diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 450 |
1 files changed, 448 insertions, 2 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 81258d38f5..8bd87582ef 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -27,6 +27,7 @@ #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) @@ -53,7 +54,7 @@ (define-public r (package (name "r") - (version "3.2.2") + (version "3.2.3") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -61,7 +62,7 @@ version ".tar.gz")) (sha256 (base32 - "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw")))) + "1hdnv77ralzcx5k5b88jq1r8l6zqnywpq00g2qs949rqh63psfxr")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -1497,3 +1498,448 @@ grobs.") and draw tables.") (license license:gpl2+))) +(define-public r-rsqlite + (package + (name "r-rsqlite") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "RSQLite" version)) + (sha256 + (base32 + "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f")))) + (properties `((upstream-name . "RSQLite"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/rstats-db/RSQLite") + (synopsis "SQLite interface for R") + (description + "This package embeds the SQLite database engine in R and provides an +interface compliant with the DBI package. The source for the SQLite +engine (version 3.8.6) is included.") + (license license:lgpl2.0+))) + +(define-public r-rcurl + (package + (name "r-rcurl") + (version "1.95-0.1.2") + (source (origin + (method url-fetch) + (uri (string-append "http://www.bioconductor.org/packages/" + "release/extra/src/" + "contrib/RCurl_" version ".tar.gz")) + (sha256 + (base32 + "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) + (properties `((upstream-name . "RCurl"))) + (build-system r-build-system) + (inputs + `(("libcurl" ,curl))) + (propagated-inputs + `(("r-bitops" ,r-bitops))) + (home-page "http://www.omegahat.org/RCurl") + (synopsis "General network client interface for R") + (description + "The package allows one to compose general HTTP requests and provides +convenient functions to fetch URIs, GET and POST forms, etc. and process the +results returned by the Web server. This provides a great deal of control +over the HTTP/FTP/... connection and the form of the request while providing a +higher-level interface than is available just using R socket connections. +Additionally, the underlying implementation is robust and extensive, +supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, +ldap, and also supports cookies, redirects, authentication, etc.") + (license license:bsd-3))) + +(define-public r-xml + (package + (name "r-xml") + (version "3.98-1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "XML" version)) + (sha256 + (base32 + "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy")))) + (properties + `((upstream-name . "XML"))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-rcurl" ,r-rcurl))) + (home-page "http://www.omegahat.org/RSXML") + (synopsis "Tools for parsing and generating XML within R") + (description + "Many approaches for both reading and creating XML (and HTML) +documents (including DTDs), both local and accessible via HTTP or FTP. Also +offers access to an XPath \"interpreter\".") + (license license:bsd-2))) + +(define-public r-lambda-r + (package + (name "r-lambda-r") + (version "1.1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "lambda.r" version)) + (sha256 + (base32 + "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa")))) + (properties `((upstream-name . "lambda.r"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/lambda.r") + (synopsis "Functional programming extension for R") + (description + "This package provides a language extension to efficiently write +functional programs in R. Syntax extensions include multi-part function +definitions, pattern matching, guard statements, built-in (optional) type +safety.") + (license license:lgpl3+))) + +(define-public r-futile-options + (package + (name "r-futile-options") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "futile.options" version)) + (sha256 + (base32 + "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f")))) + (properties + `((upstream-name . "futile.options"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/futile.options") + (synopsis "Options management framework") + (description + "The futile.options subsystem provides an easy user-defined options +management system that is properly scoped. This means that options created +via @code{futile.options} are fully self-contained and will not collide with +options defined in other packages.") + (license license:lgpl3+))) + +(define-public r-futile-logger + (package + (name "r-futile-logger") + (version "1.4.1") + (source (origin + (method url-fetch) + (uri (cran-uri "futile.logger" version)) + (sha256 + (base32 + "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51")))) + (properties `((upstream-name . "futile.logger"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-options" ,r-futile-options) + ("r-lambda-r" ,r-lambda-r))) + (home-page "http://cran.r-project.org/web/packages/futile.logger") + (synopsis "Logging utility for R") + (description + "This package provides a simple yet powerful logging utility. Based +loosely on log4j, futile.logger takes advantage of R idioms to make logging a +convenient and easy to use replacement for @code{cat} and @code{print} +statements.") + (license license:lgpl3+))) + +(define-public r-snow + (package + (name "r-snow") + (version "0.4-1") + (source (origin + (method url-fetch) + (uri (cran-uri "snow" version)) + (sha256 + (base32 + "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/snow") + (synopsis "Support for simple parallel computing in R") + (description + "The snow package provides support for simple parallel computing on a +network of workstations using R. A master R process calls @code{makeCluster} +to start a cluster of worker processes; the master process then uses functions +such as @code{clusterCall} and @code{clusterApply} to execute R code on the +worker processes and collect and return the results on the master.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-sparsem + (package + (name "r-sparsem") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "SparseM" version)) + (sha256 + (base32 + "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz")))) + (properties + `((upstream-name . "SparseM"))) + (build-system r-build-system) + (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") + (synopsis "Sparse linear algebra") + (description + "This package provides some basic linear algebra functionality for sparse +matrices. It includes Cholesky decomposition and backsolving as well as +standard R subsetting and Kronecker products.") + (license license:gpl2+))) + +(define-public r-dt + (package + (name "r-dt") + (version "0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "DT" version)) + (sha256 + (base32 + "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj")))) + (properties + `((upstream-name . "DT"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr))) + (home-page "http://rstudio.github.io/DT") + (synopsis "R wrapper of the DataTables JavaScript library") + (description + "This package allows for data objects in R to be rendered as HTML tables +using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). +The 'DataTables' library has been included in this R package.") + ;; The DT package as a whole is distributed under GPLv3. The DT package + ;; inludes other software components under different licenses: + ;; + ;; * Expat: jQuery, jquery.highlight.js, DataTables + ;; * ASL2.0: selectize.js + ;; * WTFPL: noUiSlider + (license (list license:gpl3 + license:expat + license:asl2.0 + (license:non-copyleft "http://www.wtfpl.net/txt/copying/"))))) + +(define-public r-base64enc + (package + (name "r-base64enc") + (version "0.1-3") + (source (origin + (method url-fetch) + (uri (cran-uri "base64enc" version)) + (sha256 + (base32 + "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) + (build-system r-build-system) + (home-page "http://www.rforge.net/base64enc") + (synopsis "Tools for Base64 encoding") + (description + "This package provides tools for handling Base64 encoding. It is more +flexible than the orphaned \"base64\" package.") + (license license:gpl2+))) + +(define-public r-r-methodss3 + (package + (name "r-r-methodss3") + (version "1.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.methodsS3" version)) + (sha256 + (base32 + "1dg4bbrwr8jcsqisjrrwxs942mrjq72zw8yvl2br4djdm0md8zz5")))) + (properties `((upstream-name . "R.methodsS3"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/R.methodsS3") + (synopsis "S3 methods simplified") + (description + "This package provides methods that simplify the setup of S3 generic +functions and S3 methods. Major effort has been made in making definition of +methods as simple as possible with a minimum of maintenance for package +developers. For example, generic functions are created automatically, if +missing, and naming conflict are automatically solved, if possible. The +method @code{setMethodS3()} is a good start for those who in the future may +want to migrate to S4.") + (license license:lgpl2.1+))) + +(define-public r-r-oo + (package + (name "r-r-oo") + (version "1.19.