diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 202 |
1 files changed, 160 insertions, 42 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dd8965312b..47276cb95e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com> +;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -187,7 +188,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.1.0") + (version "4.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -195,7 +196,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "109732arm6dq6d6v3fl1nyx63lcvv9569j8g6r3s2b18sxcqkrp8")))) + "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -214,11 +215,14 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (substitute* "src/library/base/makebasedb.R" (("compress = TRUE") "compress = FALSE")) #t)) - (add-before 'configure 'patch-uname + (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) - (let ((uname-bin (search-input-file inputs "/bin/uname"))) + (let ((uname-bin (search-input-file inputs "/bin/uname")) + (rm-bin (search-input-file inputs "/bin/rm"))) (substitute* "src/scripts/R.sh.in" - (("uname") uname-bin))) + (("uname") uname-bin)) + (substitute* "src/unix/sys-std.c" + (("rm -Rf ") (string-append rm-bin " -Rf ")))) #t)) (add-after 'unpack 'build-reproducibly (lambda _ @@ -345,12 +349,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ texlive-latex-base texlive-latex-fancyvrb texlive-latex-graphics - texlive-latex-hyperref - texlive-latex-l3backend - texlive-latex-oberdiek + texlive-hyperref + texlive-oberdiek texlive-latex-tools texlive-latex-upquote - texlive-latex-url + texlive-url texlive-latex-xkeyval))) ("tzdata" ,tzdata-for-tests) ("xz" ,xz))) @@ -713,14 +716,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.2-11") + (version "3.2-12") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0w0gkni1w8rbmfw7yl08bl1s9lij1yhbkj4dvmxcarkkw26sjjzs")))) + "1152zpd961bzwnabkhf6q9jgb72bj68023dsn2dcdmxqdi72mps5")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -1041,14 +1044,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.6.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1bidc1xzsv5nz2glf6z4sjxqlbs6zq595wwdmiq66sc2p7cis59s")))) + "0mhz7dkjdm8ap2zav1pmivhr8s0l6p2f6piij2hy08nwszqk51nr")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1513,19 +1516,19 @@ the execution time of R expressions.") (define-public r-pryr (package (name "r-pryr") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "pryr" version)) (sha256 (base32 - "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k")))) + "02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-codetools" ,r-codetools))) - (native-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-codetools" ,r-codetools) + ("r-lobstr" ,r-lobstr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr))) (home-page "https://github.com/hadley/pryr") (synopsis "Tools for computing on the R language") (description @@ -1637,13 +1640,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.5.0") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "00ifi2kwa7kn67xf0z1w6jfdicjczygbyi5mhfw2qlzc4sbazhdf")))) + "0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1677,14 +1680,14 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.1.2") + (version "3.1.3") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "1vmwz1a756lar0jsigx6dhmj9mwk5mhywhq0prifwih3abhvszmn")))) + "1gpy90hg0bd4an0wqj0xx16a6x37fhc94z1v63y46dpiz231xfks")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -2552,13 +2555,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.4.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82")))) + "0cj5k3ykkhixgdsqm1gnmpc0d8z04l3fhvm2dr5xp7cpmhgsrpfr")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2570,7 +2573,8 @@ time-of-day values, based on the @code{difftime} class.") ("r-tibble" ,r-tibble) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) - ("r-bh" ,r-bh))) + ("r-tzdb" ,r-tzdb) + ("r-vroom" ,r-vroom))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/readr") @@ -2644,13 +2648,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.5.0.0") + (version "0.10.6.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "059qi872f9h40ns65166qsq1i1jq1mvizm29a0xmqlyn7a5y9ca3")))) + "1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2736,13 +2740,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.9") + (version "2.10") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0s46x819zhf45k8qzpiwz79i5pn4gv99jfadywcjca3wka5szrbc")))) + (base32 "1p2cc9ysj906gkl4c6ac7s8njh32p2kcx1ib4gjj3jmfz915k9jk")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2829,13 +2833,13 @@ that package, other packages are unaffected.") (define-public r-blob (package (name "r-blob") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "blob" version)) (sha256 (base32 - "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g")))) + "1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9")))) (build-system r-build-system) (propagated-inputs `(("r-rlang" ,r-rlang) @@ -2851,13 +2855,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.7") + (version "2.2.8") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1j89n4ydv42y5hqqv8nz72sa5wncws074kg527s902k1a67s69ii")))) + "1hscgi11px9hq0sx78c2lkfzq121rlvmhxmqf305xg6lgqdxr2hv")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2924,13 +2928,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.6") + (version "3.99-0.7") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0qibvacbfm7gl41ylway3vdyi1qbpa211d48rg3k5i30d48rbf58")))) + "024038g1mrzkv7b7fyrzpzpxlch3sifsnaa584g98y3c3g6jbrz0")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3410,14 +3414,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-7") + (version "1.7-8") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "1phqrx787fkiamgx56sjjmzl9nh5wgpffah0mlwd7ijrf446qz3r")))) + "16lw0pr71h00whndkkv9zh2ixm6vc8bkp8m4i5wwhmihd9abdkdb")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -3658,13 +3662,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.59.0") + (version "0.60.