diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 176 |
1 files changed, 60 insertions, 116 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9e613cd63a..904727df2b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -160,14 +160,14 @@ simulation not wholly unlike BUGS. JAGS was written with three aims in mind: (define-public libxls (package (name "libxls") - (version "1.5.2") + (version "1.5.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/libxls/libxls/releases/download/" "v" version "/libxls-" version ".tar.gz")) (sha256 - (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld")))) + (base32 "0rl513wpq5qh7wkmdk4g9c68rzffv3mcbz48p4xyg4969zrx8lnm")))) (build-system gnu-build-system) (home-page "https://github.com/libxls/libxls") (synopsis "Read binary (.xls) Excel spreadsheet files") @@ -184,7 +184,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -192,7 +192,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0ckgpihkih4b44rx48hpg9p6bv0w67j5z3qc8s4giy6qv2j29zlm")))) + "0xdy3dy2bzdiba8z94hjykyra8si8a5q15s0bri7c26scjrymg6k")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -1097,13 +1097,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.1") + (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "04wvswadlry2n9gnfqlpdqsav1wllnlzb5c9w9ydynllv4vkwfm0")))) + (base32 "0wsib5qpzn4d0w1ss3x158xmrawkms8vvsfvr3mh40pvd8g2ibad")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1187,19 +1187,21 @@ and to generate base64 encoded string from raster matrix.") (define-public r-svglite (package (name "r-svglite") - (version "1.2.3") + (version "1.2.3.2") (source (origin (method url-fetch) (uri (cran-uri "svglite" version)) (sha256 (base32 - "1zivykbi1pxdxhrkc1if1ihdn5p27j0nai2q0abca1dwry3wg2yl")))) + "00n8bg4iligl0h24v42cka417w26zmcxrr4r6k8wdal1riwhgmi5")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-gdtools" ,r-gdtools) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/svglite") (synopsis "SVG graphics device") (description @@ -1410,13 +1412,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.28") + (version "1.29") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0ai382fmpz25qrhdgchs3vph2cdvyd73xyryg4jby5fp67d03vh5")))) + "00rcwiq8znmk5h4qgrwd0639xyb38iwbjykqjk3disz3kvrcvbn1")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -1617,13 +1619,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1jik4lywg4688dfi5fh8jbnmsxvq3382ii0nsw5armjzfq3v309s")))) + "0f4rhnhyhgrv874l0yzm80ij6vcqdykfd7bzmnqs0wbgyhkxk8vq")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1635,14 +1637,14 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.0.1") + (version "3.0.3") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m")))) + "0f4yi87w6509lnaz1lhk9s8nm3bzx21ij3273s0zx7vpbp0qlxxz")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2094,14 +2096,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "02vfkqm1kw54y1qax8cmiyg2nk6bmh8j87fc3j22k7852s3y4xxj")))) + "1irc9c23hwliwkky1b3hi0dkzwalhb7zgjj08562ff1k8dqv4qf6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -2282,13 +2284,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.1.0") + (version "7.1.1") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "00s1wzx5960k8pzgpz4kikjf4k061hyhnd278y65q6n0wzv3d6vy")))) + "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx")))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew) @@ -2304,6 +2306,8 @@ tables, autolinks and strikethrough text.") ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description @@ -2314,19 +2318,20 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp")))) + "17fkc6pr8w5z3rpadg692a689p1v4j7xl5ak0y64is7c74cxgljx")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-askpass" ,r-askpass))) (home-page "https://github.com/jeroenooms/openssl") @@ -2683,13 +2688,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.2") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "196r3hq1gcr6iamxllq4k40cb109b16ng24ky0q68bwrll80q1mh")))) + (base32 "0vdjq4kcyxkr2m27588kk6yi5g53symjshj4jz4n0j18wz53shji")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2871,13 +2876,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.3") + (version "3.99-0.4") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1")))) + "1bw6wr17gp0vdnxc5hip47n15nhxwacin3a5992sc7yfb55kaxm5")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -2994,14 +2999,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.1-0") + (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh")))) + "0r83p36l6m5sy4lxfjbfajn4gcqb0wv9zh7arny02s6c7fb4756y")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -3154,13 +3159,13 @@ using the multicore functionality of the parallel package.") (define-public r-dt (package (name "r-dt") - (version "0.13") + (version "0.14") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "1db35mi4m4q3kha4vhvh693bv04y7h9pdawhsx8f234qjvz7783r")))) + "0xhinw7wasrai5wfswp3r48qfv7ppdfd9jc7py2rp63dn0bnvbab")))) (properties `((upstream-name . "DT"))) (build-system r-build-system) @@ -3233,13 +3238,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.0") + (version "4.0-2") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "1vy8v6filhw9sflk8wwnbgz2mryg70ml4iq4y1c34dlwxczcbzv8")))) + (base32 "0qdswxvdwjcnw0by15p9yfzw8laq4f2j0ivpma6q8c5zywldpxxc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -3247,7 +3252,8 @@ analysis of large sparse or dense matrices.") (propagated-inputs `(("r-foreach" ,r-foreach) ("r-matrix" ,r-matrix) - ("r-shape" ,r-shape))) + ("r-shape" ,r-shape) + ("r-survival" ,r-survival))) (home-page "https://www.jstatsoft.org/article/view/v033i01") (synopsis "Lasso and elastic-net regularized generalized linear models") (description @@ -3545,13 +3551,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.43.2") + (version "0.44.