diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1341 |
1 files changed, 1130 insertions, 211 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index adb1bf421b..40f8e82c34 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31,6 +31,8 @@ ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> +;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -95,21 +97,95 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) #:use-module (gnu packages tls) + #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) +(define-public r-brio + (package + (name "r-brio") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "brio" version)) + (sha256 + (base32 + "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb")))) + (properties `((upstream-name . "brio"))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/brio") + (synopsis "Basic R input output") + (description + "This package provides functions to handle basic input output. These +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-diffobj + (package + (name "r-diffobj") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "diffobj" version)) + (sha256 + (base32 + "0v18zz14g8ppzmj1d997rdmsfh327ml4wvpmfx168lravdsk5ym2")))) + (properties `((upstream-name . "diffobj"))) + (build-system r-build-system) + (propagated-inputs `(("r-crayon" ,r-crayon))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/brodieG/diffobj") + (synopsis "Diffs for R objects") + (description + "Generate a colorized diff of two R objects for an intuitive +visualization of their differences.") + (license license:gpl2+))) + +(define-public r-waldo + (package + (name "r-waldo") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "waldo" version)) + (sha256 + (base32 + "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz")))) + (properties `((upstream-name . "waldo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-diffobj" ,r-diffobj) + ("r-fansi" ,r-fansi) + ("r-glue" ,r-glue) + ("r-rematch2" ,r-rematch2) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/r-lib/waldo") + (synopsis "Find differences between R objects") + (description + "Compare complex R objects and reveal the key differences. This package +was designed particularly for use in testing packages where being able to +quickly isolate key differences makes understanding test failures much +easier.") + (license license:expat))) + (define-public r-rticles (package (name "r-rticles") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1ca3k5sdy9mnm6frcimqwf5k18j14wn69x5iagjnjwhq711l8dv0")))) + "1wbwva5n88dw3vvhcrlzkr58cv03hyx0dqgfmxj7d0dgf4ichr3c")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -147,14 +223,14 @@ degree elevation and curve fitting.") (define-public r-v8 (package (name "r-v8") - (version "3.3.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1d2j9p1fsz9hp8n8lrywyrkwivhfa3qx5ha5f24vin8b6l04xy67")))) + "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -255,16 +331,45 @@ ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) +(define-public r-ggalluvial + (package + (name "r-ggalluvial") + (version "0.12.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ggalluvial" version)) + (sha256 + (base32 + "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3")))) + (properties `((upstream-name . "ggalluvial"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lazyeval" ,r-lazyeval) + ("r-rlang" ,r-rlang) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://corybrunson.github.io/ggalluvial/") + (synopsis "Alluvial plots for ggplot2") + (description "This package provides alluvial plots for @code{ggplot2}. +Alluvial plots use variable-width ribbons and stacked bar plots to represent +multi-dimensional or repeated-measures data with categorical or ordinal +variables.") + (license license:gpl3))) + (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208")))) + "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -560,6 +665,30 @@ generalized linear, additive and interaction models to potentially high-dimensional data.") (license license:gpl2))) +(define-public r-shadowtext + (package + (name "r-shadowtext") + (version "0.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "shadowtext" version)) + (sha256 + (base32 + "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf")))) + (properties `((upstream-name . "shadowtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/GuangchuangYu/shadowtext/") + (synopsis "Shadow text grob and layer") + (description "This package implements @code{shadowtextGrob()} for +@code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}. +These functions draw text grob with background shadow.") + (license license:artistic2.0))) + (define-public r-sys (package (name "r-sys") @@ -585,6 +714,34 @@ interrupts and timeouts. This provides the basis for a sandboxing mechanism.") (license license:expat))) +(define-public r-ashr + (package + (name "r-ashr") + (version "2.2-47") + (source (origin + (method url-fetch) + (uri (cran-uri "ashr" version)) + (sha256 + (base32 + "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4")))) + (properties `((upstream-name . "ashr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-etrunct" ,r-etrunct) + ("r-invgamma" ,r-invgamma) + ("r-matrix" ,r-matrix) + ("r-mixsqp" ,r-mixsqp) + ("r-rcpp" ,r-rcpp) + ("r-squarem" ,r-squarem) + ("r-truncnorm" ,r-truncnorm))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/stephens999/ashr") + (synopsis "Methods for adaptive shrinkage, using empirical bayes") + (description "This package implements an empirical Bayes approach for +large-scale hypothesis testing and false discovery rate estimation.") + (license license:gpl3+))) + (define-public r-askpass (package (name "r-askpass") @@ -609,20 +766,20 @@ read a protected key.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-6") + (version "2.5-7") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k")))) + "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("r-knitr" ,r-knitr) ; needed for vignettes + ("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) - ("r-knitr" ,r-knitr) ; needed for vignettes ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -1396,13 +1553,13 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w")))) + (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs @@ -1451,20 +1608,19 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (define-public r-d3r (package (name "r-d3r") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 - "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y")))) + "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) - (srfi srfi-1) - (ice-9 popen)) + (srfi srfi-1)) #:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript @@ -1478,16 +1634,16 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (,(assoc-ref inputs "d3.v4.js") "v4/dist/d3.min.js") (,(assoc-ref inputs "d3.v5.js") - "v5/dist/d3.min.js")))) + "v5/dist/d3.min.js") + (,(assoc-ref inputs "d3.v6.js") + "v6/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) sources targets)))) #t))))) (propagated-inputs @@ -1496,7 +1652,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.") ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("esbuild" ,esbuild) ("d3.v3.js" ,(origin (method url-fetch) @@ -1517,7 +1673,14 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v5.js") (sha256 (base32 - "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))))) + "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))) + ("d3.v6.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v6.js") + (sha256 + (base32 + "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description @@ -1912,14 +2075,16 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (define-public r-colorspace (package (name "r-colorspace") - (version "1.4-1") + (version "2.0-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9")))) + (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description @@ -2058,13 +2223,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "0yns03ffd2a2cs4b6dsjjlqhv46vq2g094m8psmhf3h9i52awyaz")))) + (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -2308,14 +2473,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.10") + (version "0.4.11") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk")))) + "1s84xl7kv3qc1261xxaq4aqh64gwywhacsf5nh6yf8djw0d1w42d")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -2550,6 +2715,36 @@ quantities.") @code{melt} and @code{cast}. This package provides them.") (license license:expat))) +(define-public r-restrserve + (package + (name "r-restrserve") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RestRserve" version)) + (sha256 + (base32 "07mm65yxzpwlg6x3lsggj41v8nl4m6v9mszhqjpgj19v3yxvwgi0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-jsonlite" ,r-jsonlite) + ("r-mime" ,r-mime) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rserve" ,r-rserve) + ("r-uuid" ,r-uuid))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://restrserve.org") + (synopsis "R web API framework") + (description + "RestRserve is an R web API framework for building high-performance AND +robust microservices and app backends. With Rserve backend on UNIX-like +systems it is parallel by design. It will handle incoming requests in +parallel - each request in a separate fork.") + (license license:gpl2+))) + (define-public r-progress (package (name "r-progress") @@ -2751,14 +2946,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh")))) + "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") @@ -2769,17 +2964,36 @@ complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) +(define-public r-etrunct + (package + (name "r-etrunct") + (version "0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "etrunct" version)) + (sha256 + (base32 + "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) + (properties `((upstream-name . "etrunct"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/etrunct") + (synopsis "Computes moments of univariate truncated T distribution") + (description "This package computes moments of univariate truncated +T distribution. There is only one exported function, @code{e_trunct}, +which should be seen for details.") + (license license:expat))) + (define-public r-extremes (package (name "r-extremes") - (version "2.0-12") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2")))) + "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs @@ -2841,13 +3055,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.16") + (version "0.3.17") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj")))) + "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -2878,6 +3092,24 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and representation of intervals, including a method of coercing variables in data frames.") (license license:gpl2))) +(define-public r-invgamma + (package + (name "r-invgamma") + (version "1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "invgamma" version)) + (sha256 + (base32 + "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a")))) + (properties `((upstream-name . "invgamma"))) + (build-system r-build-system) + (home-page "https://github.com/dkahle/invgamma") + (synopsis "Inverse gamma distribution") + (description "This package provides a light weight implementation of the +standard distribution functions for the inverse gamma distribution, wrapping +those for the gamma distribution in the @code{stats} package.") + (license license:gpl2))) (define-public r-bdsmatrix (package @@ -3013,14 +3245,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-1") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl")))) + "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -3178,14 +3410,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.8") + (version "1.6.8.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0jdmjjs894mfncswmzz7sa6cy7hqbqii5fcvl3zqkmzpbadb2za2")))) + "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -3566,14 +3798,14 @@ created using basic graphics.") (define-public r-generics (package (name "r-generics") - (version "0.0.2") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 - "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) + "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb")))) (build-system r-build-system) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") @@ -3624,14 +3856,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.14") + (version "0.1.15") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0ix678aj71ml5cmfhy1j0b2ddhf5wlb1d74bjc9djr6r86xsqmcz")))) + "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3915,21 +4147,23 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.11.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq")))) + "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) + ("r-cpp11" ,r-cpp11) ("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-lattice" ,r-lattice) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") @@ -3994,14 +4228,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0b6j1mkpr7ck2nr9fmpnsjdv29jc6vg4b91cg50skmcgky1j0zi7")))) + "0l93r1hkr483hp4yd7rm7mdkgl5lp0nkvv0inahj3r1cplgfxpvs")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -4352,14 +4586,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "03zaq9yhz6gw49qdnhc66b3sw9i916ahkzyg2cgh17dhf31d2acq")))) + "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4417,13 +4651,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.4") + (version "3.4.5") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a")))) + (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -4627,14 +4861,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb")))) + "1k1mcq7jkpc55dsm0wb4k8asc1irvmi5884v3ap4sabf22c5sq0i")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -4666,14 +4900,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.6") + (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj")))) + "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -4714,14 +4948,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "02b0v8ydbfspma3rgsdpkf2cm6jl9qm3l9jsrl0xng482b06bb0q")))) + "10hbc9h1fsw91w5f4fjcaqy68b3n1wr6pml01fnkf3pdjiri5sj0")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4972,14 +5206,14 @@ provides some missing S-PLUS functionality in R.") (define-public r-ifultools (package (name "r-ifultools") - (version "2.0-5") + (version "2.0-22") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 - "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j")))) + "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -5035,14 +5269,14 @@ Fisher's method), and Sidak correction.