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-rw-r--r--gnu/packages/statistics.scm748
1 files changed, 644 insertions, 104 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 700a8957cc..40a511b6ed 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -6,6 +6,7 @@
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -101,7 +102,7 @@ be output in text, PostScript, PDF or HTML.")
(define-public r
(package
(name "r")
- (version "3.3.1")
+ (version "3.3.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -109,7 +110,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
- "1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x"))))
+ "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@@ -205,16 +206,63 @@ publication-quality data plots. A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
(license license:gpl3+)))
+(define-public r-bit
+ (package
+ (name "r-bit")
+ (version "1.1-12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bit" version))
+ (sha256
+ (base32
+ "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
+ (build-system r-build-system)
+ (home-page "http://ff.r-forge.r-project.org")
+ (synopsis "Class for vectors of 1-bit booleans")
+ (description
+ "This package provides bitmapped vectors of booleans (no @code{NA}s),
+coercion from and to logicals, integers and integer subscripts, fast boolean
+operators and fast summary statistics. With @code{bit} class vectors of true
+binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
+ (license license:gpl2)))
+
+(define-public r-bit64
+ (package
+ (name "r-bit64")
+ (version "0.9-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bit64" version))
+ (sha256
+ (base32
+ "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bit" ,r-bit)))
+ (home-page "http://ff.r-forge.r-project.org/")
+ (synopsis "S3 class for vectors of 64 bit integers")
+ (description
+ "The bit64 package provides serializable S3 atomic 64 bit (signed)
+integers that can be used in vectors, matrices, arrays and @code{data.frames}.
+Methods are available for coercion from and to logicals, integers, doubles,
+characters and factors as well as many elementwise and summary functions.
+Many fast algorithmic operations such as @code{match} and @code{order} support
+interactive data exploration and manipulation and optionally leverage
+caching.")
+ (license license:gpl2)))
+
(define-public r-colorspace
(package
(name "r-colorspace")
- (version "1.2-7")
+ (version "1.3-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "colorspace" version))
(sha256
- (base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5"))))
+ (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/colorspace")
(synopsis "Color space manipulation")
@@ -276,13 +324,13 @@ OpenSSL should be used.")
(define-public r-estimability
(package
(name "r-estimability")
- (version "1.1-1")
+ (version "1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "estimability" version))
(sha256
(base32
- "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w"))))
+ "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/estimability")
(synopsis "Tools for assessing estimability of linear predictions")
@@ -394,13 +442,13 @@ Munsell colour system.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "0.12.7")
+ (version "0.12.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb"))))
+ (base32 "0is1vql1q82g7yakad4skx707ip0fx3rgdwv9a8mi8259gly2qji"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ Integration")
@@ -440,14 +488,14 @@ and operations on them using LAPACK and SuiteSparse.")
(define-public r-mgcv
(package
(name "r-mgcv")
- (version "1.8-15")
+ (version "1.8-16")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
(base32
- "05xzmsx51y92c0r0yihac8m9d3v1sqnn8ahcgm3q75j8z6zybsjs"))))
+ "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/mgcv")
(synopsis "Mixed generalised additive model computation")
@@ -638,13 +686,13 @@ using just two functions: melt and dcast (or acast).")
(define-public r-scales
(package
(name "r-scales")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "scales" version))
(sha256
- (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5"))))
+ (base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dichromat" ,r-dichromat)
@@ -664,22 +712,22 @@ legends.")
(define-public r-ggplot2
(package
(name "r-ggplot2")
- (version "2.1.0")
+ (version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplot2" version))
(sha256
- (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj"))))
+ (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
("r-gtable" ,r-gtable)
("r-plyr" ,r-plyr)
- ("r-proto" ,r-proto)
+ ("r-lazyeval" ,r-lazyeval)
+ ("r-tibble" ,r-tibble)
("r-reshape2" ,r-reshape2)
- ("r-scales" ,r-scales)
- ("r-svglite" ,r-svglite)))
+ ("r-scales" ,r-scales)))
(home-page "http://ggplot2.org")
(synopsis "An implementation of the grammar of graphics")
(description
@@ -694,14 +742,14 @@ aesthetic attributes.")