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj")))) + "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs @@ -4211,20 +4217,22 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.0.3") + (version "3.0.4") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "0hs6mk48i9yd43rg9wfjc2nxsjjwrnpifxqvxkv8ah18kvpd6xnp")))) + "15ip3v4xiqzbanf8bc5fj90cbwdgixr72aj5jrp34jfdzdx0gxwg")))) (build-system r-build-system) (propagated-inputs `(("r-catools" ,r-catools) ("r-gdata" ,r-gdata) ("r-gtools" ,r-gtools) ("r-kernsmooth" ,r-kernsmooth))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/gplots") (synopsis "Various R programming tools for plotting data") (description @@ -4280,26 +4288,6 @@ plot can be quickly adjusted using a flexible parameter dispatching mechanism.") (license license:gpl2+))) -(define-public r-zoo - (package - (name "r-zoo") - (version "1.8-8") - (source (origin - (method url-fetch) - (uri (cran-uri "zoo" version)) - (sha256 - (base32 - "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) - (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice))) - (home-page "http://zoo.R-Forge.R-project.org/") - (synopsis "S3 infrastructure for regular and irregular time series") - (description "This package contains an S3 class with methods for totally -ordered indexed observations. It is particularly aimed at irregular time -series of numeric vectors/matrices and factors.") - (license license:gpl2+))) - (define-public r-ztable (package (name "r-ztable") @@ -4860,14 +4848,14 @@ estimation and robust multivariate analysis with high breakdown point.") (define-public r-fit-models (package (name "r-fit-models") - (version "0.5-14") + (version "0.63") (source (origin (method url-fetch) (uri (cran-uri "fit.models" version)) (sha256 (base32 - "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck")))) + "0wrrfsgngsfrqnm247f0h6g01807i7lbf5chpyx7hkfdfmm4xbxn")))) (properties `((upstream-name . "fit.models"))) (build-system r-build-system) (propagated-inputs @@ -4937,14 +4925,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-5") + (version "2.2-7") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "10504hzivbn89ip0cd5bcxd36ivbgin1lw1xhyh3xfckcm25v1a5")))) + "1xnp3j36hggfg675v39mnr6rgvp7i11pfng7nmyy3k2ldgklz0j9")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -5106,18 +5094,19 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.55") + (version "5.61") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "1zjc8p95kb0ypxa6nxp0lkdq8armkjmmhf8484m25n5f14a59qfb")))) + (base32 "0kby1crnzkdg5sczwqapfpkr58apyzrrx85khigcqggmhhwl44wk")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs - `(("r-matrix" ,r-matrix) + `(("r-conquer" ,r-conquer) + ("r-matrix" ,r-matrix) ("r-matrixmodels" ,r-matrixmodels) ("r-sparsem" ,r-sparsem))) (home-page "https://www.r-project.org") @@ -5133,14 +5122,14 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "1.2.2.1") + (version "1.2.2.2") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "1bhh2v14phzndjhiq7yw9vych6vzn5yy3vk9q35zcp3jhjjbwdyh")))) + "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr) ; for building vignettes @@ -5321,14 +5310,14 @@ normals.") (define-public r-mnormt (package (name "r-mnormt") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "mnormt" version)) (sha256 (base32 - "1gxhma0zqsx5pkc0871vszq1y7akwdmpm8rhws5b3gr6w9mx4agf")))) + "00nn0b6nksn2jbpg0np5wphryp4f9v95vqxf5v628yysnawgkcwq")))) (build-system r-build-system) (propagated-inputs `(("r-tmvnsim" ,r-tmvnsim))) @@ -5461,14 +5450,14 @@ genome-wide association studies can be analyzed efficiently.") (define-public r-cairo (package (name "r-cairo") - (version "1.5-12") + (version "1.5-12.2") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 - "02v29am4fac3fyq6y1w6r89zwbqqkxjsxrafcwb5s124ikxyl22f")))) + "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs @@ -5637,30 +5626,6 @@ tools.") parameters.") (license license:gpl3)))) -(define-public r-directlabels - (package - (name "r-directlabels") - (version "2020.1.31") - (source - (origin - (method url-fetch) - (uri (cran-uri "directlabels" version)) - (sha256 - (base32 - "08s1gnwp4bn8xahwjaq0f1qzhwh2dvybzhq3z7xyzn8cnyzmis6c")))) - (build-system r-build-system) - (propagated-inputs - `(("r-quadprog" ,r-quadprog))) - (home-page "http://directlabels.r-forge.r-project.org/") - (synopsis "Direct labels for multicolor plots") - (description - "This package provides an extensible framework for automatically placing -direct labels onto multicolor plots. Label positions are described using -positioning methods that can be re-used across several different plots. There -are heuristics for examining @code{trellis} and @code{ggplot} objects and -inferring an appropriate positioning method.") - (license license:gpl3))) - (define-public r-catterplots (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4") (revision "3")) @@ -5670,7 +5635,7 @@ inferring an appropriate positioning method.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/Gibbsdavidl/CatterPlots.git") + (url "https://github.com/Gibbsdavidl/CatterPlots") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -5693,7 +5658,7 @@ shaped points? Now you can!") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jalvesaq/colorout.git") + (url "https://github.com/jalvesaq/colorout") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -5902,24 +5867,3 @@ Java package that provides routines for various statistical distributions.") Emacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such as R, Julia, and JAGS.") (license license:gpl2+))) - -(define-public r-boruta - (package - (name "r-boruta") - (version "7.0.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "Boruta" version)) - (sha256 - (base32 - "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg")))) - (properties `((upstream-name . "Boruta"))) - (build-system r-build-system) - (propagated-inputs `(("r-ranger" ,r-ranger))) - (home-page "https://gitlab.com/mbq/Boruta/") - (synopsis - "Wrapper Algorithm for All Relevant Feature Selection") - (description - "An all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).") - (license license:gpl2+))) |