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4.17") + (version "0.4.18") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa")))) + "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -5059,14 +5293,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-47") + (version "0.10-48") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0")))) + "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) @@ -5599,14 +5833,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.3.10") + (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c")) + "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny")) (modules '((guix build utils))) (snippet '(begin @@ -6296,14 +6530,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.12.0") + (version "0.12.3") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5")))) + "0k31x19gzpffb701c76p840cip10c0dh8yv3wcs30gqi0ag1g77l")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -6864,17 +7098,16 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "1.3") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1i000czyd059dczd2nn1cb0d4n0bjykrfh51rs85s8r2zlaydn6i")))) + "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) - (propagated-inputs `(("r-xml2" ,r-xml2))) (home-page "https://geobosh.github.io/rbibutils/") (synopsis "Convert between bibliography formats") (description @@ -6887,14 +7120,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "04gk68y3cxlqhfl1aarjwz2mvx934ka0yxfgzrnw03ykhvb47fpi")))) + "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -6914,14 +7147,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.14") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h")))) + "1s9hrkdx105c1plpxywv68bmp8hvvxbdizhwx81fxr79fhj62x5j")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -7176,14 +7409,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.10.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1r4val3hvc43zailfmq6wcbg366s0bi0ysib476a49k1x6h8b6ji")))) + "1m95xfvai1kbzqxdggjvdbk6ax2dg4v2lrfpqn7v607g2n77n2k0")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7310,14 +7543,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.5.11") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4")))) + "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -7330,6 +7563,8 @@ functions.") ("r-rmarkdown" ,r-rmarkdown) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description @@ -7556,14 +7791,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.7") + (version "4.6.8") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk")))) + "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -7642,14 +7877,14 @@ procedures to speed up calculations in R.") (define-public r-blockfest (package (name "r-blockfest") - (version "1.6") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 - "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) + "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) @@ -7749,13 +7984,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-47") + (version "0.1-48") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9")))) + (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -8038,14 +8273,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.3-13") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7")))) + "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -8599,17 +8834,48 @@ conveniently wrapped into a data frame.") multiple-imputation datasets.") (license license:gpl2))) +(define-public r-mixsqp + (package + (name "r-mixsqp") + (version "0.3-43") + (source (origin + (method url-fetch) + (uri (cran-uri "mixsqp" version)) + (sha256 + (base32 + "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q")))) + (properties `((upstream-name . "mixsqp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-irlba" ,r-irlba) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/stephenslab/mixsqp") + (synopsis + "Sequential quadratic programming for maximum-likelihood estimation") + (description + "This package provides an optimization method based on sequential +quadratic programming for maximum likelihood estimation of the mixture +proportions in a finite mixture model where the component densities are +known. The algorithm is expected to obtain solutions that are at least +as accurate as the state-of-the-art MOSEK interior-point solver, and they +are expected to arrive at solutions more quickly when the number of +samples is large and the number of mixture components is not too large.") + (license license:expat))) + (define-public r-magick (package (name "r-magick") - (version "2.5.0") + (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1fhwr34xff6793ifbzqmij8b8qg7hrnr4birqpg33ib0mdd6flkf")))) + "0myvryya7b4bbw0hs4jqflrbdffmg78kz28gbybw3yc7zwc7sqxx")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -9016,14 +9282,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-14") + (version "1.4-15") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "14a55isy1sp745s109nirlk5fryy144cri6dl8y9d9wjhfxz336a")))) + "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) @@ -9280,14 +9546,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.7.5") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0l6q7v96m9asqa0p55k0gpzy8hddf8srkhc9r7zf4hv0dscbi9dv")))) + "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -9307,14 +9573,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1vkc87vbhw7l626pdnpiravnpsa5j0iv73lbwy3m309lnfvv0cqx")))) + "0ai1pp6k0pmmjgpj7hc53s0h258c4mljln8lv3nd9r7kzrmic0gc")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9334,14 +9600,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.16.