diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
-rw-r--r-- | gnu/packages/statistics.scm | 145 |
1 files changed, 94 insertions, 51 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8cfc9507ca..01d5e25a1a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> @@ -18,6 +18,7 @@ ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com> ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com> +;;; Copyright © 2023 Felix Gruber <felgru@posteo.net> ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> ;;; ;;; This file is part of GNU Guix. @@ -508,14 +509,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-28.1") + (version "1.3-29") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "0lzz08fpn80qzm197s4806hr6skanr3r3rlx6bx7zk4cripygkfl")))) + "1zgvy7n01qyxk52yhk43d7z7c36nr54z98vqwmjdlmhx4zyj0s7f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -801,14 +802,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.5-7") + (version "3.5-8") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0bi76kr5xkcs98r795lz9nvsj6zzxq0w6zn1938z0ffx5b9js3nm")))) + "1d0qvw4200mjldna9n0acis0fk8xj28wwzqb8c3d4537l92zivbi")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) @@ -997,19 +998,20 @@ OpenSSL should be used.") (define-public r-estimability (package (name "r-estimability") - (version "1.4.1") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "estimability" version)) (sha256 (base32 - "090i1xwdp4fwj8jr8nk13w49516lfkk5mq1w7l0lff9g8lgaynn6")))) + "0s6w8vnq0jc136d2mpf6pgg45rbxccrlsgdy89pgksnbaxhmyb5k")))) (build-system r-build-system) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/estimability") (synopsis "Tools for assessing estimability of linear predictions") - (description "Provides tools for determining estimability of linear -functions of regression coefficients, and @code{epredict} methods that handle -non-estimable cases correctly.") + (description "This package provides tools for determining estimability of +linear functions of regression coefficients, and @code{epredict} methods that +handle non-estimable cases correctly.") (license license:gpl2+))) (define-public r-labeling @@ -1413,13 +1415,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "0w7dpp1zg8w0mback1mk0a0vp51hf4njmrxz1i3j1xq5b1jfyiz4")))) + "10d7sl9nk1gkkbinmvplyp2hg9zgxgs03llamrvbf4a5cnrs0mcd")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1518,6 +1520,36 @@ it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.") (license license:gpl3+))) +(define-public r-httpgd + (let ((commit "3f5f55822c4dce930155b91cedcfd4d483e3294e") + (revision "1")) + (package + (name "r-httpgd") + (version (git-version "2.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nx10/httpgd") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14i7mhbv1vcz2886w9lii9zhgr4zhhc844349syb989nhhzg552n")))) + (properties `((upstream-name . "httpgd"))) + (build-system r-build-system) + (propagated-inputs (list r-asioheaders r-cpp11 r-unigd)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/nx10/httpgd") + (synopsis "'HTTP' Server Graphics Device") + (description + "This package provides a graphics device for R that is accessible via +network protocols. This package was created to make it easier to embed live R +graphics in integrated development environments and other applications. The +included HTML/@code{JavaScript} client (plot viewer) aims to provide a better +overall user experience when dealing with R graphics. The device +asynchronously serves graphics via HTTP and @code{WebSockets}'.") + (license license:gpl2+)))) + (define-public r-mime (package (name "r-mime") @@ -3548,14 +3580,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "2.0-2") + (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0ym5z2zngkqvs1cd7c3k16k9ipsli6xc6qp0nmr77va34d8v0n4q")))) + "1f89v6zbxwl6yhx3qi7wrr3rndnxfwaf49mygw357f7cf3i8ma77")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3793,13 +3825,13 @@ using the multicore functionality of the parallel package.") "datatables-extensions/Buttons")))) (package (name "r-dt") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "11wwd76x1bk9aswi8w4bmvbf51j8hlmb5gsyqzfjdi6ihjkl4vwm")) + "0nvj2bc441b9h13085fa7q281f86lgx4k0d8lr64xgdpbmbvkl21")) (modules '((guix build utils) (ice-9 match))) (snippet @@ -4363,13 +4395,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.45.