diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 132 |
1 files changed, 84 insertions, 48 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 224c19cea3..482eea9178 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -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 "4.0.0") + (version "4.0.1") (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 - "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6")))) + "0ckgpihkih4b44rx48hpg9p6bv0w67j5z3qc8s4giy6qv2j29zlm")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -513,14 +513,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-79") + (version "0.8-80") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg")))) + "0wjdi3qn9famsxmpdyyahidaid0yhxlpx4ad9k8vrxhxd6xspasp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -599,13 +599,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-147") + (version "3.1-148") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "1rqc3wy3lmy0wczsvsn8yszzsxhppfwg4iznb1j6ki2qawpdij7g")))) + (base32 "1cmf43r82kar1hpj9dhqfi3rbjka0z5s6cbdy7fklwh99xj3phkp")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -702,14 +702,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.1-12") + (version "3.2-3") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "07zj3gpwncw89hbiwjb6ih9axv5zwdqnbgz9yw9xzws6nrpdcbmn")))) + "07h76r2y23w889257krlijcw4n4d7ssx92x7i5qb1xyv5gyvl3rx")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -1097,13 +1097,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.0") + (version "3.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0j21am605kqqzlwhm45kaj0m2irnmy2vz0j7kzi9f0qdzrv3q3ij")))) + (base32 "04wvswadlry2n9gnfqlpdqsav1wllnlzb5c9w9ydynllv4vkwfm0")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1117,6 +1117,8 @@ using just two functions: melt and dcast (or acast).") ("r-scales" ,r-scales) ("r-svglite" ,r-svglite) ; Needed for 'ggsave' ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://ggplot2.tidyverse.org") (synopsis "An implementation of the grammar of graphics") (description @@ -1665,27 +1667,25 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.8.5") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0602b4a9nffxx67q57csqp87nkrv33nn9wlaw1458yys9fzx6l2p")))) + "1wxi7pzw1mqkgay2s9hwlkpkxfzydngf56wrf7k93n14rlqm3dmz")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-bh" ,r-bh) - ("r-ellipsis" ,r-ellipsis) + `(("r-ellipsis" ,r-ellipsis) + ("r-generics" ,r-generics) ("r-glue" ,r-glue) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) - ("r-pkgconfig" ,r-pkgconfig) - ("r-plogr" ,r-plogr) ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/dplyr") @@ -1703,21 +1703,23 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "1.4.3") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39")))) + "1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) + ("r-blob" ,r-blob) ("r-dbi" ,r-dbi) ("r-dplyr" ,r-dplyr) ("r-glue" ,r-glue) ("r-lifecycle" ,r-lifecycle) + ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) @@ -2052,13 +2054,13 @@ jackknifed confidence intervals are available for most estimates.") (define-public r-rversions (package (name "r-rversions") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "rversions" version)) (sha256 (base32 - "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i")))) + "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -2092,14 +2094,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.6") + (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "170rphqq28j0pcr28g6dxv3isp436ajhyzkpri31pn0lfm3szs6h")))) + "02vfkqm1kw54y1qax8cmiyg2nk6bmh8j87fc3j22k7852s3y4xxj")))) (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") @@ -2589,13 +2591,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.870.2.0") + (version "0.9.900.1.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v")))) + "1zisw2yrb9qmmrs7q8y83mrm7lh1c2786h70gs8jwc0si16x0lq5")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2681,13 +2683,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg")))) + (base32 "196r3hq1gcr6iamxllq4k40cb109b16ng24ky0q68bwrll80q1mh")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2702,6 +2704,8 @@ certain criterion, e.g., it contains a certain regular file.") ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml) ("ghc-pandoc" ,ghc-pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description @@ -3229,16 +3233,17 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "3.0-2") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl")))) + (base32 "1vy8v6filhw9sflk8wwnbgz2mryg70ml4iq4y1c34dlwxczcbzv8")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-foreach" ,r-foreach) ("r-matrix" ,r-matrix) @@ -3572,13 +3577,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "0pfb6qk4yb6xaya8i1wvx6dnc3jj4s2g94sq2kzv4p8zn4pf24l1")))) + "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -3699,14 +3704,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.0.3") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "18ypk63nifp5jj5d9880m49zdv7n4a18gac59wj5z5xk6qr7vfal")))) + "0vqj5dakb35axv4l0yrihpa16vnz2b5bhaaqg7l0gsqbb04qcb00")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -4071,14 +4076,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm")))) + "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -5215,13 +5220,13 @@ bootstrap test for generalized linear mixed models.") (define-public r-cardata (package (name "r-cardata") - (version "3.0-3") + (version "3.0-4") (source (origin (method url-fetch) (uri (cran-uri "carData" version)) (sha256 - (base32 "0cg2yxzn0pdjqykr60my1fzpfkqac21fll5hv3m9w5c9sayq8swq")))) + (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd")))) (properties `((upstream-name . "carData"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/car/") @@ -5234,13 +5239,13 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-7") + (version "3.0-8") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "11sfk1l41j27mrfy16g7b02c570n3gy9icvpcrfjh1biykqa565d")))) + (base32 "0ig1691kxbzkrsq8xi5a6fq2f0vq22j1dn54jxdkldqr5vri1m57")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -5284,18 +5289,49 @@ computations taking place in C++ code, and support for interrupting those comput even in multithreaded code, typically using OpenMP.") (license license:gpl3+))) +(define-public r-tmvnsim + (package + (name "r-tmvnsim") + (version "1.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tmvnsim" version)) + (sha256 + (base32 + "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp")))) + (properties `((upstream-name . "tmvnsim"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://www.r-project.org") + (synopsis "Truncated multivariate normal simulation") + (description + "This package implements importance sampling from the truncated +multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK) +simulator. Unlike Gibbs sampling which can get stuck in one truncation +sub-region depending on initial values, this package allows truncation based +on disjoint regions that are created by truncation of absolute values. The +GHK algorithm uses simple Cholesky transformation followed by recursive +simulation of univariate truncated normals hence there are also no convergence +issues. Importance sample is returned along with sampling weights, based on +which, one can calculate integrals over truncated regions for multivariate +normals.") + (license license:gpl2))) + (define-public r-mnormt (package (name "r-mnormt") - (version "1.5-7") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "mnormt" version)) (sha256 (base32 - "1y0vlvh02wza2wvfd29wxjlw3jg9rnwnx3kph5qz4179kz87fgfg")))) + "1gxhma0zqsx5pkc0871vszq1y7akwdmpm8rhws5b3gr6w9mx4agf")))) (build-system r-build-system) + (propagated-inputs + `(("r-tmvnsim" ,r-tmvnsim))) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") @@ -5330,14 +5366,14 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "0snri2k8qslb7478c5jz4a5xxmmb1ipmp8x1jizi8mhj2cjic1w0")))) + "179xb7yb8br99aa5awm2yxsy0v5w1kdhv6a7ifaliz2y64677m1g")))) (build-system r-build-system) (propagated-inputs `(("r-mnormt" ,r-mnormt) @@ -5461,14 +5497,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.8") + (version "1.7.9") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0g2m9dyhgds4shdrk76w7rqdl9msam4rii2qrhz12gipzhi9k89x")))) + "0wnjzvfkrgp2hkr8g5r5vcgcxmsq8bhdmkzkk0m93wr3fgh5xyfb")))) (build-system r-build-system) (propagated-inputs `(("r-generics" ,r-generics) |