(define-public r-gdtools
(package
(name "r-gdtools")
- (version "0.1.1")
+ (version "0.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "gdtools" version))
(sha256
(base32
- "1l9d759x9s4ddz51sls8kcjps2i9kwfbc72dnagrdavh82h0al8n"))))
+ "1prh814lw3qkgnf0760cvpic1k68jhlkpcxlksv8chjkvsrnnf09"))))
(build-system r-build-system)
(native-inputs
`(("r-rcpp" ,r-rcpp)
@@ -720,14 +768,14 @@ and to generate base64 encoded string from raster matrix.")
(define-public r-svglite
(package
(name "r-svglite")
- (version "1.1.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "svglite" version))
(sha256
(base32
- "11ryicjglfi6jvkk4jgg5kra42qbs5z2zid7jjhlslpjcljfwc70"))))
+ "1s1gvmlmmna5y4jsn9h6438pg5b86fl4nwfvkgm6n4h6ljfgqyx3"))))
(build-system r-build-system)
(native-inputs `(("r-rcpp" ,r-rcpp)))
(propagated-inputs
@@ -803,13 +851,13 @@ R/DBMS implementations.")
(define-public r-bh
(package
(name "r-bh")
- (version "1.60.0-2")
+ (version "1.62.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "BH" version))
(sha256
(base32
- "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4"))))
+ "01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p"))))
(build-system r-build-system)
(home-page "https://github.com/eddelbuettel/bh")
(synopsis "R package providing subset of Boost headers")
@@ -926,13 +974,13 @@ syntax that can be converted to XHTML or other formats.")
(define-public r-yaml
(package
(name "r-yaml")
- (version "2.1.13")
+ (version "2.1.14")
(source (origin
(method url-fetch)
(uri (cran-uri "yaml" version))
(sha256
(base32
- "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
+ "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/yaml/")
(synopsis "Methods to convert R data to YAML and back")
@@ -944,18 +992,17 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.14")
+ (version "1.15.1")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds"))))
+ "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
("r-digest" ,r-digest)
- ("r-formatr" ,r-formatr)
("r-highr" ,r-highr)
("r-markdown" ,r-markdown)
("r-stringr" ,r-stringr)
@@ -1323,13 +1370,13 @@ and density estimation.")
(define-public r-chron
(package
(name "r-chron")
- (version "2.3-47")
+ (version "2.3-48")
(source (origin
(method url-fetch)
(uri (cran-uri "chron" version))
(sha256
(base32
- "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
+ "1q1d0p2wq19w3mpfqnrg8nmspxqmhv4ap52r393s6y3abl36ccac"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/chron")
(synopsis "Chronological R objects which can handle dates and times")
@@ -1341,16 +1388,14 @@ times.")
(define-public r-data-table
(package
(name "r-data-table")
- (version "1.9.6")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (cran-uri "data.table" version))
(sha256
(base32
- "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
+ "1168arn4wjd1jj7kgr4sb8xd52hr8p8iqp85g5jwp3mkz4p76qfg"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-chron" ,r-chron)))
(home-page "https://github.com/Rdatatable/data.table/wiki")
(synopsis "Enhanced version of data.frame R object")
(description
@@ -1394,13 +1439,7 @@ and fast file reading.")
