diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 427 |
1 files changed, 346 insertions, 81 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c2e623705..c91b0ee75e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> -;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com> @@ -83,6 +83,25 @@ #:use-module (gnu packages web) #:use-module (gnu packages xorg)) +(define-public r-bezier + (package + (name "r-bezier") + (version "1.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "bezier" version)) + (sha256 + (base32 + "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bezier/") + (synopsis "Bezier curve and spline toolkit") + (description + "This package is a toolkit for working with Bezier curves and splines. +The package provides functions for point generation, arc length estimation, +degree elevation and curve fitting.") + (license license:gpl2+))) + (define-public r-clipr (package (name "r-clipr") @@ -102,6 +121,36 @@ the system clipboards.") (license license:gpl3))) +(define-public r-ggpmisc + (package + (name "r-ggpmisc") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (cran-uri "ggpmisc" version)) + (sha256 + (base32 + "0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-lubridate" ,r-lubridate) + ("r-mass" ,r-mass) + ("r-plyr" ,r-plyr) + ("r-polynom" ,r-polynom) + ("r-splus2r" ,r-splus2r) + ("r-tibble" ,r-tibble) + ("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (home-page "https://www.r4photobiology.info/") + (synopsis "Miscellaneous Extensions to @code{ggplot2}") + (description "This package provides extensions to @code{ggplot2}, +respecting the grammar of its graphics paradigm.") + (license license:gpl2+))) + (define-public r-oenb (package (name "r-oenb") @@ -177,6 +226,30 @@ legends.") control over dimensions and appearance.") (license license:gpl2+))) +(define-public r-ecp + (package + (name "r-ecp") + (version "3.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "ecp" version)) + (sha256 + (base32 + "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/ecp/") + (synopsis "Multiple change-point analysis of multivariate data") + (description + "This package implements various procedures for finding multiple +change-points. Two methods make use of dynamic programming and pruning, with +no distributional assumptions other than the existence of certain absolute +moments in one method. Hierarchical and exact search methods are included. +All methods return the set of estimated change-points as well as other summary +information.") + (license license:gpl2+))) + (define-public r-ellipsis (package (name "r-ellipsis") @@ -449,6 +522,27 @@ small, reproducible, and runnable examples on code-oriented websites or email. such as copy/paste from an R session.") (license license:expat))) +(define-public r-reordercluster + (package + (name "r-reordercluster") + (version "1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "ReorderCluster" version)) + (sha256 + (base32 + "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gplots" ,r-gplots) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/ReorderCluster") + (synopsis "Reordering the dendrogram according to the class labels") + (description "This package provides tools for performing the leaf reordering +for the dendrogram that preserves the hierarchical clustering result and at the +same time tries to group instances from the same class together.") + (license license:gpl3+))) + (define-public r-callr (package (name "r-callr") @@ -1027,13 +1121,13 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.7.5") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a")))) + (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs @@ -1677,13 +1771,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx")))) + (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -1910,17 +2004,19 @@ multi-dimensional data.") (define-public r-powerlaw (package (name "r-powerlaw") - (version "0.70.4") + (version "0.70.6") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 - (base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk")))) + (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs - `(("r-vgam" ,r-vgam))) + `(("r-pracma" ,r-pracma))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description @@ -2029,14 +2125,14 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "2.2-14") + (version "2.2-14.2") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw")))) + "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) (home-page "http://ff.r-forge.r-project.org/") @@ -2176,14 +2272,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-23") + (version "0.4-24") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x")))) + "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -2293,14 +2389,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.0-6") + (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429")))) + "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") @@ -2400,6 +2496,27 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and ;; Any version of the LGPL. (license license:lgpl3+))) +(define-public r-inum + (package + (name "r-inum") + (version "1.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "inum" version)) + (sha256 + (base32 + "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-libcoin" ,r-libcoin))) + (home-page "https://cran.r-project.org/web/packages/inum/") + (synopsis "Interval and enum-type representation of vectors") + (description + "This package provides an enum-type representation of vectors and +representation of intervals, including a method of coercing variables +in data frames.") + (license license:gpl2))) + (define-public r-bdsmatrix (package (name "r-bdsmatrix") @@ -3105,14 +3222,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx")))) + "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -3124,6 +3241,8 @@ by base R methods related to model fitting.") ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description @@ -3926,14 +4045,14 @@ timeout. It can also poll several processes at once.") (define-public r-tsp (package (name "r-tsp") - (version "1.1-9") + (version "1.1-10") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 - "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7")))) + "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach))) @@ -4195,14 +4314,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9")))) + "0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -6456,14 +6575,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.8.2") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj")))) + "0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -6965,14 +7084,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.2") + (version "1.8.2.1") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l")))) + "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -7313,14 +7432,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.0-12") + (version "3.1-5") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg")))) + "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -8324,14 +8443,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.4.5") + (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm")))) + "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -8339,6 +8458,8 @@ Hothorn, Westfall, 2010, CRC Press).") ("r-numderiv" ,r-numderiv) ("r-plyr" ,r-plyr) ("r-xtable" ,r-xtable))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description @@ -8557,14 +8678,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.5.3") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz")))) + "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -8611,14 +8732,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.14.2") + (version "0.14.3") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw")))) + "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -8799,14 +8920,14 @@ terminals that do not support Unicode.") (define-public r-usethis (package (name "r-usethis") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146")))) + "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -9395,14 +9516,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.100.50") + (version "0.100.54") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay")))) + "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -9534,14 +9655,14 @@ features (e.g. local modes).") (define-public r-arm (package (name "r-arm") - (version "1.10-1") + (version "1.11-1") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 - "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) + "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -11478,14 +11599,14 @@ library.") (define-public r-protviz (package (name "r-protviz") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7")))) + "1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -11528,14 +11649,14 @@ JASA, 94:496-509.") (define-public r-etm (package (name "r-etm") - (version "1.0.5.1") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 - "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7")))) + "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -11736,14 +11857,14 @@ them in distributed compute environments.") (define-public r-future (package (name "r-future") - (version "1.16.0") + (version "1.17.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm")))) + "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -11768,14 +11889,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk")))) + "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (propagated-inputs @@ -13234,14 +13355,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-1") + (version "0.9-2") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4")))) + "01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -13730,17 +13851,19 @@ authoring books and technical documents with R Markdown.") (define-public r-optparse (package (name "r-optparse") - (version "1.6.4") + (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d")))) + "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description @@ -14900,18 +15023,19 @@ external dependencies. This package has is implemented purely in R.") (define-public r-rex (package (name "r-rex") - (version "1.1.2") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 - "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x")))) + "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval) - ("r-magrittr" ,r-magrittr))) + `(("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description @@ -15242,20 +15366,89 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") ;; whole is distributed under the terms of the AGPL 3. (license license:agpl3))) +(define-public r-ingredients + (package + (name "r-ingredients") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ingredients" version)) + (sha256 + (base32 + "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967")))) + (properties `((upstream-name . "ingredients"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-scales" ,r-scales))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://ModelOriented.github.io/ingredients/") + (synopsis "Effects and importances of model ingredients") + (description + "This is a collection of tools for assessment of feature importance and +feature effects. Key functions are: + +@itemize +@item @code{feature_importance()} for assessment of global level feature + importance, +@item @code{ceteris_paribus()} for calculation of the what-if plots, +@item @code{partial_dependence()} for partial dependence plots, +@item @code{conditional_dependence()} for conditional dependence plots, +@item @code{accumulated_dependence()} for accumulated local effects plots, +@item @code{aggregate_profiles()} and @code{cluster_profiles()} for + aggregation of ceteris paribus profiles, +@item generic @code{print()} and @code{plot()} for better usability of + selected explainers, +@item generic @code{plotD3()} for interactive, D3 based explanations, and +@item generic @code{describe()} for explanations in natural language. +@end itemize\n") + (license license:gpl3))) + +(define-public r-ibreakdown + (package + (name "r-ibreakdown") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "iBreakDown" version)) + (sha256 + (base32 + "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk")))) + (properties `((upstream-name . "iBreakDown"))) + (build-system r-build-system) + (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://ModelOriented.github.io/iBreakDown/") + (synopsis "Model agnostic instance level variable attributions") + (description + "This package provides a model agnostic tool for decomposition of +predictions from black boxes. It supports additive attributions and +attributions with interactions. The Break Down Table shows contributions of +every variable to a final prediction. The Break Down Plot presents variable +contributions in a concise graphical way. This package works for +classification and regression models.") + (license license:gpl3))) + (define-public r-dalex (package (name "r-dalex") - (version "1.0.