diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 203 |
1 files changed, 173 insertions, 30 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d8fde36cd3..aa2094ecdb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -43,6 +43,7 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system ant) + #:use-module (guix build-system cmake) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system r) @@ -54,12 +55,15 @@ #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bash) + #:use-module (gnu packages bison) + #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages emacs) #:use-module (gnu packages emacs-xyz) + #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) @@ -90,6 +94,7 @@ #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) + #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -647,13 +652,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (define-public r-lattice (package (name "r-lattice") - (version "0.21-8") + (version "0.21-9") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 - "0af3c0mk0s3gnpmg7xmd4hjjynwv4ym3iv4grjvcmrk28abxdlwa")))) + "0ak9k6s6drd1a25m7mwzb426ms92a2p3ps04h2pacifwnk74ca59")))) (build-system r-build-system) (home-page "https://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") @@ -667,14 +672,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.6-1") + (version "1.6-1.1") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "01qcrv4y1fm3ah5h4j90xvzlwvzcnbpa10cpg6k9hp363xh0pip5")))) + "1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -1091,13 +1096,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (define-public r-plyr (package (name "r-plyr") - (version "1.8.8") + (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 - (base32 "030706kwgqa2s5jd93ck271iqb0pj3fshrj9frg4wgp1pfs12cm7")))) + (base32 "00z1mvqisnzbbwcwax1gm9ilahpgp21kk4l7hqdz8fym27vygd8m")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "http://had.co.nz/plyr") @@ -1446,13 +1451,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "1f92kjlds2nckmsjxx07xm2pikpc9x6hcvc0538xf5w9xsfcjy1i")))) + "0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") @@ -1532,13 +1537,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "1az5l2dnrdfx36kcdi5x8qnrbwmylf0wqd6a4hg2l9m8q1vpgs8d")))) + "0201v3spgl8a5c5xkddac5a3z9zh8d0nm9yg6alyhhj4cjwmgibh")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally @@ -1864,14 +1869,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "2.3.3") + (version "2.3.4") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1d3m7bhd8n5l0x1phfwzgrw2kwfyahb9yd61bbcnryd6m8c8kr3w")))) + "1b6y1jhf5ix4vry165vwid5nqm0d99q61vxak6aw3vfkj379vgk9")))) (build-system r-build-system) (propagated-inputs (list r-blob @@ -2234,6 +2239,32 @@ modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms.") (license license:asl2.0))) +(define-public python-chaospy + (package + (name "python-chaospy") + (version "4.3.13") + (source (origin ;; PyPI misses Pytest fixtures. + (method git-fetch) + (uri (git-reference + (url "https://github.com/jonathf/chaospy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata python-numpoly + python-numpy python-scipy)) + (native-inputs (list python-pytest python-scikit-learn)) + (home-page "https://chaospy.readthedocs.io/en/master/") + (synopsis "Numerical tool for performing uncertainty quantification") + (description "Chaospy is a numerical toolbox for performing uncertainty +quantification using polynomial chaos expansions, advanced Monte Carlo +methods implemented in Python. It also include a full suite of tools for +doing low-discrepancy sampling, quadrature creation, polynomial manipulations, +and a lot more.") + (license license:expat))) + (define-public python-patsy (package (name "python-patsy") @@ -2265,6 +2296,30 @@ building design matrices.") ;; and is covered by the PSFL. (license (list license:bsd-2 license:psfl)))) +(define-public python-mapie + (package + (name "python-mapie") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "MAPIE" version)) + (sha256 + (base32 + "1nvi547avvwrck1n7rf5jh7d0ml6jaqjs2p59iwcq2a5xjmdsmsc")))) + (build-system pyproject-build-system) + (native-inputs (list python-pandas python-pytest)) + (propagated-inputs (list python-numpy python-scikit-learn)) + (home-page "https://github.com/scikit-learn-contrib/MAPIE") + (synopsis "Module for estimating prediction intervals") + (description "MAPIE allows you to easily estimate prediction intervals +(or prediction sets) using your favourite scikit-learn-compatible model for +single-output regression or multi-class classification settings. + +Prediction intervals output by MAPIE encompass both aleatoric and epistemic +uncertainties and are backed by strong theoretical guarantees thanks to +conformal prediction methods intervals.") + (license license:bsd-3))) + (define-public python-statsmodels (package (name "python-statsmodels") @@ -2319,6 +2374,94 @@ statistical computations including descriptive statistics and estimation and inference for statistical models.") (license license:bsd-3))) +(define-public python-openturns + (package + (name "python-openturns") + (version "1.21") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openturns/openturns") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05lbx8npvvk7jyakvfpgi9ggdp6cnzwv2hjmjrkji2s42axv0q6d")))) + (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (delete 