(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)))))
+ (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
@@ -1416,15 +1455,10 @@ 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))
- (properties `((python2-variant . ,(delay python2-patsy))))))
+ (license (list license:bsd-2 license:psfl))))
(define-public python2-patsy
- (let ((patsy (package-with-python2 (strip-python2-variant python-patsy))))
- (package (inherit patsy)
- (native-inputs
- `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs patsy))))))
+ (package-with-python2 python-patsy))
(define-public python-statsmodels
(package
@@ -1455,11 +1489,13 @@ building design matrices.")
line)))
#t))
(add-after 'install 'check
- (lambda _
- (with-directory-excursion "/tmp"
- (zero? (system* "nosetests"
- "--stop"
- "-v" "statsmodels"))))))))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Make installed package available for running the tests
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "/tmp"
+ (zero? (system* "nosetests"
+ "--stop"
+ "-v" "statsmodels"))))))))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
@@ -1487,24 +1523,19 @@ inference for statistical models.")
("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))))))
+ ("python2-matplotlib" ,python2-matplotlib))))))
(define-public r-coda
(package
(name "r-coda")
- (version "0.18-1")
+ (version "0.19-1")
(source (origin
(method url-fetch)
(uri (cran-uri "coda" version))
(sha256
(base32
- "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958"))))
+ "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-lattice" ,r-lattice)))
(home-page "http://cran.r-project.org/web/packages/coda")
(synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
(description "This package provides functions for summarizing and plotting
@@ -1516,14 +1547,14 @@ chain.")
(define-public r-ade4
(package
(name "r-ade4")
- (version "1.7-4")
+ (version "1.7-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ade4" version))
(sha256
(base32
- "17sbicash7z4b63dlrbaf8xx2pbwh62vykzvhdjs43h8jkl881y7"))))
+ "0aaqbnydm5fb37nrvqj4bx6hxax7255j426cwh2lh88nyvznbq37"))))
(build-system r-build-system)
(home-page "http://pbil.univ-lyon1.fr/ADE-4")
(synopsis "Multivariate data analysis and graphical display")
@@ -1788,14 +1819,14 @@ collation, and NAMESPACE files.")
(define-public r-openssl
(package
(name "r-openssl")
- (version "0.9.5")
+ (version "0.9.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "1lal8mmcwjhhln10mfi96ipv3d364k0wiviiln220wvhddcpr9pp"))))
+ "0ffwllii8xl6sa2v66134g0fwaw1y3zn3mvaa4nrc120vv5d3mkd"))))
(build-system r-build-system)
(inputs
`(("openssl" ,openssl)))
@@ -1845,13 +1876,13 @@ functions make it easy to control additional request components.")
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.15.0")
+ (version "0.18.0")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8"))))
+ "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi"))))
(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
@@ -1938,14 +1969,14 @@ were originally a part of the r-devtools package.")
(define-public r-hms
(package
(name "r-hms")
- (version "0.2")
+ (version "0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
- "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds"))))
+ "127znf522r5mn3k6frhdd7pqh063bs3l85gn9h7cx50hpjf2as4k"))))
(build-system r-build-system)
(home-page "https://github.com/rstats-db/hms")
(synopsis "Pretty time of day")
@@ -1982,13 +2013,13 @@ disk (or a connection).")
(define-public r-plotrix
(package
(name "r-plotrix")
- (version "3.6-3")
+ (version "3.6-4")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
- "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91"))))
+ "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@@ -2061,13 +2092,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.7.500.0.0")
+ (version "0.7.600.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps"))
+ "0k1wniip184j0ckcg9kcjy2q4mcfj5jpd1nkk4l0ab75ad8znywv"))
(modules '((guix build utils)))
;; Remove bundled armadillo sources
(snippet
@@ -2142,27 +2173,50 @@ ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc.")
(license license:gpl3+)))
+(define-public r-rprojroot
+ (package
+ (name "r-rprojroot")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rprojroot" version))
+ (sha256
+ (base32
+ "04ywfpar4d2hyi4rh4fbixrbzd665gpa2jhx67g8857cr70pp0nh"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-backports" ,r-backports)))
+ (home-page "https://github.com/krlmlr/rprojroot")
+ (synopsis "Finding files in project subdirectories")
+ (description
+ "This package helps accessing files relative to a project root. It
+provides helpers for robust, reliable and flexible paths to files below a
+project root. The root of a project is defined as a directory that matches a
+certain criterion, e.g., it contains a certain regular file.")
