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-rw-r--r--gnu/packages/statistics.scm589
1 files changed, 515 insertions, 74 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9c197f4977..3d0faf7572 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -40,6 +40,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages java)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages multiprecision)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -97,7 +98,7 @@ be output in text, PostScript, PDF or HTML.")
(define-public r
(package
(name "r")
- (version "3.2.3")
+ (version "3.2.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -105,7 +106,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
- "1hdnv77ralzcx5k5b88jq1r8l6zqnywpq00g2qs949rqh63psfxr"))))
+ "1dc0iybjk9kr1nghz3fpir6mb9hb9rnrz9bgh00w5pg5vir5cx30"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@@ -224,14 +225,19 @@ effects of different types of color-blindness.")
(define-public r-digest
(package
(name "r-digest")
- (version "0.6.8")
+ (version "0.6.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
- (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
+ (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm"))))
(build-system r-build-system)
+ ;; Vignettes require r-knitr, which requires r-digest, so we have to
+ ;; disable them and the tests.
+ (arguments
+ `(#:tests? #f
+ #:configure-flags (list "--no-build-vignettes")))
(home-page "http://dirk.eddelbuettel.com/code/digest.html")
(synopsis "Create cryptographic hash digests of R objects")
(description
@@ -305,13 +311,13 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
(define-public r-munsell
(package
(name "r-munsell")
- (version "0.4.2")
+ (version "0.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "munsell" version))
(sha256
- (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
+ (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)))
@@ -325,13 +331,13 @@ Munsell colour system.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "0.12.0")
+ (version "0.12.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
+ (base32 "1lyhyaxrnb5w4igi3l1p378s4jblcnrv6h7h5ym42ljm54mm44w3"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ Integration")
@@ -408,14 +414,14 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
(define-public r-stringi
(package
(name "r-stringi")
- (version "0.5-5")
+ (version "1.0-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
- "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
+ "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77"))))
(build-system r-build-system)
(inputs `(("icu4c" ,icu4c)))
(native-inputs `(("pkg-config" ,pkg-config)))
@@ -480,13 +486,13 @@ using just two functions: melt and dcast (or acast).")
(define-public r-scales
(package
(name "r-scales")
- (version "0.3.0")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "scales" version))
(sha256
- (base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl"))))
+ (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dichromat" ,r-dichromat)
@@ -506,13 +512,13 @@ legends.")
(define-public r-ggplot2
(package
(name "r-ggplot2")
- (version "2.0.0")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplot2" version))
(sha256
- (base32 "07r5zw0ccv4sf1mdxcz9wa86p2c6j61cnnq18qdjrh3zhhcbmdp2"))))
+ (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@@ -593,13 +599,13 @@ R/DBMS implementations.")
(define-public r-bh
(package
(name "r-bh")
- (version "1.58.0-1")
+ (version "1.60.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "BH" version))
(sha256
(base32
- "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf"))))
+ "08gc3b0irgvpjl59irdxs8jhlbky4yp4fvs3zi4pq0wdwj43cfsk"))))
(build-system r-build-system)
(home-page "https://github.com/eddelbuettel/bh")
(synopsis "R package providing subset of Boost headers")
@@ -611,13 +617,13 @@ for template use among CRAN packages.")
(define-public r-evaluate
(package
(name "r-evaluate")
- (version "0.8")
+ (version "0.8.3")
(source (origin
(method url-fetch)
(uri (cran-uri "evaluate" version))
(sha256
(base32
- "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq"))))
+ "08d6164m9wqf9qq6yh1s9a0qxwqzqpsq7312hilzy79gxf9gixzr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-stringr" ,r-stringr)))
@@ -633,13 +639,13 @@ adapted for other output formats, such as HTML or LaTeX.")
(define-public r-formatr
(package
(name "r-formatr")
- (version "1.2.1")
+ (version "1.3")
(source (origin
(method url-fetch)
(uri (cran-uri "formatR" version))
(sha256
(base32
- "0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr"))))
+ "09fsd0z6nhksc1h921h8q28f87hr6d1q8d6dmpxphjylb9r5xmj4"))))
(build-system r-build-system)
(home-page "http://yihui.name/formatR")
(synopsis "Format R code automatically")
@@ -734,13 +740,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.11")
+ (version "1.12.3")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd"))))
+ "1v3rzv6wq8mvpdrljsaqk4z3f8323jnv385js24wmn4fglqly6dz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
@@ -763,13 +769,13 @@ generation in R using Literate Programming techniques.")