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5")))) + "18diwssc5vij5g7zh9mv0ppcv3xgfi2jqzfx9srxfahg05sr1xdq")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9364,14 +9630,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0shx19ahw13wrn7jlyyvzvngqk66d6jiw9i51mx3psdn3hdnhy9s")))) + "1rbl63b1c7z9llznnwvclqrcgdd4hfmc7y66v7raqqf2a4nadqa5")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -9454,23 +9720,50 @@ files to an structured list. Users can manipulate this resulting list with back to file after modifications.") (license license:gpl3))) +(define-public r-gitcreds + (package + (name "r-gitcreds") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gitcreds" version)) + (sha256 + (base32 + "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi")))) + (properties `((upstream-name . "gitcreds"))) + (build-system r-build-system) + (inputs `(("git" ,git-minimal))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/r-lib/gitcreds") + (synopsis "Query git credentials from R") + (description + "Query, set, and delete credentials from the git credential store. +Manage GitHub tokens and other git credentials. This package is to be used by +other packages that need to authenticate to GitHub and/or other git +repositories.") + (license license:expat))) + (define-public r-gh (package (name "r-gh") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy")))) + "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) + ("r-gitcreds" ,r-gitcreds) ("r-httr" ,r-httr) ("r-ini" ,r-ini) ("r-jsonlite" ,r-jsonlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description @@ -10001,14 +10294,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.16") + (version "0.0.17") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr")))) + "0z4dpvk2hmh817709l70jdl1vvnzn0vb9wlr5m8jza24sn9w14ac")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -10491,14 +10784,14 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-5") + (version "0.1-6") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) + "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) @@ -10536,14 +10829,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-7") + (version "0.7-8") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) + "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -10923,14 +11216,14 @@ diagnostics for controlling type-1 errors are also provided.") (define-public r-flare (package (name "r-flare") - (version "1.6.0.2") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 - "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) + "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) @@ -11023,14 +11316,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "02jdxz3w423k9b5wldky4pnnq0cs2zlfi52jxjw1mk24z756j692")))) + "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -11492,14 +11785,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-1") + (version "0.8-2") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr")))) + "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs @@ -12281,19 +12574,20 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.41") + (version "2.42") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5")))) + "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs `(("r-cmprsk" ,r-cmprsk) ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) ("r-etm" ,r-etm) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) @@ -12439,14 +12733,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.13.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "1ch9m7fxclfhfa38b743wcm7w1bkx9kmivc6l7phpbgs6h9jhrcc")))) + "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools))) @@ -12460,22 +12754,51 @@ simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.") (license license:lgpl2.1+))) +(define-public r-parallelly + (package + (name "r-parallelly") + (version "1.21.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "parallelly" version)) + (sha256 + (base32 + "1hlr81khr7z4x9gprymdh19mdq3nw6wm8d2795sd2pa3ya6phnb0")))) + (properties `((upstream-name . "parallelly"))) + (build-system r-build-system) + (home-page "https://github.com/HenrikBengtsson/parallelly") + (synopsis "Enhancements of the parallel package") + (description + "This package provides utility functions that enhance the @code{parallel} +package and support the built-in parallel backends of the @code{future} +package. For example, @code{availableCores} gives the number of CPU cores +available to your R process as given by R options and environment variables, +including those set by job schedulers on high-performance compute clusters. +If none is set, it will fall back to @code{parallel::detectCores}. Another +example is @code{makeClusterPSOCK}, which is backward compatible with +@code{parallel::makePSOCKcluster} while doing a better job in setting up +remote cluster workers without the need for configuring the firewall to do +port-forwarding to your local computer.") + (license license:lgpl2.1+))) + (define-public r-future (package (name "r-future") - (version "1.19.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "12f483h7g172ygafbg7h43vykv0f7xz9miwqf5q8dyv7gpgqi5fl")))) + "14k00g8c9zgf77d6q7x2vibvlivzk2rzj7lwn7v7d9nr6prqzlb6")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-globals" ,r-globals) - ("r-listenv" ,r-listenv))) + ("r-listenv" ,r-listenv) + ("r-parallelly" ,r-parallelly))) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") @@ -12761,14 +13084,14 @@ Coefficient Logit Models.") (define-public r-tensora (package (name "r-tensora") - (version "0.36.1") + (version "0.36.2") (source (origin (method url-fetch) (uri (cran-uri "tensorA" version)) (sha256 (base32 - "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) + "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf")))) (properties `((upstream-name . "tensorA"))) (build-system r-build-system) (home-page "http://www.stat.boogaart.de/tensorA") @@ -13947,14 +14270,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-29") + (version "0.2-3") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv")))) + "0kin1hsd6dj36kkg7n328mzp21wwn9jm69lvgg2rvbf6bq7q091d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -14211,13 +14534,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.0-1") + (version "6.1-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq")))) + (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -14395,32 +14718,6 @@ effects. It is applicable to backcrosses, doubled haploids, recombinant inbred lines, F2 intercrosses, and association mapping populations.") (license license:gpl2))) -(define-public r-ldheatmap - (package - (name "r-ldheatmap") - (version "1.0-4") - (source - (origin - (method url-fetch) - (uri (cran-uri "LDheatmap" version)) - (sha256 - (base32 - "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) - (properties `((upstream-name . "LDheatmap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) - (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") - (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") - (description - "This package provides tools to produce a graphical display, as a heat -map, of measures of pairwise linkage disequilibria between SNPs. Users may -optionally include the physical locations or genetic map distances of each SNP -on the plot.") - (license license:gpl3))) - (define-public r-hwde (package (name "r-hwde") @@ -15132,14 +15429,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.") (define-public r-ggraph (package (name "r-ggraph") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 - "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq")))) + "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -15155,7 +15452,8 @@ databases, including ENA, PDB or ChEMBL are also accessible.") ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis))) + ("r-viridis" ,r-viridis) + ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ggraph/") @@ -15240,22 +15538,22 @@ discriminant analysis for the purpose of classifying high dimensional data.") (define-public r-ggvis (package (name "r-ggvis") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "ggvis" version)) (sha256 (base32 - "1k40mkfxj66qvwbsp849maihv6vxkdprhhzjkwffwn0lwl78lsz1")))) + "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) ("r-shiny" ,r-shiny))) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") @@ -15941,14 +16239,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-57") + (version "0.3-58") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf")))) + "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/clue/") @@ -16084,14 +16382,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.1-27") + (version "3.1-32") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml")))) + "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -16229,24 +16527,25 @@ results and plots in a unified style using the @code{ggplot2} package.") (define-public r-refmanager (package (name "r-refmanager") - (version "1.2.12") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 - "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp")))) + "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs - `(("r-bibtex" ,r-bibtex) - ("r-httr" ,r-httr) + `(("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lubridate" ,r-lubridate) ("r-plyr" ,r-plyr) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description @@ -16326,14 +16625,14 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.6.0") + (version "0.2.7.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f")))) + "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab")))) (build-system r-build-system) (propagated-inputs `(("r-openssl" ,r-openssl) @@ -16353,14 +16652,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd")))) + "1iqvircvlxyd68n5279a0cwn5rc3pshxs7w1gqrns9c602xd6mhy")))) (build-system r-build-system) (propagated-inputs `(("r-dqrng" ,r-dqrng) @@ -16512,14 +16811,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.4") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "0cj98s1d9771dahn2xwdb1hpkw51jsfmgvzpam34c7i57fj37hn2")))) + "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs @@ -16540,14 +16839,14 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (define-public r-patchwork (package (name "r-patchwork") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02")))) + "13vswvcfmadmjz7pw0qdqdr6x85zbza4gljx2nx3a39hldj71yck")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -16865,14 +17164,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.9.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "17jjmy1qnx25ldvasrwhmal45nl1sr8qjxprbi8fcjwra9af6cr6")))) + "1xvjvsdd0hql209f7v2l1nw7gy8jkj5qp0699p5m2h55a01jl778")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -17512,14 +17811,14 @@ server-side.") (define-public r-sysfonts (package (name "r-sysfonts") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 - "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994")))) + "1gapsiva0vjd2myxgm1avav6my5x00rmy2hx0qll7dm7v1isznbv")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs @@ -17560,14 +17859,14 @@ package.") (define-public r-showtext (package (name "r-showtext") - (version "0.9") + (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 - "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid")))) + "1hq346k2lm7rv49hw7srn3ab5gcp6b0r4zc1kgsdmswyh3q1asra")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs @@ -17681,14 +17980,14 @@ regression models.") (define-public r-abtest (package (name "r-abtest") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 - "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0")))) + "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs @@ -18375,14 +18674,14 @@ the @code{aroma.affymetrix} package.") (define-public r-r-filesets (package (name "r-r-filesets") - (version "2.13.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (cran-uri "R.filesets" version)) (sha256 (base32 - "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) + "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) (propagated-inputs @@ -19028,21 +19327,124 @@ metrics to quantify time accumulation strategies based on minute level actigraphy-measured activity counts data.") (license license:gpl3))) +(define-public r-ash + (package + (name "r-ash") + (version "1.0-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "ash" version)) + (sha256 + (base32 + "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) + (properties `((upstream-name . "ash"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ash/") + (synopsis "David Scott's ASH routines") + (description + "This package provides David Scott's ASH routines ported from S-PLUS to +R.") + (license license:gpl2+))) + +(define-public r-hdrcde + (package + (name "r-hdrcde") + (version "3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "hdrcde" version)) + (sha256 + (base32 + "0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab")))) + (properties `((upstream-name . "hdrcde"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ash" ,r-ash) + ("r-ggplot2" ,r-ggplot2) + ("r-kernsmooth" ,r-kernsmooth) + ("r-ks" ,r-ks) + ("r-locfit" ,r-locfit) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://pkg.robjhyndman.com/hdrcde") + (synopsis "Highest density regions and conditional density estimation") + (description + "This is a package for the computation of highest density regions in one +and two dimensions, kernel estimation of univariate density functions +conditional on one covariate, and multimodal regression.") + (license license:gpl3))) + +(define-public r-rainbow + (package + (name "r-rainbow") + (version "3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "rainbow" version)) + (sha256 + (base32 + "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3")))) + (properties `((upstream-name . "rainbow"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-colorspace" ,r-colorspace) + ("r-hdrcde" ,r-hdrcde) + ("r-ks" ,r-ks) + ("r-mass" ,r-mass) + ("r-pcapp" ,r-pcapp))) + (home-page "https://cran.r-project.org/web/packages/rainbow/") + (synopsis "Bagplots, boxplots and rainbow plots for functional data") + (description + "This is a package for visualizing functional data and identifying +functional outliers with bagplots, boxplots and rainbow plots.") + (license license:gpl3))) + +(define-public r-fds + (package + (name "r-fds") + (version "1.