+ (license license:gpl3)))
+
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "1.1")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0"))))
+ "1vvxyf3zhyxx6k697lia299456hryp8nh3zr0fc27f3107a8mcjf"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
`(("r-catools" ,r-catools)
("r-evaluate" ,r-evaluate)
- ("r-tibble" ,r-tibble)
("r-htmltools" ,r-htmltools)
("r-jsonlite" ,r-jsonlite)
("r-base64enc" ,r-base64enc)
("r-knitr" ,r-knitr)
+ ("r-rprojroot" ,r-rprojroot)
("r-yaml" ,r-yaml)
("ghc-pandoc" ,ghc-pandoc)))
(home-page "http://rmarkdown.rstudio.com")
@@ -2215,20 +2269,44 @@ grobs.")
and draw tables.")
(license license:gpl2+)))
+(define-public r-plogr
+ (package
+ (name "r-plogr")
+ (version "0.1-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "plogr" version))
+ (sha256
+ (base32
+ "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/krlmlr/plogr")
+ (synopsis "R bindings for the plog C++ logging library")
+ (description
+ "This package provides the header files for a stripped-down version of
+the plog header-only C++ logging library, and a method to log to R's standard
+error stream.")
+ (license license:expat)))
+
(define-public r-rsqlite
(package
(name "r-rsqlite")
- (version "1.0.0")
+ (version "1.1-1")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
- "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
+ "11vnzds5gidgakdmsbdn0bvnsz064ym1savwb7l6gc1bjn7xa2k4"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
- `(("r-dbi" ,r-dbi)))
+ `(("r-dbi" ,r-dbi)
+ ("r-bh" ,r-bh)
+ ("r-memoise" ,r-memoise)
+ ("r-plogr" ,r-plogr)
+ ("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/rstats-db/RSQLite")
(synopsis "SQLite interface for R")
(description
@@ -2271,20 +2349,18 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(define-public r-xml
(package
(name "r-xml")
- (version "3.98-1.4")
+ (version "3.98-1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw"))))
+ "0dcdj7ryn8lm7wmv4hqhh9jxa5k97l6ad8xyvb932yfkwj1g1byy"))))
(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
@@ -2432,13 +2508,13 @@ worker processes and collect and return the results on the master.")
(define-public r-sparsem
(package
(name "r-sparsem")
- (version "1.72")
+ (version "1.74")
(source (origin
(method url-fetch)
(uri (cran-uri "SparseM" version))
(sha256
(base32
- "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka"))))
+ "1fpfhld887y5lyb8jydprmv5krqm1fk6n53z942b4g4z1v4g04j7"))))
(properties
`((upstream-name . "SparseM")))
(inputs
@@ -2966,13 +3042,13 @@ maintenance for package developers.")
(define-public r-r-utils
(package
(name "r-r-utils")
- (version "2.4.0")
+ (version "2.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.utils" version))
(sha256
(base32
- "0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj"))))
+ "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s"))))
(properties `((upstream-name . "R.utils")))
(build-system r-build-system)
(propagated-inputs
@@ -3014,13 +3090,13 @@ persistent (on the file system).")
(define-public r-r-rsp
(package
(name "r-r-rsp")
- (version "0.30.0")
+ (version "0.40.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.rsp" version))
(sha256
(base32
- "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2"))))
+ "1hz5fnxz30m3cc7x7ha1swx4pn8c2244z6ka6v9m3l5lpdgc1367"))))
(properties `((upstream-name . "R.rsp")))
(build-system r-build-system)
(propagated-inputs
@@ -3216,13 +3292,13 @@ features present in other programming languages.")