(define-public r-microbenchmark
(package
(name "r-microbenchmark")
- (version "1.4-2")
+ (version "1.4-2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "microbenchmark" version))
(sha256
(base32
- "05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg"))))
+ "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)))
@@ -822,13 +828,13 @@ understand the language at a deeper level.")
(define-public r-memoise
(package
(name "r-memoise")
- (version "0.2.1")
+ (version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "memoise" version))
(sha256
(base32
- "19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4"))))
+ "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)))
@@ -862,20 +868,42 @@ New styles can also be created easily. This package was inspired by the
\"chalk\" JavaScript project.")
(license license:expat)))
+(define-public r-praise
+ (package
+ (name "r-praise")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "praise" version))
+ (sha256
+ (base32
+ "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/gaborcsardi/praise")
+ (synopsis "Functions to praise users")
+ (description
+ "This package provides template functions to assist in building friendly
+R packages that praise their users.")
+ (license license:expat)))
+
(define-public r-testthat
(package
(name "r-testthat")
- (version "0.10.0")
+ (version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "testthat" version))
(sha256
(base32
- "0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw"))))
+ "1ci1y54kaz7g4di79fcibp0m0wkkxn2glchhs6v8jfg6374ka410"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
- ("r-crayon" ,r-crayon)))
+ ("r-crayon" ,r-crayon)
+ ("r-magrittr" ,r-magrittr)
+ ("r-praise" ,r-praise)
+ ("r-r6" ,r-r6)))
(home-page "https://github.com/hadley/testthat")
(synopsis "Unit testing for R")
(description
@@ -886,21 +914,14 @@ flexible and easy to set up.")
(define-public r-r6
(package
(name "r-r6")
- (version "2.1.1")
+ (version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "R6" version))
(sha256
(base32
- "16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m"))))
+ "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-knitr" ,r-knitr)
- ("r-microbenchmark" ,r-microbenchmark)
- ("r-pryr" ,r-pryr)
- ("r-testthat" ,r-testthat)
- ("r-ggplot2" ,r-ggplot2)
- ("r-scales" ,r-scales)))
(home-page "https://github.com/wch/R6/")
(synopsis "Classes with reference semantics in R")
(description
@@ -944,6 +965,110 @@ matter where it is stored, whether in a data frame, a data table or
database.")
(license license:expat)))
+(define-public r-acepack
+ (package
+ (name "r-acepack")
+ (version "1.3-3.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "acepack" version))
+ (sha256
+ (base32
+ "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://cran.r-project.org/web/packages/acepack")
+ (synopsis "Functions for regression transformations")
+ (description
+ "This package provides ACE and AVAS methods for choosing regression
+transformations.")
+ (license license:expat)))
+
+(define-public r-cluster
+ (package
+ (name "r-cluster")
+ (version "2.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "cluster" version))
+ (sha256
+ (base32
+ "1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://cran.r-project.org/web/packages/cluster")
+ (synopsis "Methods for data cluster analysis")
+ (description
+ "This package provides tools that are useful in finding groups in data.
+It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
+Groups in Data\".")
+ (license license:gpl2+)))
+
+(define-public r-foreign
+ (package
+ (name "r-foreign")
+ (version "0.8-66")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "foreign" version))
+ (sha256
+ (base32
+ "19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/foreign")
+ (synopsis "Read data stored by other statistics software in R")
+ (description
+ "This package provides functions for reading and writing data stored by
+some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and
+for reading and writing some dBase files.")
+ (license license:gpl2+)))
+
+(define-public r-formula
+ (package
+ (name "r-formula")
+ (version "1.2-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Formula" version))
+ (sha256
+ (base32
+ "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
+ (properties `((upstream-name . "Formula")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/Formula")
+ (synopsis "Extended model formulas")
+ (description
+ "This package provides a new class @code{Formula}, which extends the base
+class @code{formula}. It supports extended formulas with multiple parts of
+regressors on the right-hand side and/or multiple responses on the left-hand
+side.")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-locfit
+ (package
+ (name "r-locfit")
+ (version "1.5-9.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "locfit" version))
+ (sha256
+ (base32
+ "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/locfit")
+ (synopsis "Local regression, likelihood and density estimation")
+ (description
+ "This package provides functions used for local regression, likelihood
+and density estimation.")