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fds" version)) + (sha256 + (base32 + "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0")))) + (properties `((upstream-name . "fds"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rainbow" ,r-rainbow) + ("r-rcurl" ,r-rcurl))) + (home-page "https://cran.r-project.org/web/packages/fds/") + (synopsis "Functional data sets") + (description "This package contains a list of functional time series, +sliced functional time series, and functional data sets. Functional time +series is a special type of functional data observed over time. Sliced +functional time series is a special type of functional time series with a time +variable observed over time.") + (license license:gpl2+))) + (define-public r-fda (package (name "r-fda") - (version "5.1.5.1") + (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm")))) + "1r8hfi6x1maw5zz8k95wfcr7v69lg4zl3mcj69cvvq2mkg4y3158")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + `(("r-fds" ,r-fds) + ("r-matrix" ,r-matrix))) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description @@ -20418,14 +20820,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2020.03.16") + (version "2020.12.04") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn")))) + "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -20440,14 +20842,14 @@ character codes as well as the UN M.49 area codes.") (define-public r-stopwords (package (name "r-stopwords") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 - "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw")))) + "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs @@ -21510,13 +21912,13 @@ recommendations for developers.") (define-public r-loo (package (name "r-loo") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "loo" version)) (sha256 - (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr")))) + (base32 "01a15ikfnyxhjhrgvy3ag929rg45dxp3wji1j38r4hg4q1yz4ma9")))) (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs @@ -21812,14 +22214,14 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx")))) + "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (propagated-inputs @@ -22428,17 +22830,109 @@ connection, user authentication and file transfer. A simple R client is included in this package as well.") (license license:gpl2))) +(define-public r-gamm4 + (package + (name "r-gamm4") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamm4" version)) + (sha256 + (base32 + "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap")))) + (properties `((upstream-name . "gamm4"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv))) + (home-page "https://cran.r-project.org/web/packages/gamm4/") + (synopsis "Generalized additive mixed models using mgcv and lme4") + (description + "Estimate generalized additive mixed models via a version of function +@code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor +estimation.") + (license license:gpl2+))) + +(define-public r-optimx + (package + (name "r-optimx") + (version "2020-4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "optimx" version)) + (sha256 + (base32 + "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3")))) + (properties `((upstream-name . "optimx"))) + (build-system r-build-system) + (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/optimx/") + (synopsis "Expanded replacement and extension of the optim function") + (description + "This package provides a replacement and extension of the @code{optim} +function to call to several function minimization codes in R in a single +statement. These methods handle smooth, possibly box constrained functions of +several or many parameters. Note that the function @code{optimr} was prepared +to simplify the incorporation of minimization codes going forward. This +package also implements some utility codes and some extra solvers, including +safeguarded Newton methods. Many methods previously separate are now included +here.") + (license license:gpl2))) + +(define-public r-projpred + (package + (name "r-projpred") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "projpred" version)) + (sha256 + (base32 + "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg")))) + (properties `((upstream-name . "projpred"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-gamm4" ,r-gamm4) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-loo" ,r-loo) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-optimx" ,r-optimx) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rngtools" ,r-rngtools) + ("r-rstantools" ,r-rstantools) + ("r-tidyverse" ,r-tidyverse))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://mc-stan.org/projpred/") + (synopsis "Projection predictive feature selection") + (description + "This package performs projection predictive feature selection for +generalized linear models and generalized linear and additive multilevel +models. The package is compatible with the @code{rstanarm} and @code{brms} +packages, but other reference models can also be used. See the package +vignette for more information and examples.") + (license license:gpl3))) + (define-public r-brms (package (name "r-brms") - (version "2.14.0") + (version "2.14.4") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0s8dl1xm3bpivfv3hw94zv9cifjg8cgs5137yd8d755kc2v0fdmf")))) + "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -22456,6 +22950,7 @@ included in this package as well.") ("r-mgcv" ,r-mgcv) ("r-nleqslv" ,r-nleqslv) ("r-nlme" ,r-nlme) + ("r-projpred" ,r-projpred) ("r-rcpp" ,r-rcpp) ("r-rstan" ,r-rstan) ("r-rstantools" ,r-rstantools) @@ -22655,14 +23150,14 @@ counting and recursive k-means partitioning.") (define-public r-hardhat (package (name "r-hardhat") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 - "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs")))) + "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs @@ -23060,14 +23555,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "1.4-3") + (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9")))) + "17vbf48g1mh8iigzzlaa9j4mw087hib7f1kkbl3c50xjcrr5iw6b")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -23150,14 +23645,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "1avcip33bldzz0rhkl43b4sljrbb8i24684xxmr9il5bijcpyy97")))) + "08lrmpfkwh1w290a5ikhs9yn1vn32wbgvbzb4n3zb2indb8s5g69")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -23964,27 +24459,26 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1")))) + "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-foreach" ,r-foreach) + ("r-generics" ,r-generics) ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-gpfit" ,r-gpfit) ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) ("r-recipes" ,r-recipes) @@ -24286,20 +24780,19 @@ model-related packages.") (define-public r-tidymodels (package (name "r-tidymodels") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 - "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4")))) + "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) @@ -24357,6 +24850,82 @@ censored data with competing risks (see data set @code{menopause}). The package also provides functions to visualize the observed data and the MLE.") (license