(define-public r-plotly
(package
(name "r-plotly")
- (version "4.5.2")
+ (version "4.5.6")
(source (origin
(method url-fetch)
(uri (cran-uri "plotly" version))
(sha256
(base32
- "08shs0qhy9js0fpj3d4rzfbwmw11ki3z5vg8jszfm6m69mfkgzw1"))))
+ "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -3272,6 +3348,128 @@ noncentral hypergeometric distribution (also called extended hypergeometric
distribution).")
(license license:gpl3+)))
+(define-public r-rematch
+ (package
+ (name "r-rematch")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rematch" version))
+ (sha256
+ (base32
+ "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/MangoTheCat/rematch")
+ (synopsis "Match regular expressions with a nicer API")
+ (description
+ "This package provides a small wrapper on @code{regexpr} to extract the
+matches and captured groups from the match of a regular expression to a
+character vector.")
+ (license license:expat)))
+
+(define-public r-cellranger
+ (package
+ (name "r-cellranger")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "cellranger" version))
+ (sha256
+ (base32
+ "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rematch" ,r-rematch)
+ ("r-tibble" ,r-tibble)))
+ (home-page "https://github.com/rsheets/cellranger")
+ (synopsis "Translate spreadsheet cell ranges to rows and columns")
+ (description
+ "This package provides helper functions to work with spreadsheets and the
+@code{A1:D10} style of cell range specification.")
+ (license license:expat)))
+
+(define-public r-googlesheets
+ (package
+ (name "r-googlesheets")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "googlesheets" version))
+ (sha256
+ (base32
+ "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cellranger" ,r-cellranger)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-purrr" ,r-purrr)
+ ("r-readr" ,r-readr)
+ ("r-stringr" ,r-stringr)
+ ("r-tidyr" ,r-tidyr)
+ ("r-xml2" ,r-xml2)))
+ (home-page "https://github.com/jennybc/googlesheets")
+ (synopsis "Manage Google spreadsheets from R")
+ (description "This package provides tools to interact with Google Sheets
+from within R.")
+ (license license:expat)))
+
+(define-public r-spams
+ (package
+ (name "r-spams")
+ (version "2.5-svn2014-07-04")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://gforge.inria.fr/frs/download.php/33815/"
+ "spams-R-v" version ".tar.gz"))
+ (sha256
+ (base32
+ "1k459jg9a334slkw31w63l4d39xszjzsng7dv5j1mp78zifz7hvx"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "spams") #t))
+ ;; Since R 3.3.0 including R headers inside of an extern "C" block
+ ;; causes C headers to be included, which results in a lot of
+ ;; duplicate definitions. This can be avoided by defining
+ ;; NO_C_HEADERS before including the R headers.
+ (add-after 'chdir 'patch-use-of-R-headers
+ (lambda _
+ (substitute* "src/spams.cpp"
+ (("#include <R.h>" line)
+ (string-append "#define NO_C_HEADERS\n" line)))
+ #t))
+ ;; This looks like a syntax error.
+ (add-after 'chdir 'patch-isnan
+ (lambda _
+ (substitute* '"src/spams/linalg/linalg.h"
+ (("if isnan\\(lambda\\) \\{")
+ "if (isnan(lambda)) {"))
+ #t)))))
+ (home-page "http://spams-devel.gforge.inria.fr")
+ (synopsis "Toolbox for solving sparse estimation problems")
+ (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
+for solving various sparse estimation problems. It includes tools for the
+following problems:
+
+@enumerate
+@item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
+ component analysis} (PCA), ...)
+@item Solving sparse decomposition problems with LARS, coordinate descent,
+ OMP, SOMP, proximal methods
+@item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
+ group lasso, tree-structured regularization, structured sparsity with
+ overlapping groups,...).
+@end enumerate\n")
+ (license license:gpl3+)))
+
(define-public r-rpart
(package
(name "r-rpart")
@@ -3311,40 +3509,59 @@ definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
curves, Cox models, and parametric accelerated failure time models.")