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-chron
(package
(name "r-chron")
@@ -984,6 +1109,26 @@ fast ordered joins, fast add/modify/delete of columns by group, column listing
and fast file reading.")
(license license:gpl3+)))
+(define-public r-xtable
+ (package
+ (name "r-xtable")
+ (version "1.8-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "xtable" version))
+ (sha256
+ (base32
+ "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "http://xtable.r-forge.r-project.org/")
+ (synopsis "Export R tables to LaTeX or HTML")
+ (description
+ "This package provides tools to export R data as LaTeX and HTML tables.")
+ (license license:gpl2+)))
+
(define-public python-patsy
(package
(name "python-patsy")
@@ -1180,13 +1325,13 @@ module, Java Server Pages, and Python's psp module.")
(define-public r-roxygen2
(package
(name "r-roxygen2")
- (version "5.0.0")
+ (version "5.0.1")
(source (origin
(method url-fetch)
(uri (cran-uri "roxygen2" version))
(sha256
(base32
- "0xjdphjs7l1v71lylmqgp76cbcxzvm9z1a40jgkdwvz072nn08vr"))))
+ "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-brew" ,r-brew)
@@ -1201,21 +1346,51 @@ module, Java Server Pages, and Python's psp module.")
collation, and NAMESPACE files.")
(license license:gpl2+)))
+(define-public r-openssl
+ (package
+ (name "r-openssl")
+ (version "0.9.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "openssl" version))
+ (sha256
+ (base32
+ "1dbsaciz39zvsmcyxkmpfm5yxzrpw2iv2nb86525wn80q0cyv0cb"))))
+ (build-system r-build-system)
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://github.com/jeroenooms/openssl")
+ (synopsis "Toolkit for encryption, signatures and certificates")
+ (description
+ "This package provides R bindings to OpenSSL libssl and libcrypto, plus
+custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
+and P-521. Cryptographic signatures can either be created and verified
+manually or via x509 certificates. AES block cipher is used in CBC mode for
+symmetric encryption; RSA for asymmetric (public key) encryption. High-level
+envelope functions combine RSA and AES for encrypting arbitrary sized data.
+Other utilities include key generators, hash functions (md5, sha1, sha256,
+etc), base64 encoder, a secure random number generator, and @code{bignum} math
+methods for manually performing crypto calculations on large multibyte
+integers.")
+ (license license:expat)))
+
(define-public r-httr
(package
(name "r-httr")
- (version "1.0.0")
+ (version "1.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "httr" version))
(sha256
(base32
- "1yprw8p4g8026jhravgg1hdwj1g51cpdgycyr5a58jwm4i5f79cq"))))
+ "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
("r-digest" ,r-digest)
("r-jsonlite" ,r-jsonlite)
+ ("r-openssl" ,r-openssl)
("r-mime" ,r-mime)
("r-r6" ,r-r6)
("r-stringr" ,r-stringr)))
@@ -1231,13 +1406,13 @@ functions make it easy to control additional request components.")
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.11.0")
+ (version "0.14.0")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "1h5ag8sm512jsn2sp4yhiqspc7hjq5y8z0kqz24sdznxa3b7rpn9"))))
+ "0jkkrggffpflaaw0gn2hnm1wz83xs31amriim481g73zf30g2bpr"))))
(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
@@ -1257,13 +1432,13 @@ pure C implementation of the Git core methods.")
(define-public r-rstudioapi
(package
(name "r-rstudioapi")
- (version "0.3.1")
+ (version "0.5")
(source (origin
(method url-fetch)
(uri (cran-uri "rstudioapi" version))
(sha256
(base32
- "0q7671d924nzqsqhs8d9p7l907bcam56wjwm7vvz44xgj0saj8bs"))))
+ "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/rstudioapi")
(synopsis "Safely access the RStudio API")
@@ -1275,13 +1450,13 @@ informative error messages when it's not available.")
(define-public r-devtools
(package
(name "r-devtools")
- (version "1.10.0")
+ (version "1.11.0")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
- "11x51bqhjwypbxv5sfnrnxx06b92k8kzmmx7zrwk3537r072b6pa"))))
+ "101j15d0f9107pnmdpdwqyvk2ncykq48336rl8lnqp6idiq8id2q"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@@ -1346,13 +1521,13 @@ disk (or a connection).")
