diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 421 |
1 files changed, 415 insertions, 6 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f854a44d96..0ffd4955bb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -24,6 +24,7 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system r) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) @@ -35,11 +36,18 @@ #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) #:use-module (gnu packages readline) + #:use-module (gnu packages ssh) #:use-module (gnu packages texlive) #:use-module (gnu packages texinfo) + #:use-module (gnu packages tls) #:use-module (gnu packages base) - #:use-module (gnu packages xorg)) + #:use-module (gnu packages web) + #:use-module (gnu packages xml) + #:use-module (gnu packages xorg) + #:use-module (gnu packages zip) + #:use-module (srfi srfi-1)) (define-public r (package @@ -913,9 +921,9 @@ database.") times.") (license license:gpl2))) -(define-public r-data.table +(define-public r-data-table (package - (name "r-data.table") + (name "r-data-table") (version "1.9.6") (source (origin (method url-fetch) @@ -929,7 +937,408 @@ times.") (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") (description - "The R data.table package provides functions for fast aggregation of -large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of -columns by group, column listing and fast file reading.") + "The R package @code{data.table} is an extension of @code{data.frame} +providing functions for fast aggregation of large data (e.g. 100GB in RAM), +fast ordered joins, fast add/modify/delete of columns by group, column listing +and fast file reading.") + (license license:gpl3+))) + +(define-public python-patsy + (package + (name "python-patsy") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (string-append "https://pypi.python.org/packages/source/" + "p/patsy/patsy-" version ".zip")) + (sha256 + (base32 + "1kbs996xc2haxalmhd19rr1wh5fa4gbbxf81czkf5w4kam7h7wz4")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))) + (add-after 'unpack 'prevent-generation-of-egg-archive + (lambda _ + (substitute* "setup.py" + (("from setuptools import setup") + "from distutils.core import setup")) + #t))))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" ,python-nose) + ("unzip" ,unzip))) + (home-page "https://github.com/pydata/patsy") + (synopsis "Describe statistical models and build design matrices") + (description + "Patsy is a Python package for describing statistical models and for +building design matrices.") + ;; The majority of the code is distributed under BSD-2. The module + ;; patsy.compat contains code derived from the Python standard library, + ;; and is covered by the PSFL. + (license (list license:bsd-2 license:psfl)))) + +(define-public python2-patsy + (let ((patsy (package-with-python2 python-patsy))) + (package (inherit patsy) + (native-inputs + `(("python2-setuptools" ,python2-setuptools) + ,@(package-native-inputs patsy))) + (propagated-inputs + `(("python2-numpy" ,python2-numpy) + ("python2-scipy" ,python2-scipy) + ,@(alist-delete "python-numpy" + (alist-delete "python-scipy" + (package-propagated-inputs patsy)))))))) + +(define-public python-statsmodels + (package + (name "python-statsmodels") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://pypi.python.org/packages/source/" + "s/statsmodels/statsmodels-" version ".tar.gz")) + (sha256 + (base32 + "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; tests must be run after installation + (delete 'check) + (add-after 'unpack 'set-matplotlib-backend-to-agg + (lambda _ + ;; Set the matplotlib backend to Agg to avoid problems using the + ;; GTK backend without a display. + (substitute* (find-files "statsmodels/graphics/tests" "\\.py") + (("import matplotlib\\.pyplot as plt" line) + (string-append "import matplotlib;matplotlib.use('Agg');" + line))) + #t)) + (add-after 'install 'check + (lambda _ + (with-directory-excursion "/tmp" + (zero? (system* "nosetests" + "--stop" + "-v" "statsmodels")))))))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-pandas" ,python-pandas) + ("python-patsy" ,python-patsy) + ("python-matplotlib" ,python-matplotlib))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-sphinx" ,python-sphinx))) + (home-page "http://statsmodels.sourceforge.net/") + (synopsis "Statistical modeling and econometrics in Python") + (description + "Statsmodels is a Python package that provides a complement to scipy for +statistical computations including descriptive statistics and estimation and +inference for statistical models.") + (license license:bsd-3))) + +(define-public python2-statsmodels + (let ((stats (package-with-python2 python-statsmodels))) + (package (inherit stats) + (propagated-inputs + `(("python2-numpy" ,python2-numpy) + ("python2-scipy" ,python2-scipy) + ("python2-pandas" ,python2-pandas) + ("python2-patsy" ,python2-patsy) + ("python2-matplotlib" ,python2-matplotlib))) + (native-inputs + `(("python2-setuptools" ,python2-setuptools) + ,@(package-native-inputs stats)))))) + +(define-public r-xml2 + (package + (name "r-xml2") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "xml2" version)) + (sha256 + (base32 + "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c")))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-bh" ,r-bh))) + (home-page "https://github.com/hadley/xml2") + (synopsis "Parse XML with R") + (description + "This package provides a simple, consistent interface to working with XML +files in R. It is built on top of the libxml2 C library.") + (license license:gpl2+))) + +(define-public r-rversions + (package + (name "r-rversions") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "rversions" version)) + (sha256 + (base32 + "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/metacran/rversions") + (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") + (description + "This package provides functions to query the main R repository to find +the versions that @code{r-release} and @code{r-oldrel} refer to, and also all +previous R versions and their release dates.") + (license license:expat))) + +(define-public r-whisker + (package + (name "r-whisker") + (version "0.3-2") + (source (origin + (method url-fetch) + (uri (cran-uri "whisker" version)) + (sha256 + (base32 + "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28")))) + (build-system r-build-system) + (home-page "http://github.com/edwindj/whisker") + (synopsis "Logicless mustache templating for R") + (description + "This package provides logicless templating, with a syntax that is not +limited to R.") + (license license:gpl3+))) + +(define-public r-brew + (package + (name "r-brew") + (version "1.0-6") + (source (origin + (method url-fetch) + (uri (cran-uri "brew" version)) + (sha256 + (base32 + "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/brew") + (synopsis "Templating framework for report generation") + (description + "The brew package implements a templating framework for mixing text and R +code for report generation. The template syntax is similar to PHP, Ruby's erb +module, Java Server Pages, and Python's psp module.") + (license license:gpl2+))) + +(define-public r-roxygen2 + (package + (name "r-roxygen2") + (version "5.