (base32 + "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk")))) + (properties `((upstream-name . "rworldmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fields" ,r-fields) + ("r-maptools" ,r-maptools) + ("r-sp" ,r-sp))) + (home-page + "https://github.com/AndySouth/rworldmap/") + (synopsis "Mapping Global Data") + (description + "Enables mapping of country level and gridded user datasets.") + (license license:gpl2+))) + +(define-public r-rtweet + (package + (name "r-rtweet") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rtweet" version)) + (sha256 + (base32 + "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n")))) + (properties `((upstream-name . "rtweet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-progress" ,r-progress) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://docs.ropensci.org/rtweet/") + (synopsis "Collecting Twitter Data") + (description + "An implementation of calls designed to collect and organize Twitter data +via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream +Application Program Interfaces (API)}.") + (license license:expat))) + +(define-public r-intervals + (package + (name "r-intervals") + (version "0.15.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "intervals" version)) + (sha256 + (base32 + "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) + (properties `((upstream-name . "intervals"))) + (build-system r-build-system) + (home-page "https://github.com/edzer/intervals") + (synopsis + "Tools for Working with Points and Intervals") + (description + "Tools for working with and comparing sets of points and intervals.") + (license license:artistic2.0))) + +(define-public r-eyelinker + (package + (name "r-eyelinker") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "eyelinker" version)) + (sha256 + (base32 + "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2")))) + (properties `((upstream-name . "eyelinker"))) + (build-system r-build-system) + (propagated-inputs + `(("r-intervals" ,r-intervals) + ("r-readr" ,r-readr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/a-hurst/eyelinker") + (synopsis + "Import ASC Files from EyeLink Eye Trackers") + (description + "Imports plain-text ASC data files from EyeLink eye trackers into +(relatively) tidy data frames for analysis and visualization.") + (license license:gpl3))) + +(define-public r-btm + (package + (name "r-btm") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "BTM" version)) + (sha256 + (base32 + "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb")))) + (properties `((upstream-name . "BTM"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bnosac/BTM") + (synopsis "Biterm Topic Models for Short Text") + (description + "Biterm Topic Models find topics in collections of short texts. It is a +word co-occurrence based topic model that learns topics by modeling word-word +co-occurrences patterns which are called biterms. This in contrast to +traditional topic models like Latent Dirichlet Allocation and Probabilistic +Latent Semantic Analysis which are word-document co-occurrence topic models. A +biterm consists of two words co-occurring in the same short text window. This +context window can for example be a twitter message, a short answer on a +survey, a sentence of a text or a document identifier. The techniques are +explained in detail in the paper 'A Biterm Topic Model For Short Text' by +Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) +@url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ +BTM-WWW13.pdf}.") + (license license:asl2.0))) + +(define-public r-textplot + (package + (name "r-textplot") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "textplot" version)) + (sha256 + (base32 + "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy")))) + (properties `((upstream-name . "textplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/bnosac/textplot") + (synopsis "Text Plots") + (description + "Visualise complex relations in texts. This is done by providing +functionalities for displaying text co-occurrence networks, text correlation +networks, dependency relationships as well as text clustering. Feel free to +join the effort of providing interesting text visualisations.") + (license license:gpl2))) |