(define-public r-plotrix
(package
(name "r-plotrix")
- (version "3.6")
+ (version "3.6-1")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
- "0zn6k8azh40v0lg7q9yd4sy30a26bcc0fjvndn4z7k36avlw4i25"))))
+ "1y8xnlpy4zba70af9lwj2sshvfdfcmfdh92wamyzj8z9gciailfr"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@@ -1398,16 +1573,40 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is
also flexible enough to handle most nonstandard requirements.")
(license license:gpl2+)))
+(define-public r-latticeextra
+ (package
+ (name "r-latticeextra")
+ (version "0.6-28")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "latticeExtra" version))
+ (sha256
+ (base32
+ "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
+ (properties `((upstream-name . "latticeExtra")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://latticeextra.r-forge.r-project.org/")
+ (synopsis "Extra graphical utilities based on lattice")
+ (description
+ "Building on the infrastructure provided by the lattice package, this
+package provides several new high-level graphics functions and methods, as
+well as additional utilities such as panel and axis annotation functions.")
+ (license license:gpl2+)))
+
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.6.200.2.0")
+ (version "0.6.700.3.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "137wqqga776yj6synx5awhrzgkz7mmqnvgmggh9l4k6d99vwp9gj"))
+ "1mc62b6my568ni18w4clgs6l6ggqrwzsm3lgx0c1prf4rap69s8w"))
(modules '((guix build utils)))
;; Remove bundled armadillo sources
(snippet
@@ -1485,14 +1684,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "0.8.1")
+ (version "0.9.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "07q5g9dvac5j3vnf4sjc60mnkij1k6y7vnzjz6anf499rwdwbxza"))))
+ "1zz98jxvw3lzva5kkj1n37gbhjwqd96gjs04y6h37pqy6qmkhk8c"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
@@ -1511,13 +1710,13 @@ variety of formats.")
(define-public r-gtable
(package
(name "r-gtable")
- (version "0.1.2")
+ (version "0.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "gtable" version))
(sha256
(base32
- "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
+ "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
(properties `((upstream-name . "gtable")))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/gtable")
@@ -1530,13 +1729,13 @@ grobs.")
(define-public r-gridextra
(package
(name "r-gridextra")
- (version "2.0.0")
+ (version "2.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "gridExtra" version))
(sha256
(base32
- "19yyrfd37c5hxlavb9lca9l26wjhc80rlqhgmfj9k3xhbvvpdp17"))))
+ "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
(properties `((upstream-name . "gridExtra")))
(build-system r-build-system)
(propagated-inputs
@@ -1607,13 +1806,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(define-public r-xml
(package
(name "r-xml")
- (version "3.98-1.3")
+ (version "3.98-1.4")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy"))))
+ "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@@ -1629,6 +1828,34 @@ 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-xnomial
+ (package
+ (name "r-xnomial")
+ (version "1.0.4")
+ (source
+ (origin (method url-fetch)
+ (uri (cran-uri "XNomial" version))
+ (sha256
+ (base32
+ "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
+ (properties (quasiquote ((upstream-name . "XNomial"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/XNomial")
+ (synopsis "Goodness-of-Fit test for multinomial data")
+ (description
+ "This package provides an exact Goodness-of-Fit test for
+multinomial data with fixed probabilities. It can be used to
+determine whether a set of counts fits a given expected ratio. To see
+whether a set of observed counts fits an expectation, one can examine
+all possible outcomes with @code{xmulti()} or a random sample of them
+with @code{xmonte()} and find the probability of an observation
+deviating from the expectation by at least as much as the observed.
+As a measure of deviation from the expected, one can use the
+log-likelihood ratio, the multinomial probability, or the classic
+chi-square statistic. A histogram of the test statistic can also be
+plotted and compared with the asymptotic curve.")
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-lambda-r
(package
(name "r-lambda-r")
@@ -1881,16 +2108,175 @@ The 'DataTables' library has been included in this R package.")
flexible than the orphaned \"base64\" package.")
