diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 262 |
1 files changed, 201 insertions, 61 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 592200bb13..ad8c6ebe67 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -421,14 +421,14 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "3.3.2") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh")))) + "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -619,14 +619,14 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 - "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh")))) + "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -2472,14 +2472,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-6") + (version "1.7-7") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh")))) + "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -2821,14 +2821,14 @@ Optimization problems by using the simplex algorithm.") (define-public r-geometry (package (name "r-geometry") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8")))) + "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) @@ -3745,18 +3745,20 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "1.1.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g")))) + "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon))) + ("r-crayon" ,r-crayon) + ("r-fansi" ,r-fansi) + ("r-glue" ,r-glue))) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build @@ -4121,31 +4123,6 @@ functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) -(define-public r-metap - (package - (name "r-metap") - (version "1.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "metap" version)) - (sha256 - (base32 - "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0")))) - (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-rdpack" ,r-rdpack))) - (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") - (synopsis "Meta-analysis of significance values") - (description - "The canonical way to perform meta-analysis involves using effect sizes. -When they are not available this package provides a number of methods for -meta-analysis of significance values including the methods of Edgington, -Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate -published results; and a routine for graphical display.") - (license license:gpl2))) - (define-public r-network (package (name "r-network") @@ -4191,6 +4168,30 @@ supports arbitrary vertex/edge/graph attributes.") software developed by the Statnet Project.") (license license:gpl3))) +(define-public r-statcheck + (package + (name "r-statcheck") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "statcheck" version)) + (sha256 + (base32 + "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rmarkdown" ,r-rmarkdown))) + (home-page "https://cran.r-project.org/web/packages/statcheck/") + (synopsis "Extract statistics from articles and recompute p-values") + (description "This package can automatically extract statistical +null-hypothesis significant testing (NHST) results from articles and recompute +the p-values based on the reported test statistic and degrees of freedom to +detect possible inconsistencies.") + (license license:gpl2))) + (define-public r-sna (package (name "r-sna") @@ -4215,6 +4216,35 @@ methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) +(define-public r-tfisher + (package + (name "r-tfisher") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "TFisher" version)) + (sha256 + (base32 + "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx")))) + (properties `((upstream-name . "TFisher"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sn" ,r-sn))) + (home-page "https://cran.r-project.org/web/packages/TFisher/") + (synopsis "Optimal thresholding Fisher's p-value combination method") + (description + "This package provides the @dfn{cumulative distribution function} (CDF), +quantile, and statistical power calculator for a collection of thresholding +Fisher's p-value combination methods, including Fisher's p-value combination +method, truncated product method and, in particular, soft-thresholding +Fisher's p-value combination method which is proven to be optimal in some +context of signal detection. The p-value calculator for the omnibus version +of these tests are also included.") + (license license:gpl2))) + (define-public r-ttr (package (name "r-ttr") @@ -4515,14 +4545,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) + "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -4683,22 +4713,50 @@ ordered factor data types.") exponentiation.") (license license:gpl2))) +(define-public r-egg + (package + (name "r-egg") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "egg" version)) + (sha256 + (base32 + "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m")))) + (properties `((upstream-name . "egg"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable))) + (home-page "https://cran.r-project.org/web/packages/egg") + (synopsis "Extensions for ggplot2") + (description + "This package provides miscellaneous functions to help customize ggplot2 +objects. High-level functions are provided to post-process ggplot2 layouts +and allow alignment between plot panels, as well as setting panel sizes to +fixed values. Other functions include a custom @code{geom}, and helper +functions to enforce symmetric scales or add tags to facetted plots.") + (license license:gpl3))) + (define-public r-heatmaply (package (name "r-heatmaply") - (version "0.16.