(license license:lgpl2.0+)))
+(define-public r-base64
+ (package
+ (name "r-base64")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "base64" version))
+ (sha256
+ (base32
+ "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-openssl" ,r-openssl)))
+ (home-page "http://cran.r-project.org/web/packages/base64")
+ (synopsis "Base64 encoder and decoder")
+ (description
+ "This package is a compatibility wrapper to replace the orphaned package
+by Romain Francois. New applications should use the openssl or base64enc
+package instead.")
+ (license license:expat)))
+
(define-public r-hmisc
(package
(name "r-hmisc")
- (version "4.0-0")
+ (version "4.0-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "Hmisc" version))
(sha256
(base32
- "0azxmg9h9c456biydc0wpi9xhljmd37m8bv0zaadbvc93g7x0l4b"))))
+ "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr"))))
(properties `((upstream-name . "Hmisc")))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
`(("r-acepack" ,r-acepack)
- ("r-cluster" ,r-cluster)
+ ("r-base64" ,r-base64)
+ ("r-base64enc" ,r-base64enc)
("r-data-table" ,r-data-table)
- ("r-foreign" ,r-foreign)
("r-formula" ,r-formula)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-gtable" ,r-gtable)
- ("r-lattice" ,r-lattice)
;; Hmisc needs survival >= 2.40.1, so it cannot use the survival
- ;; package that comes with R 3.3.1.
+ ;; package that comes with R 3.3.2.
("r-survival" ,r-survival)
("r-latticeextra" ,r-latticeextra)
("r-htmltable" ,r-htmltable)
("r-htmltools" ,r-htmltools)
- ("r-viridis" ,r-viridis)
- ("r-nnet" ,r-nnet)
- ("r-rpart" ,r-rpart)))
+ ("r-viridis" ,r-viridis)))
(home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
(synopsis "Miscellaneous data analysis and graphics functions")
(description
@@ -3375,6 +3592,224 @@ conversion of R objects to LaTeX code, and recoding variables.")
framework, with additional code inspection and report generation tools.")
(license license:gpl2+)))
+(define-public r-dynamictreecut
+ (package
+ (name "r-dynamictreecut")
+ (version "1.63-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dynamicTreeCut" version))
+ (sha256
+ (base32
+ "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
+ (properties `((upstream-name . "dynamicTreeCut")))
+ (build-system r-build-system)
+ (home-page
+ "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
+ (synopsis "Detect clusters in hierarchical clustering dendrograms")
+ (description
+ "This package contains methods for the detection of clusters in
+hierarchical clustering dendrograms.")
+ (license license:gpl2+)))
+
+(define-public r-preprocesscore
+ (package
+ (name "r-preprocesscore")
+ (version "1.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "preprocessCore" version))
+ (sha256
+ (base32
+ "1n8y12q7145f385gm2k3c6y3vwvin7jlb47la4mnl7mar6pq9kmp"))))
+ (properties
+ `((upstream-name . "preprocessCore")))
+ (build-system r-build-system)
+ (home-page "https://github.com/bmbolstad/preprocessCore")
+ (synopsis "Collection of pre-processing functions")
+ (description
+ "This package provides a library of core pre-processing and normalization
+routines.")
+ (license license:lgpl2.0+)))
+
+(define-public r-fastcluster
+ (package
+ (name "r-fastcluster")
+ (version "1.1.22")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fastcluster" version))
+ (sha256
+ (base32
+ "006k9isra5biyavqwci61avladw19mhp6kmkjj3777rl1r4r8b9z"))))
+ (build-system r-build-system)
+ (home-page "http://danifold.net/fastcluster.html")
+ (synopsis "Fast hierarchical clustering routines")
+ (description
+ "This package implements fast hierarchical, agglomerative clustering
+routines. Part of the functionality is designed as drop-in replacement for
+existing routines: @code{linkage()} in the SciPy package
+@code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
+and the @code{flashClust} package. It provides the same functionality with
+the benefit of a much faster implementation. Moreover, there are
+memory-saving routines for clustering of vector data, which go beyond what the
+existing packages provide.")