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "178baqrd7rbin3l10zyrkps5sda0q9mdqil9r12b3n99mlk8fhh7")))) + "08azjib5pwqs683dpgr3p5gid0silddcq6baqmvmazncrw1r7q0f")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments @@ -5444,14 +5448,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.12.1") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w")))) + "02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -6215,3 +6219,117 @@ various statistical models with linear predictors.") factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.") (license license:gpl2))) + +(define-public r-norm + (package + (name "r-norm") + (version "1.0-9.5") + (source (origin + (method url-fetch) + (uri (cran-uri "norm" version)) + (sha256 + (base32 + "01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/norm/") + (synopsis "Analysis of multivariate normal datasets with missing values") + (description "Multiple imputation of multivariate continuous data under a +normal model.") + ;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE. + (license (license:non-copyleft "file://LICENSE")))) + +(define-public r-naniar + (package + (name "r-naniar") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (cran-uri "naniar" version)) + (sha256 + (base32 + "0l3l2x85v3srilww483kpgp4zlwixyml257b0cqly8kcpwawlinm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-norm" ,r-norm) + ("r-forcats" ,r-forcats) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-upsetr" ,r-upsetr) + ("r-viridis" ,r-viridis) + ("r-visdat" ,r-visdat))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/njtierney/naniar") + (synopsis + "Data structures, summaries, and visualisations for missing data") + (description + "Missing values are ubiquitous in data and need to be explored and +handled in the initial stages of analysis. The package provides data structures +and functions that facilitate the plotting of missing values and examination of +imputations. This allows missing data dependencies to be explored with minimal +deviation from the common work patterns of @code{ggplot2} and tidy data.") + (license license:expat))) + +(define-public r-glinternet + (package + (name "r-glinternet") + (version "1.0.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "glinternet" version)) + (sha256 + (base32 + "1lqph2hj0h826gcfyk290ahkfalpnrd6jzymm60xi2qxia14lzk5")))) + (build-system r-build-system) + (home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf") + (synopsis "Learning interactions via hierarchical group-lasso regularization") + (description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction +models that satisfy strong hierarchy: if an interaction coefficient is estimated +to be nonzero, then its two associated main effects also have nonzero estimated +coefficients. Accommodates categorical variables (factors) with arbitrary +numbers of levels, continuous variables, and combinations thereof. Implements +the machinery described in the paper \"Learning interactions via hierarchical +group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3). +Michael Lim & Trevor Hastie (2015)") + (license license:gpl2))) + +(define-public r-datasaurus + (package + (name "r-datasaurus") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "datasauRus" version)) + (sha256 + (base32 + "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl")))) + (properties `((upstream-name . "datasauRus"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/lockedata/datasauRus") + (synopsis "Datasets from the Datasaurus Dozen") + (description + "The Datasaurus Dozen is a set of datasets with the same summary +statistics. They retain the same summary statistics despite having radically +different distributions. The datasets represent a larger and quirkier object +lesson that is typically taught via Anscombe's Quartet (available in the +'datasets' package). Anscombe's Quartet contains four very different +distributions with the same summary statistics and as such highlights the value +of visualisation in understanding data, over and above summary statistics. As +well as being an engaging variant on the Quartet, the data is generated in a +novel way. The simulated annealing process used to derive datasets from the +original Datasaurus is detailed in \"Same Stats, Different Graphs: Generating +Datasets with Varied Appearance and Identical Statistics through Simulated +Annealing\" @url{doi:10.1145/3025453.3025912}.") + (license license:expat))) |