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0")))) + "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ibreakdown" ,r-ibreakdown) + ("r-ingredients" ,r-ingredients))) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description @@ -15317,14 +15510,14 @@ includes data sets from oceanography.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.9") + (version "0.4.10") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5")))) + "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -15833,22 +16026,22 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "0.1.1") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z")))) + "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (inputs `(("fontconfig" ,fontconfig) - ("freetype" ,freetype) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description @@ -15862,14 +16055,14 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0")))) + "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs @@ -16756,28 +16949,61 @@ for original research. A variety of user defined options and formatting are included.") (license license:gpl3))) +(define-public r-qgam + (package + (name "r-qgam") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "qgam" version)) + (sha256 + (base32 + "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7")))) + (properties `((upstream-name . "qgam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-mgcv" ,r-mgcv) + ("r-plyr" ,r-plyr) + ("r-shiny" ,r-shiny))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/qgam/") + (synopsis "Smooth additive quantile regression models") + (description + "This package provides smooth additive quantile regression models, fitted +using the methods of Fasiolo et al. (2017). Differently from @code{quantreg}, +the smoothing parameters are estimated automatically by marginal loss +minimization, while the regression coefficients are estimated using either +PIRLS or Newton algorithm. The learning rate is determined so that the +Bayesian credible intervals of the estimated effects have approximately the +correct coverage. The main function is @code{qgam()} which is similar to +@code{gam()} in the @code{mgcv} package, but fits non-parametric quantile +regression models.") + (license license:gpl2+))) + (define-public r-abtest (package (name "r-abtest") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 - "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws")))) + "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm) ("r-plotrix" ,r-plotrix) + ("r-qgam" ,r-qgam) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-sn" ,r-sn) - ("r-truncnorm" ,r-truncnorm) - ("r-vgam" ,r-vgam))) + ("r-truncnorm" ,r-truncnorm))) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description @@ -18107,14 +18333,14 @@ actigraphy-measured activity counts data.") (define-public r-fda (package (name "r-fda") - (version "2.4.8.1") + (version "5.1.4") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a")))) + "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs @@ -18569,14 +18795,14 @@ functions.") (define-public r-univoutl (package (name "r-univoutl") - (version "0.1-5") + (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 - "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi")))) + "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v")))) (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs @@ -19513,17 +19739,20 @@ character codes as well as the UN M.49 area codes.") (define-public r-stopwords (package (name "r-stopwords") - (version "1.0") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 - "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv")))) + "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) - (propagated-inputs `(("r-isocodes" ,r-isocodes))) + (propagated-inputs + `(("r-desc" ,r-desc) + ("r-isocodes" ,r-isocodes) + ("r-usethis" ,r-usethis))) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description @@ -19627,14 +19856,14 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-9") + (version "0.2-11") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0")))) + "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw")))) (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (native-inputs @@ -19990,19 +20219,18 @@ estimate parameters given observed data.") (define-public r-kutils (package (name "r-kutils") - (version "1.69") + (version "1.70") (source (origin (method url-fetch) (uri (cran-uri "kutils" version)) (sha256 (base32 - "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8")))) + "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37")))) (properties `((upstream-name . "kutils"))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) - ("r-lavaan" ,r-lavaan) ("r-openxlsx" ,r-openxlsx) ("r-plyr" ,r-plyr) ("r-runit" ,r-runit) @@ -21404,3 +21632,40 @@ infinite-precision rational arithmetic.") Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and download images.") (license license:gpl2))) + +(define-public r-rserve + (package + (name "r-rserve") + (version "1.8-6") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_" + version ".tar.gz")) + (sha256 + (base32 + "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-mime" ,r-mime) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-uuid" ,r-uuid))) + (inputs + `(("openssl" ,openssl) + ("zlib" ,zlib))) + (home-page "https://github.com/s-u/Rserve") + (synopsis + "Server providing access to R from many languages and systems") + (description + "Rserve acts as a socket server (TCP/IP or local sockets) which allows +binary requests to be sent to R. Every connection has a separate workspace +and working directory. Client-side implementations are available for popular +languages such as C/C++ and Java, allowing any application to use facilities +of R without the need of linking to R code. Rserve supports remote +connection, user authentication and file transfer. A simple R client is +included in this package as well.") + (license license:gpl2))) |