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1")))) + "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-colorspace" ,r-colorspace) ("r-dendextend" ,r-dendextend) + ("r-egg" ,r-egg) ("r-ggplot2" ,r-ggplot2) ("r-htmlwidgets" ,r-htmlwidgets) ("r-magrittr" ,r-magrittr) @@ -5335,18 +5393,17 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.1.3") + (version "4.1.4") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "087zivh9xdh1kk8zci67ys0m2xq0slzwgnf0jl05yy4gsgb6nmyx")))) + "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) ("r-stringi" ,r-stringi) ("r-zip" ,r-zip))) (home-page "https://github.com/awalker89/openxlsx") @@ -5541,14 +5598,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.8.3") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0034jlaq7z40q3hcpkjlaff37dpn46kvxvzw4scbwlw4x9q8sx9j")))) + "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (home-page "https://rstudio.github.io/renv") @@ -5868,14 +5925,14 @@ structured in groups, etc. and hierarchical cluster analysis.") (define-public r-factoextra (package (name "r-factoextra") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "factoextra" version)) (sha256 (base32 - "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) + "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -9204,14 +9261,14 @@ image formats, including PNG, Postscript, SVG, PGF.") (define-public r-multicool (package (name "r-multicool") - (version "0.1-10") + (version "0.1-11") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 - "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) + "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/multicool/") @@ -10996,13 +11053,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.4-0") + (version "2.5-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "0xb7a0x1i93kzijr518m9plzmg8s3mxh5anwfx9xrkg5ipldvz10")))) + (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) @@ -11451,14 +11508,14 @@ by change of variable.") (define-public r-listenv (package (name "r-listenv") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 - "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1")))) + "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) (build-system r-build-system) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ; vignette builder @@ -11474,14 +11531,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.12.4") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br")))) + "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools))) @@ -12392,14 +12449,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.0.2") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp")))) + "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -14662,6 +14719,89 @@ they are often difficult to interpret. Rex allows you to build complex regular expressions from human readable expressions") (license license:expat))) +(define-public r-xmlparsedata + (package + (name "r-xmlparsedata") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "xmlparsedata" version)) + (sha256 + (base32 + "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh")))) + (properties `((upstream-name . "xmlparsedata"))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/xmlparsedata#readme") + (synopsis "Parse data of @code{R} code as an @code{XML} tree") + (description + "This package provides tools to convert the output of +@code{utils::getParseData()} to an @code{XML} tree, that one can search via +@code{XPath}, and is easier to manipulate in general.") + (license license:expat))) + +(define-public r-cyclocomp + (package + (name "r-cyclocomp") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "cyclocomp" version)) + (sha256 + (base32 + "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd")))) + (properties `((upstream-name . "cyclocomp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) + ("r-remotes" ,r-remotes) + ("r-withr" ,r-withr))) + (home-page "https://github.com/MangoTheCat/cyclocomp") + (synopsis "Cyclomatic complexity of R code") + (description + "Cyclomatic complexity is a software metric, used to indicate the +complexity of a program. It is a quantitative measure of the number of +linearly independent paths through a program's source code. This package +provides tools to compute this metric.") + (license license:expat))) + +(define-public r-lintr + (package + (name "r-lintr") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "lintr" version)) + (sha256 + (base32 + "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb")))) + (properties `((upstream-name . "lintr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-crayon" ,r-crayon) + ("r-cyclocomp" ,r-cyclocomp) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-rex" ,r-rex) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringdist" ,r-stringdist) + ("r-testthat" ,r-testthat) + ("r-xml2" ,r-xml2) + ("r-xmlparsedata" ,r-xmlparsedata))) + (home-page "https://github.com/jimhester/lintr") + (synopsis "Linter for R code") + (description "This package checks adherence to a given style, syntax +errors and possible semantic issues. It supports on the fly checking of R +code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") + (license license:expat))) + (define-public r-sctransform (package (name "r-sctransform") @@ -15098,14 +15238,14 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.3.1") + (version "0.2.4.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d")))) + "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch")))) (build-system r-build-system) (propagated-inputs `(("r-openssl" ,r-openssl) @@ -15123,14 +15263,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n")))) + "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj")))) (build-system r-build-system) (propagated-inputs `(("r-dqrng" ,r-dqrng) |