(license license:gpl2+)))
+(define-public r-irlba
+ (package
+ (name "r-irlba")
+ (version "2.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "irlba" version))
+ (sha256
+ (base32
+ "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/irlba")
+ (synopsis "Methods for eigendecomposition of large matrices")
+ (description
+ "This package provides fast and memory efficient methods for truncated
+singular and eigenvalue decompositions, as well as for principal component
+analysis of large sparse or dense matrices.")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-pkgmaker
+ (package
+ (name "r-pkgmaker")
+ (version "0.22")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pkgmaker" version))
+ (sha256
+ (base32
+ "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-codetools" ,r-codetools)
+ ("r-digest" ,r-digest)
+ ("r-registry" ,r-registry)
+ ("r-stringr" ,r-stringr)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://renozao.github.io/pkgmaker")
+ (synopsis "Package development utilities")
+ (description
+ "This package provides some low-level utilities to use for R package
+development. It currently provides managers for multiple package specific
+options and registries, vignette, unit test and bibtex related utilities.")
+ (license license:gpl2+)))
+
+ (define-public r-registry
+ (package
+ (name "r-registry")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "registry" version))
+ (sha256
+ (base32
+ "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/registry")
+ (synopsis "Infrastructure for R package registries")
+ (description
+ "This package provides a generic infrastructure for creating and using R
+package registries.")
+ (license license:gpl2+)))
+
+(define-public r-rngtools
+ (package
+ (name "r-rngtools")
+ (version "1.2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rngtools" version))
+ (sha256
+ (base32
+ "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-pkgmaker" ,r-pkgmaker)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://renozao.github.io/rngtools")
+ (synopsis "Utility functions for working with random number generators")
+ (description
+ "This package contains a set of functions for working with Random Number
+Generators (RNGs). In particular, it defines a generic S4 framework for
+getting/setting the current RNG, or RNG data that are embedded into objects
+for reproducibility. Notably, convenient default methods greatly facilitate
+the way current RNG settings can be changed.")
+ (license license:gpl3+)))
+
+(define-public r-nmf
+ (package
+ (name "r-nmf")
+ (version "0.20.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NMF" version))
+ (sha256
+ (base32
+ "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
+ (properties `((upstream-name . "NMF")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cluster" ,r-cluster)
+ ("r-colorspace" ,r-colorspace)
+ ("r-digest" ,r-digest)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-pkgmaker" ,r-pkgmaker)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-registry" ,r-registry)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rngtools" ,r-rngtools)
+ ("r-stringr" ,r-stringr)))
+ (home-page "http://renozao.github.io/NMF")
+ (synopsis "Algorithms and framework for nonnegative matrix factorization")
+ (description
+ "This package provides a framework to perform Non-negative Matrix
+Factorization (NMF). The package implements a set of already published
+algorithms and seeding methods, and provides a framework to test, develop and
+plug new or custom algorithms. Most of the built-in algorithms have been
+optimized in C++, and the main interface function provides an easy way of
+performing parallel computations on multicore machines.")
+ (license license:gpl2+)))
+
+(define-public r-igraph
+ (package
+ (name "r-igraph")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "igraph" version))
+ (sha256
+ (base32
+ "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("gmp" ,gmp)
+ ("libxml2" ,libxml2)))
+ (propagated-inputs
+ `(("r-irlba" ,r-irlba)
+ ("r-magrittr" ,r-magrittr)
+ ("r-nmf" ,r-nmf)))
+ (home-page "http://igraph.org")
+ (synopsis "Network analysis and visualization")
+ (description
+ "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+ (license license:gpl2+)))
+
(define-public r-r-methodss3
(package
(name "r-r-methodss3")
- (version "1.7.0")
+ (version "1.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "R.methodsS3" version))
(sha256
(base32
- "1dg4bbrwr8jcsqisjrrwxs942mrjq72zw8yvl2br4djdm0md8zz5"))))
+ "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
(properties `((upstream-name . "R.methodsS3")))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/R.methodsS3")
@@ -1908,13 +2294,13 @@ want to migrate to S4.")
(define-public r-r-oo
(package
(name "r-r-oo")
- (version "1.19.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.oo" version))
(sha256
(base32
- "15rm1qb9a212bqazhcpk7m48hcp7jq8rh4yhd9c6zfyvdqszfmsb"))))
+ "1l1x4r69mdchjyi6sq52p580fz3b3bqv6dpn1706y9n4vq47qx24"))))
(properties `((upstream-name . "R.oo")))
(build-system r-build-system)
(propagated-inputs
@@ -1931,13 +2317,13 @@ maintenance for package developers.")