+ (license license:bsd-2)))
+
+(define-public r-sfsmisc
+ (package
+ (name "r-sfsmisc")
+ (version "1.1-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sfsmisc" version))
+ (sha256
+ (base32
+ "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/sfsmisc")
+ (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
+ (description
+ "This package provides useful utilities from Seminar fuer Statistik ETH
+Zurich, including many that are related to graphics.")
+ (license license:gpl2+)))
+
+(define-public r-gtools
+ (package
+ (name "r-gtools")
+ (version "3.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gtools" version))
+ (sha256
+ (base32
+ "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/gtools")
+ (synopsis "Various R programming tools")
+ (description
+ "This package contains a collection of various functions to assist in R
+programming, such as tools to assist in developing, updating, and maintaining
+R and R packages, calculating the logit and inverse logit transformations,
+tests for whether a value is missing, empty or contains only @code{NA} and
+@code{NULL} values, and many more.")
+ (license license:gpl2)))
+
+(define-public r-gdata
+ (package
+ (name "r-gdata")
+ (version "2.17.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gdata" version))
+ (sha256
+ (base32
+ "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0"))))
+ (build-system r-build-system)
+ (inputs
+ `(("perl" ,perl)))
+ (propagated-inputs
+ `(("r-gtools" ,r-gtools)))
+ (home-page "http://cran.r-project.org/web/packages/gdata")
+ (synopsis "Various R programming tools for data manipulation")
+ (description
+ "This package provides various R programming tools for data manipulation,
+including:
+
+@itemize
+@item medical unit conversions
+@item combining objects
+@item character vector operations
+@item factor manipulation
+@item obtaining information about R objects
+@item manipulating MS-Excel formatted files
+@item generating fixed-width format files
+@item extricating components of date and time objects
+@item operations on columns of data frames
+@item matrix operations
+@item operations on vectors and data frames
+@item value of last evaluated expression
+@item wrapper for @code{sample} that ensures consistent behavior for
+ both scalar and vector arguments
+@end itemize\n")
+ (license license:gpl2+)))
+
+(define-public r-gplots
+ (package
+ (name "r-gplots")
+ (version "3.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gplots" version))
+ (sha256
+ (base32
+ "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-catools" ,r-catools)
+ ("r-gdata" ,r-gdata)
+ ("r-gtools" ,r-gtools)
+ ("r-kernsmooth" ,r-kernsmooth)))
+ (home-page "http://cran.r-project.org/web/packages/gplots")
+ (synopsis "Various R programming tools for plotting data")
+ (description
+ "This package provides various R programming tools for plotting data,
+including:
+
+@itemize
+@item calculating and plotting locally smoothed summary function
+@item enhanced versions of standard plots
+@item manipulating colors
+@item calculating and plotting two-dimensional data summaries
+@item enhanced regression diagnostic plots
+@item formula-enabled interface to @code{stats::lowess} function
+@item displaying textual data in plots
+@item baloon plots
+@item plotting \"Venn\" diagrams
+@item displaying Open-Office style plots
+@item plotting multiple data on same region, with separate axes
+@item plotting means and confidence intervals
+@item spacing points in an x-y plot so they don't overlap
+@end itemize\n")
+ (license license:gpl2+)))
+
+(define-public r-rocr
+ (package
+ (name "r-rocr")
+ (version "1.0-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ROCR" version))
+ (sha256
+ (base32
+ "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
+ (properties `((upstream-name . "ROCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gplots" ,r-gplots)))
+ (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
+ (synopsis "Visualizing the performance of scoring classifiers")
+ (description
+ "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
+curves by freely combining two from over 25 performance measures (new
+performance measures can be added using a standard interface). Curves from
+different cross-validation or bootstrapping runs can be averaged by different
+methods, and standard deviations, standard errors or box plots can be used to
+visualize the variability across the runs. The parameterization can be
+visualized by printing cutoff values at the corresponding curve positions, or
+by coloring the curve according to cutoff. All components of a performance
+plot can be quickly adjusted using a flexible parameter dispatching
+mechanism.")