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "roxygen2" version)) + (sha256 + (base32 + "0xjdphjs7l1v71lylmqgp76cbcxzvm9z1a40jgkdwvz072nn08vr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-brew" ,r-brew) + ("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/klutometis/roxygen") + (synopsis "In-source documentation system for R") + (description + "Roxygen2 is a Doxygen-like in-source documentation system for Rd, +collation, and NAMESPACE files.") + (license license:gpl2+))) + +(define-public r-httr + (package + (name "r-httr") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "httr" version)) + (sha256 + (base32 + "1yprw8p4g8026jhravgg1hdwj1g51cpdgycyr5a58jwm4i5f79cq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-jsonlite" ,r-jsonlite) + ("r-mime" ,r-mime) + ("r-r6" ,r-r6) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/hadley/httr") + (synopsis "Tools for working with URLs and HTTP") + (description + "The aim of httr is to provide a wrapper for RCurl customised to the +demands of modern web APIs. It provides useful tools for working with HTTP +organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration +functions make it easy to control additional request components.") + (license license:expat))) + +(define-public r-git2r + (package + (name "r-git2r") + (version "0.11.0") + (source (origin + (method url-fetch) + (uri (cran-uri "git2r" version)) + (sha256 + (base32 + "1h5ag8sm512jsn2sp4yhiqspc7hjq5y8z0kqz24sdznxa3b7rpn9")))) + (build-system r-build-system) + ;; This R package contains modified sources of libgit2. This modified + ;; version of libgit2 is built as the package is built. Hence libgit2 is + ;; not among the inputs of this package. + (inputs + `(("libssh2" ,libssh2) + ("openssl" ,openssl) + ("zlib" ,zlib))) + (home-page "https://github.com/ropensci/git2r") + (synopsis "Access Git repositories with R") + (description + "This package provides an R interface to the libgit2 library, which is a +pure C implementation of the Git core methods.") + ;; GPLv2 only with linking exception. + (license license:gpl2))) + +(define-public r-rstudioapi + (package + (name "r-rstudioapi") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "rstudioapi" version)) + (sha256 + (base32 + "0q7671d924nzqsqhs8d9p7l907bcam56wjwm7vvz44xgj0saj8bs")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/rstudioapi") + (synopsis "Safely access the RStudio API") + (description + "This package provides functions to access the RStudio API and provide +informative error messages when it's not available.") + (license license:expat))) + +(define-public r-devtools + (package + (name "r-devtools") + (version "1.9.1") + (source (origin + (method url-fetch) + (uri (cran-uri "devtools" version)) + (sha256 + (base32 + "10ycx3kkiz5x8nmgw31d9wa5hhlx2fhda2nqzxfrczqpz1jik6ci")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-digest" ,r-digest) + ("r-evaluate" ,r-evaluate) + ("r-git2r" ,r-git2r) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-memoise" ,r-memoise) + ("r-roxygen2" ,r-roxygen2) + ("r-rstudioapi" ,r-rstudioapi) + ("r-rversions" ,r-rversions) + ("r-whisker" ,r-whisker))) + (home-page "https://github.com/hadley/devtools") + (synopsis "Tools to make developing R packages easier") + (description "The devtools package is a collection of package development +tools to simplify the devolpment of R packages.") + (license license:gpl2+))) + +(define-public r-readr + (package + (name "r-readr") + (version "0.2.2") + (source (origin + (method url-fetch) + (uri (cran-uri "readr" version)) + (sha256 + (base32 + "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-rcpp" ,r-rcpp) + ("r-bh" ,r-bh))) + (home-page "https://github.com/hadley/readr") + (synopsis "Read tabular data") + (description + "This package provides functions to read flat or tabular text files from +disk (or a connection).") + (license license:gpl2+))) + +(define-public r-plotrix + (package + (name "r-plotrix") + (version "3.6") + (source (origin + (method url-fetch) + (uri (cran-uri "plotrix" version)) + (sha256 + (base32 + "0zn6k8azh40v0lg7q9yd4sy30a26bcc0fjvndn4z7k36avlw4i25")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/plotrix") + (synopsis "Various plotting functions") + (description + "This package provides lots of plotting, various labeling, axis and color +scaling functions for R.") + (license license:gpl2+))) + +(define-public r-gridbase + (package + (name "r-gridbase") + (version "0.4-7") + (source (origin + (method url-fetch) + (uri (cran-uri "gridBase" version)) + (sha256 + (base32 + "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/gridBase") + (synopsis "Integration of base and grid graphics") + (description + "This package provides an integration of base and grid graphics for R.") + (license license:gpl2+))) + +(define-public r-lattice + (package + (name "r-lattice") + (version "0.20-33") + (source (origin + (method url-fetch) + (uri (cran-uri "lattice" version)) + (sha256 + (base32 + "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg")))) + (build-system r-build-system) + (home-page "http://lattice.r-forge.r-project.org/") + (synopsis "High-level data visualization system") + (description + "The lattice package provides a powerful and elegant high-level data +visualization system inspired by Trellis graphics, with an emphasis on +multivariate data. Lattice is sufficient for typical graphics needs, and is +also flexible enough to handle most nonstandard requirements.") (license license:gpl2+))) |