(define-public r-r-utils
(package
(name "r-r-utils")
- (version "2.1.0")
+ (version "2.3.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.utils" version))
(sha256
(base32
- "03pi6pkcsq65fv7cn4x74cj050dc8x5d4xyg930p6f7flk788xaz"))))
+ "0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647"))))
(properties `((upstream-name . "R.utils")))
(build-system r-build-system)
(propagated-inputs
@@ -1979,13 +2365,13 @@ persistent (on the file system).")
(define-public r-r-rsp
(package
(name "r-r-rsp")
- (version "0.20.0")
+ (version "0.21.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.rsp" version))
(sha256
(base32
- "06vq9qq5hdz3hqc99q82622mab6ix7jwap20h4za6ap6gnwqs0fv"))))
+ "0snc6ps75s3ci6sy8mil1wg2i9xmlr1ygh9n244y1brdvp43dfsw"))))
(properties `((upstream-name . "R.rsp")))
(build-system r-build-system)
(propagated-inputs
@@ -2010,13 +2396,13 @@ vignettes.")
(define-public r-matrixstats
(package
(name "r-matrixstats")
- (version "0.15.0")
+ (version "0.50.1")
(source (origin
(method url-fetch)
(uri (cran-uri "matrixStats" version))
(sha256
(base32
- "1068k85s6rlwfzlszw790c2rndydvrsw7rpck6k6z17896m8drfa"))))
+ "08l32abp7dfnsc49ca4hzznh934y60n5z01x5ga2ixky5961s57c"))))
(properties `((upstream-name . "matrixStats")))
(build-system r-build-system)
(native-inputs
@@ -2034,13 +2420,13 @@ memory usage.")
(define-public r-viridis
(package
(name "r-viridis")
- (version "0.3.1")
+ (version "0.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "viridis" version))
(sha256
(base32
- "0zz9i874s1fwhl9bcbiprlzaz7zsy1rj6c729zn3k525d63qbnj7"))))
+ "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -2057,26 +2443,81 @@ 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-tidyr
+ (package
+ (name "r-tidyr")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidyr" version))
+ (sha256
+ (base32
+ "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-lazyeval" ,r-lazyeval)
+ ("r-magrittr" ,r-magrittr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-stringi" ,r-stringi)))
+ (home-page "https://github.com/hadley/tidyr")
+ (synopsis "Tidy data with `spread()` and `gather()` functions")
+ (description
+ "tidyr is a reframing of the reshape2 package designed to accompany the
+tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
+a solid pipeline for data analysis. It is designed specifically for tidying
+data, not the general reshaping that reshape2 does, or the general aggregation
+that reshape did. In particular, built-in methods only work for data frames,
+and tidyr provides no margins or aggregation.")
+ (license license:expat)))
+
+(define-public r-hexbin
+ (package
+ (name "r-hexbin")
+ (version "1.27.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hexbin" version))
+ (sha256
+ (base32
+ "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://github.com/edzer/hexbin")
+ (synopsis "Hexagonal binning routines")
+ (description
+ "This package provides binning and plotting functions for hexagonal bins.
+It uses and relies on grid graphics and formal (S4) classes and methods.")
+ (license license:gpl2+)))
+
(define-public r-plotly
(package
(name "r-plotly")
- (version "2.0.3")
+ (version "3.4.13")
(source (origin
(method url-fetch)
(uri (cran-uri "plotly" version))
(sha256
(base32
- "16pqycns8qf0y1j21n009qf242lv0izwyidlx40zv88izxhg1vs0"))))
+ "1pfl9w35iwin8a1hfwcihajyps2ngjbyrmvi61b9lspcdbk39lf8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
("r-digest" ,r-digest)
("r-ggplot2" ,r-ggplot2)
+ ("r-hexbin" ,r-hexbin)
("r-htmlwidgets" ,r-htmlwidgets)
("r-httr" ,r-httr)
("r-jsonlite" ,r-jsonlite)
("r-magrittr" ,r-magrittr)
("r-plyr" ,r-plyr)
+ ("r-scales" ,r-scales)
+ ("r-tidyr" ,r-tidyr)
("r-viridis" ,r-viridis)))
(home-page "https://plot.ly/r")
(synopsis "Create interactive web graphics")