+ (license license:gpl2+)))
+
(define-public r-kernsmooth
(package
(name "r-kernsmooth")
@@ -3402,16 +3837,14 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
(define-public r-zoo
(package
(name "r-zoo")
- (version "1.7-13")
+ (version "1.7-14")
(source (origin
(method url-fetch)
(uri (cran-uri "zoo" version))
(sha256
(base32
- "0m67bnrg7r1jxvs9p7rpa430szp5qfp65r056yb8bivpc16jd98c"))))
+ "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-lattice" ,r-lattice)))
(home-page "http://zoo.R-Forge.R-project.org/")
(synopsis "S3 infrastructure for regular and irregular time series")
(description "This package contains an S3 class with methods for totally
@@ -3439,3 +3872,110 @@ with alternating row colors) in LaTeX and HTML formats easily from
@code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
@code{cbind.mytable} objects.")
(license license:gpl2+)))
+
+(define-public r-vipor
+ (package
+ (name "r-vipor")
+ (version "0.4.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "vipor" version))
+ (sha256
+ (base32
+ "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/vipor")
+ (synopsis "Plot categorical data using noise and density estimates")
+ (description
+ "This package provides tools to generate a violin point plot, a
+combination of a violin/histogram plot and a scatter plot by offsetting points
+within a category based on their density using quasirandom noise.")
+ (license license:gpl2+)))
+
+(define-public r-beeswarm
+ (package
+ (name "r-beeswarm")
+ (version "0.2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "beeswarm" version))
+ (sha256
+ (base32
+ "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
+ (build-system r-build-system)
+ (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
+ (synopsis "Implementation of bee swarm plots")
+ (description
+ "This package provides an implementation of bee swarm plots. The bee
+swarm plot is a one-dimensional scatter plot like stripchart, but with
+closely-packed, non-overlapping points.")
+ (license license:artistic2.0)))
+
+(define-public r-sourcetools
+ (package
+ (name "r-sourcetools")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sourcetools" version))
+ (sha256
+ (base32
+ "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/sourcetools")
+ (synopsis "Tools for reading, tokenizing and parsing R code")
+ (description
+ "The sourcetools package provides both an R and C++ interface for the
+tokenization of R code, and helpers for interacting with the tokenized
+representation of R code.")
+ (license license:expat)))
+
+(define-public r-ggbeeswarm
+ (package
+ (name "r-ggbeeswarm")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ggbeeswarm" version))
+ (sha256
+ (base32
+ "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beeswarm" ,r-beeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-vipor" ,r-vipor)))
+ (home-page "https://github.com/eclarke/ggbeeswarm")
+ (synopsis "Categorical scatter (violin point) plots")
+ (description
+ "This package provides two methods of plotting categorical scatter plots
+such that the arrangement of points within a category reflects the density of
+data at that region, and avoids over-plotting.")
+ (license license:gpl2+)))
+
+(define-public r-statmod
+ (package
+ (name "r-statmod")
+ (version "1.4.27")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "statmod" version))
+ (sha256
+ (base32
+ "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/statmod")
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (synopsis "Statistical modeling")
+ (description
+ "This package provides a collection of algorithms and functions to aid
+statistical modeling. It includes growth curve comparisons, limiting dilution
+analysis (aka ELDA), mixed linear models, heteroscedastic regression,
+inverse-Gaussian probability calculations, Gauss quadrature and a secure
+convergence algorithm for nonlinear models. It also includes advanced
+generalized linear model functions that implement secure convergence,
+dispersion modeling and Tweedie power-law families.")
+ ;; Statmod is distributed under either license
+ (license (list license:gpl2 license:gpl3))))
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