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "192x8cvna1j0sx37xh3ha8bjjyx39pn5wnxzn5gs3z5j93a4d055")))) + "1frkgjc2mzvjnay8g5nky1bvxv60wvsypmmdj6mbsfjnzq7ni7qs")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (arguments @@ -6776,8 +6808,8 @@ Java package that provides routines for various statistical distributions.") (license license:gpl2+))) (define-public emacs-ess - (let ((commit "3691ecc642eab5d016887e42699648e0eeeef566") - (version "18.10.2") + (let ((commit "ab2faeca1ba6c456333312c58f58ef9e5ef4aa8b") + (version "24.01.1") (revision "1")) (package (name "emacs-ess") @@ -6789,7 +6821,7 @@ Java package that provides routines for various statistical distributions.") (url "https://github.com/emacs-ess/ESS") (commit commit))) (sha256 - (base32 "19p8djsbgvahpsx1w8i6h3qvpbdr4isjwm3wi82yk2648ri0qsq1")) + (base32 "0jfdfqpa3x1zm65cllkzhqir057xd3hxi4z2ddii1i26zy56iikf")) (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet @@ -6807,9 +6839,6 @@ Java package that provides routines for various statistical distributions.") ;; Stop install-info from trying to update the info directory. (substitute* "doc/Makefile" ((".*/dir.*") "")) - ;; Fix r-help-mode test. - (substitute* "test/ess-test-r.el" - (("\\(equal ess-help-object \"plot.default\")") "t")) ;; Avoid generating ess-autoloads.el twice. (substitute* "Makefile" (("all: lisp doc etc autoloads") @@ -6839,9 +6868,6 @@ Java package that provides routines for various statistical distributions.") #~(modify-phases %standard-phases (delete 'configure) (add-before 'check 'skip-failing-tests - ;; The command-without-trailing-newline-test and other - ;; tests fail for unknown reasons (see: - ;; https://github.com/emacs-ess/ESS/issues/1272). (lambda _ (let-syntax ((disable-tests @@ -6853,22 +6879,7 @@ Java package that provides routines for various statistical distributions.") (((string-append "^\\(ert-deftest " test-name ".*") all) (string-append all "(skip-unless nil)\n")) - ...)))) - (disable-etests ;different test syntax - (syntax-rules () - ((_ file ()) - (syntax-error "test names list must not be empty")) - ((_ file (test-name ...)) - (emacs-batch-edit-file file - '(progn - (mapc (lambda (test) - (goto-char (point-min)) - (search-forward - (format "etest-deftest %s " test)) - (beginning-of-line) - (kill-sexp)) - (list test-name ...)) - (basic-save-buffer))))))) + ...))))) (disable-tests (list "test/ess-test-inf.el" "test/ess-test-r.el") ("ess--derive-connection-path" @@ -6878,15 +6889,10 @@ Java package that provides routines for various statistical distributions.") "ess-r-load-ESSR-github-fetch-no" "ess-r-load-ESSR-github-fetch-yes" "ess-set-working-directory-test" - "ess-test-r-startup-directory")) - (disable-etests "test/ess-test-r-eval.el" - ("ess-r-eval-ns-env-roxy-tracebug-test" - "ess-r-eval-sink-freeze-test")) - (disable-etests - "test/ess-test-inf.el" - ("command-without-trailing-newline-test"))))) + "ess-test-r-startup-directory"))))) (replace 'check - (lambda _ (invoke "make" "test"))))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? (invoke "make" "test")))))))) (native-inputs (list perl r-roxygen2 texinfo)) (inputs (list emacs-minimal r-minimal)) (propagated-inputs (list emacs-julia-mode)) @@ -7775,3 +7781,40 @@ weighting schemes.") statistical summary in arrays and enumerables.") (home-page "https://github.com/mrkn/enumerable-statistics") (license license:expat))) + +(define-public python-pgmpy + (package + (name "python-pgmpy") + (version "0.1.24") + (source + (origin + (method git-fetch) ;pypi package does not include test data + (uri (git-reference + (url "https://github.com/pgmpy/pgmpy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-daft + python-joblib + python-networkx + python-numpy + python-opt-einsum + python-pandas + python-pyparsing + python-pytorch + python-scikit-learn + python-scipy + python-statsmodels + python-tqdm)) + (native-inputs (list python-mock + python-pytest)) + (home-page "https://github.com/pgmpy/pgmpy") + (synopsis "Probabilistic Graphical Models library") + (description "This package provides a library for Probabilistic +Graphical Models. It can be used for learning (Structure and Parameter), +inference (Probabilistic and Causal), and simulations in Bayesian +Networks.") + (license license:expat))) |