'check) + ;; This is a Python package which is fully managed by CMake. In + ;; cmake-build-system the check phase runs before install, but the + ;; Python modules required for testing are only installed in the + ;; install phase. Move check to after the install phase. + (add-after 'install 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "--exclude-regex" + ;; XXX: Cpp tests fail in 'No such file or directory', + ;; skip for now and only run the Python tests. + ;; TODO: To pass the Python tests below, Ipopt must be + ;; built with MUMPS support, but simply adding mumps + ;; to the inputs doesn't work for it to be found, + ;; possibly because MUMPS doesn't generate a .pc file. + (string-join + (list "^cpp" + "pyinstallcheck_Bonmin_std" + "pyinstallcheck_Bonmin_4dsoo" + "pyinstallcheck_Bonmin_MIT15" + "pyinstallcheck_Bonmin_swiler2014" + "pyinstallcheck_Ipopt_std" + "pyinstallcheck_example_plot_optimization_bonmin" + "pyinstallcheck_coupling_tools") + "|")))))))) + (native-inputs + (list bison + dvisvgm + flex + python-numpydoc + python-sphinx + ;; python-sphinx-gallery ;; Currently broken + swig)) + (inputs + (list openblas ; the only required dependency + ;; The dependecies below are all optional. + bonmin + boost + cbc ;; Maybe this should be propagated by Bonmin? + ceres + cminpack + dlib + hdf5 + hmat + ipopt + libxml2 + mpc + mpfr + nlopt + pagmo + primesieve + python-wrapper + spectra + tbb)) + (propagated-inputs + (list python-chaospy + python-dill + python-matplotlib + python-numpy + python-pandas + python-scipy)) + (home-page "https://openturns.github.io/www/") + (synopsis "Uncertainty treatment library") + (description + "OpenTURNS is a scientific C++ and Python library including an internal +data model and algorithms dedicated to the treatment of uncertainties. The +main goal of this library is giving to specific applications all the +functionalities needed to treat uncertainties in studies.") + (license license:lgpl3+))) + (define-public r-coda (package (name "r-coda") @@ -2673,14 +2816,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0fg5avcrjjn7sv6rzbp19y6jwjjr77xpldxg4xssp5s1p832wnk2")))) + "1p2bnr4z4vx3yqq5isqb3z4d9vg2isiz8i0h3vxdb5ramzwjd9zs")))) (properties `((upstream-name . "openssl") (updater-extra-inputs . ("openssl")))) @@ -2826,13 +2969,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.5.0") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "1h4bzj0am9lawbh1cam1jmgk1xjmn9da14r90w3q984hswz7nc9p")))) + "1kndhxl0fxn40v9yx0iglilani3ym3ywbjf6zbg1pnb52ncf0nm9")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3055,13 +3198,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.24") + (version "2.25") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "11ixspf7w5zsr02c5545w0ra7l9c8kb4bls97dhx5cgldnjfywrq")))) + (base32 "0m814598vc67sjwk83xh9g17n72618l32dgg7fz8y0gycqk6dr06")))) (properties `((upstream-name . "rmarkdown") (updater-extra-propagated-inputs . ("pandoc")))) @@ -3837,13 +3980,13 @@ using the multicore functionality of the parallel package.") extensions))))) (package (name "r-dt") - (version "0.29") + (version "0.30") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "1b9qshrjv9xaak92rvg65vkak4pyci9js4j7nkfcg0p19ghnvlm8")) + "13k9zyapx6rqfsrl5afpgaqyni57qq88hxa1j3y3wjcv5bim66ig")) (modules '((guix build utils) (ice-9 match))) (snippet @@ -3926,7 +4069,7 @@ using the multicore functionality of the parallel package.") (list js-selectize)) (native-inputs `(("r-knitr" ,r-knitr) - ("uglifyjs" ,node-uglify-js) + ("esbuild" ,esbuild) ("datatables-plugins" ,(let ((version "1.13.4")) (origin @@ -5782,13 +5925,13 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.1-8") + (version "1.1-9") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 - (base32 "1k6i18ywfh0xlc7ipgvz1g9gdgkyz5phf1cwyfv8mn2nwgag3h6l")))) + (base32 "1l5gn6495k8vqp2b4hj4g5ani7j4cli2p7n8fwkw7bmc42q13m6l")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (native-inputs @@ -6305,14 +6448,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "19s4cm6a73b9q519mmgf2qxjmd2bsjff19ds3hk8ksgz98d46xl9")))) + "1zvzycng2hsks9d7552nb93abzjrs43c975rc16s3c1is8318vib")))) (build-system r-build-system) (propagated-inputs (list r-generics r-timechange)) @@ -6913,18 +7056,18 @@ Methods are provided for a variety of fitted models, including @code{lm()} and (define-public r-puniform (package (name "r-puniform") - (version "0.2.6") + (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "puniform" version)) (sha256 (base32 - "1rfd7d14an28hba1rhldxn418qagnlk8ngvimb86i3774ll9blvi")))) + "15q5wlcps7387rjz7p1f5kifg1fl5yxxy7gjx6fvspvqwjkjbs4z")))) (properties `((upstream-name . "puniform"))) (build-system r-build-system) (propagated-inputs - (list r-adgoftest r-metafor r-rcpp r-rcpparmadillo)) + (list r-adgoftest r-metafor r-numderiv r-rcpp r-rcpparmadillo)) (home-page "https://github.com/RobbievanAert/puniform") (synopsis @@ -7082,14 +7225,14 @@ various statistical models with linear predictors.") (define-public r-bayesfactor (package (name "r-bayesfactor") - (version "0.9.12-4.4") + (version "0.9.12-4.5") (source (origin (method url-fetch) (uri (cran-uri "BayesFactor" version)) (sha256 (base32 - "02bhlamnkxp9wqi2cp1i0dxmqdf3y3l872ad9z39xwripbi4kc7a")))) + "10bclqzczawpssjwa3b177xpab4mdhczfj1qj23xn2yvrrw1z9mh")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) (propagated-inputs |