license:gpl2+))) +(define-public r-metafor + (package + (name "r-metafor") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "metafor" version)) + (sha256 + (base32 + "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn")))) + (properties `((upstream-name . "metafor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme))) + (home-page "https://cran.r-project.org/web/packages/metafor/") + (synopsis "Meta-analysis package for R") + (description + "This package provides a comprehensive collection of functions for +conducting meta-analyses in R. The package includes functions to calculate +various effect sizes or outcome measures, fit fixed-, random-, and +mixed-effects models to such data, carry out moderator and meta-regression +analyses, and create various types of meta-analytical plots (e.g., forest, +funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial +and person-time data, the package also provides functions that implement +specialized methods, including the Mantel-Haenszel method, Peto's method, and +a variety of suitable generalized linear (mixed-effects) models (i.e. +mixed-effects logistic and Poisson regression models). Finally, the package +provides functionality for fitting meta-analytic multivariate/multilevel +models that account for non-independent sampling errors and/or true +effects (e.g. due to the inclusion of multiple treatment studies, multiple +endpoints, or other forms of clustering). Network meta-analyses and +meta-analyses accounting for known correlation structures (e.g. due to +phylogenetic relatedness) can also be conducted.") + (license license:gpl2+))) + +(define-public r-altmeta + (package + (name "r-altmeta") + (version "3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "altmeta" version)) + (sha256 + (base32 + "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0")))) + (properties `((upstream-name . "altmeta"))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda) + ("r-lme4" ,r-lme4) + ("r-matrix" ,r-matrix) + ("r-metafor" ,r-metafor) + ("r-rjags" ,r-rjags))) + (home-page "https://cran.r-project.org/web/packages/altmeta/") + (synopsis "Alternative meta-analysis methods") + (description + "This package provides alternative statistical methods for meta-analysis, +including: + +@enumerate +@item bivariate generalized linear mixed models for synthesizing odds ratios, + relative risks, and risk differences +@item heterogeneity tests and measures that are robust to outliers; +@item measures, tests, and visualization tools for publication bias or + small-study effects; +@item meta-analysis of diagnostic tests for synthesizing sensitivities, + specificities, etc.; +@item meta-analysis methods for synthesizing proportions; +@item models for multivariate meta-analysis. +@end enumerate +") + (license license:gpl2+))) + (define-public r-perm (package (name "r-perm") @@ -24573,14 +25142,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-14") + (version "0.9-15") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4")))) + "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -24656,3 +25225,353 @@ orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) +(define-public r-decon + (package + (name "r-decon") + (version "1.2-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "decon" version)) + (sha256 + (base32 + "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s")))) + (properties `((upstream-name . "decon"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page + "https://cran.r-project.org/web/packages/decon/") + (synopsis "Deconvolution Estimation in Measurement Error Models") + (description + "This package contains a collection of functions to deal with +nonparametric measurement error problems using deconvolution +kernel methods. We focus two measurement error models in the +package: (1) an additive measurement error model, where the +goal is to estimate the density or distribution function from +contaminated data; (2) nonparametric regression model with +errors-in-variables. The R functions allow the measurement errors +to be either homoscedastic or heteroscedastic. To make the +deconvolution estimators computationally more efficient in R, +we adapt the \"Fast Fourier Transform\" (FFT) algorithm for +density estimation with error-free data to the deconvolution +kernel estimation. Several methods for the selection of the +data-driven smoothing parameter are also provided in the package. +See details in: Wang, X.F. and Wang, B. (2011). Deconvolution +estimation in measurement error models: The R package decon. +Journal of Statistical Software, 39(10), 1-24.") + (license license:gpl3+))) + +(define-public r-locpol + (package + (name "r-locpol") + (version "0.7-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "locpol" version)) + (sha256 + (base32 + "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm")))) + (properties `((upstream-name . "locpol"))) + (build-system r-build-system) + (home-page + "https://cran.r-project.org/web/packages/locpol/") + (synopsis "Kernel Local Polynomial Regression") + (description + "Computes local polynomial estimators for the regression and +also density. It comprises several different utilities to handle +kernel estimators.") + (license license:gpl2+))) + +(define-public r-lpme + (package + (name "r-lpme") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lpme" version)) + (sha256 + (base32 + "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448")))) + (properties `((upstream-name . "lpme"))) + (build-system r-build-system) + (propagated-inputs + `(("r-decon" ,r-decon) + ("r-flexmix" ,r-flexmix) + ("r-locpol" ,r-locpol) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page + "https://cran.r-project.org/web/packages/lpme/") + (synopsis "Nonparametric Estimation of Measurement Error Models") + (description + "Provide nonparametric methods for mean regression model, +modal regression and conditional density estimation in the +presence/absence of measurement error. Bandwidth selection is +also provided for each method.") + (license license:gpl2+))) + +(define-public r-aws-signature + (package + (name "r-aws-signature") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aws.signature" version)) + (sha256 + (base32 + "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp")))) + (properties `((upstream-name . "aws.signature"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest))) + (home-page "https://github.com/cloudyr/aws.signature") + (synopsis "Amazon Web Services Request Signatures") + (description + "This package generates version 2 and 4 request signatures for Amazon Web +Services (AWS) and provides a mechanism for retrieving credentials from +environment variables, AWS credentials files, and EC2 instance metadata. For +use on EC2 instances, the package 'aws.ec2metadata' is suggested.") + (license license:gpl2+))) + +(define-public r-aws-s3 + (package + (name "r-aws-s3") + (version "0.3.21") + (source + (origin + (method url-fetch) + (uri (cran-uri "aws.s3" version)) + (sha256 + (base32 + "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx")))) + (properties `((upstream-name . "aws.s3"))) + (build-system r-build-system) + (propagated-inputs + `(("r-aws-signature" ,r-aws-signature) + ("r-base64enc" ,r-base64enc) + ("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/cloudyr/aws.s3") + (synopsis "AWS S3 Client Package") + (description + "This package provides a simple client package for the Amazon Web +Services (AWS) Simple Storage Service (S3) REST API.") + (license license:gpl2+))) + +(define-public r-lgr + (package + (name "r-lgr") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (cran-uri "lgr" version)) + (sha256 + (base32 + "196553hmni1ha9y6494f4g3ds0lwcl81v7k4r8wwap4a6acdrgd9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-r6" ,r-r6))) + (home-page "https://s-fleck.github.io/lgr/") + (synopsis "Fully featured logging framework") + (description "This package offers a flexible, feature-rich yet +light-weight logging framework based on @code{R6} classes. It supports +hierarchical loggers, custom log levels, arbitrary data fields in log events, +logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as +well as email and push notifications.") + (license license:expat))) + +(define-public r-mlr3measures + (package + (name "r-mlr3measures") + (version "0.3.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3measures" version)) + (sha256 + (base32 + "106lfaxphz0kh96ddq14hic7wvxjqp871zdp9kkkfk1kwfg35abw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-prroc" ,r-prroc))) + (home-page "https://mlr3measures.mlr-org.com/") + (synopsis "Performance measures for mlr3") + (description "This package implements multiple performance measures for +supervised learning. It includes over 40 measures for regression and +classification. Additionally, meta information about the performance measures +can be queried, e.g. what the best and worst possible performances scores +are.") + (license license:lgpl3))) + +(define-public r-mlr3misc + (package + (name "r-mlr3misc") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3misc" version)) + (sha256 + (base32 + "1q63i2059bf7cf61kwm0dqnk5vd60i0j4flziswwdk07fjxqh8xr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-backports" ,r-backports) + ("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-r6" ,r-r6))) + (home-page "https://mlr3misc.mlr-org.com/") + (synopsis "Helper functions for mlr3") + (description "@code{mlr3misc} provides frequently used helper functions +and assertions used in @code{mlr3} and its companion packages. It comes with +helper functions for functional programming, for printing, to work with +@code{data.table}, as well as some generally useful @code{R6} classes. This +package also supersedes the package @code{BBmisc}.") + (license license:lgpl3))) + +(define-public r-paradox + (package + (name "r-paradox") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (cran-uri "paradox" version)) + (sha256 + (base32 + "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-backports" ,r-backports) + ("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-mlr3misc" ,r-mlr3misc) + ("r-r6" ,r-r6))) + (home-page "https://paradox.mlr-org.com/") + (synopsis "Define and work with parameter spaces for complex algorithms") + (description "With this package it is possible to define parameter spaces, +constraints and dependencies for arbitrary algorithms, and to program on such +spaces. It also includes statistical designs and random samplers. Objects are +implemented as @code{R6} classes.") + (license license:lgpl3))) + +(define-public r-mlr3 + (package + (name "r-mlr3") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3" version)) + (sha256 + (base32 + "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-r6" ,r-r6) + ("r-backports" ,r-backports) + ("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-future-apply" ,r-future-apply) + ("r-lgr" ,r-lgr) + ("r-mlbench" ,r-mlbench) + ("r-mlr3measures" ,r-mlr3measures) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-uuid" ,r-uuid))) + (home-page "https://mlr3.mlr-org.com/") + (synopsis "Machine Learning in R - Next Generation") + (description "@code{mlr3} enables efficient, object-oriented programming +on the building blocks of machine learning. It provides @code{R6} objects for +tasks, learners, resamplings, and measures. The package is geared towards +scalability and larger datasets by supporting parallelization and out-of-memory +data-backends like databases. While @code{mlr3} focuses on the core +computational operations, add-on packages provide additional functionality.") + (license license:lgpl3))) + +(define-public r-mlr3learners + (package + (name "r-mlr3learners") + (version "0.4.3") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3learners" version)) + (sha256 + (base32 + "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-mlr3" ,r-mlr3) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://mlr3learners.mlr-org.com/") + (synopsis "Recommended Learners for @code{mlr3}") + (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} +with interfaces to essential machine learning packages on CRAN. This includes, +but is not limited to: (penalized) linear and logistic regression, linear and +quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support +vector machines, and gradient boosting.") + (license license:lgpl3))) + +(define-public r-bbotk + (package + (name "r-bbotk") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bbotk" version)) + (sha256 + (base32 + "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv")))) + (properties `((upstream-name . "bbotk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-lgr" ,r-lgr) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://bbotk.mlr-org.com") + (synopsis "Black-Box Optimization Toolkit") + (description "This package provides a common framework for optimization of +black-box functions for other packages, e.g. @code{mlr3}. It offers various +optimization methods e.g. grid search, random search and generalized simulated +annealing.") + (license license:lgpl3))) + +(define-public r-mlr3tuning + (package + (name "r-mlr3tuning") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3tuning" version)) + (sha256 + (base32 + "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbotk" ,r-bbotk) + ("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-lgr" ,r-lgr) + ("r-mlr3" ,r-mlr3) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://mlr3tuning.mlr-org.com/") + (synopsis "Tuning for @code{mlr3}") + (description "@code{mlr3tuning} implements methods for hyperparameter +tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various +termination criteria can be set and combined. The class @code{AutoTuner} provides a +convenient way to perform nested resampling in combination with @code{mlr3}.") + (license license:lgpl3))) |