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.oo" version)) + (sha256 + (base32 + "15rm1qb9a212bqazhcpk7m48hcp7jq8rh4yhd9c6zfyvdqszfmsb")))) + (properties `((upstream-name . "R.oo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3))) + (home-page "https://github.com/HenrikBengtsson/R.oo") + (synopsis "R object-oriented programming with or without references") + (description + "This package provides methods and classes for object-oriented +programming in R with or without references. Large effort has been made on +making definition of methods as simple as possible with a minimum of +maintenance for package developers.") + (license license:lgpl2.1+))) + +(define-public r-r-utils + (package + (name "r-r-utils") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.utils" version)) + (sha256 + (base32 + "03pi6pkcsq65fv7cn4x74cj050dc8x5d4xyg930p6f7flk788xaz")))) + (properties `((upstream-name . "R.utils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo))) + (home-page "https://github.com/HenrikBengtsson/R.utils") + (synopsis "Various programming utilities") + (description + "This package provides utility functions useful when programming and +developing R packages.") + (license license:lgpl2.1+))) + +(define-public r-r-cache + (package + (name "r-r-cache") + (version "0.12.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.cache" version)) + (sha256 + (base32 + "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx")))) + (properties `((upstream-name . "R.cache"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.cache") + (synopsis "Light-weight caching of objects and results") + (description + "This package provides methods for caching or memoization of objects and +results. With this package, any R object can be cached in a key-value storage +where the key can be an arbitrary set of R objects. The cache memory is +persistent (on the file system).") + (license license:lgpl2.1+))) + +(define-public r-r-rsp + (package + (name "r-r-rsp") + (version "0.20.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.rsp" version)) + (sha256 + (base32 + "06vq9qq5hdz3hqc99q82622mab6ix7jwap20h4za6ap6gnwqs0fv")))) + (properties `((upstream-name . "R.rsp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-cache" ,r-r-cache) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.rsp") + (synopsis "Dynamic generation of scientific reports") + (description + "The RSP markup language provides a powerful markup for controlling the +content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr +documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary +to many other literate programming languages, with RSP it is straightforward +to loop over mixtures of code and text sections, e.g. in month-by-month +summaries. RSP has also several preprocessing directives for incorporating +static and dynamic contents of external files (local or online) among other +things. RSP is ideal for self-contained scientific reports and R package +vignettes.") + (license license:lgpl2.1+))) + +(define-public r-matrixstats + (package + (name "r-matrixstats") + (version "0.15.0") + (source (origin + (method url-fetch) + (uri (cran-uri "matrixStats" version)) + (sha256 + (base32 + "1068k85s6rlwfzlszw790c2rndydvrsw7rpck6k6z17896m8drfa")))) + (properties `((upstream-name . "matrixStats"))) + (build-system r-build-system) + (native-inputs + `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes + (home-page "https://github.com/HenrikBengtsson/matrixStats") + (synopsis "Methods applying to vectors and matrix rows and columns") + (description + "This package provides methods operating on rows and columns of matrices, +e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are +also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and +@code{weightedMedians()}. All methods have been optimized for speed and +memory usage.") + (license license:artistic2.0))) + +(define-public r-viridis + (package + (name "r-viridis") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "viridis" version)) + (sha256 + (base32 + "0zz9i874s1fwhl9bcbiprlzaz7zsy1rj6c729zn3k525d63qbnj7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra))) + (home-page "https://github.com/sjmgarnier/viridis") + (synopsis "Matplotlib default color map") + (description + "This package is a port of the new @url{matplotlib, +http://matplotlib.org/} color maps (@code{viridis}--the default--, +@code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are +designed in such a way that they will analytically be perfectly +perceptually-uniform, both in regular form and also when converted to +black-and-white. They are also designed to be perceived by readers with the +most common form of color blindness.") + (license license:x11))) + +(define-public r-plotly + (package + (name "r-plotly") + (version "2.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "plotly" version)) + (sha256 + (base32 + "16pqycns8qf0y1j21n009qf242lv0izwyidlx40zv88izxhg1vs0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-viridis" ,r-viridis))) + (home-page "https://plot.ly/r") + (synopsis "Create interactive web graphics") + (description + "This package enables the translation of ggplot2 graphs to an interactive +web-based version and/or the creation of custom web-based visualizations +directly from R. Once uploaded to a plotly account, plotly graphs (and the +data behind them) can be viewed and modified in a web browser.") + (license license:x11))) + |