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-rw-r--r--gnu/packages/statistics.scm507
1 files changed, 440 insertions, 67 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 838428fde9..1bc5aa78ff 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -41,6 +41,7 @@
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pcre)
@@ -237,13 +238,13 @@ effects of different types of color-blindness.")
(define-public r-digest
(package
(name "r-digest")
- (version "0.6.9")
+ (version "0.6.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
- (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm"))))
+ (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
@@ -300,6 +301,30 @@ non-estimable cases correctly.")
\"tables\" of grobs.")
(license license:gpl2+)))
+(define-public r-pheatmap
+ (package
+ (name "r-pheatmap")
+ (version "1.0.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pheatmap" version))
+ (sha256
+ (base32
+ "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gtable" ,r-gtable)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-scales" ,r-scales)))
+ (home-page
+ "http://cran.r-project.org/web/packages/pheatmap")
+ (synopsis "Pretty heatmaps")
+ (description
+ "This package provides an implementation of heatmaps that offers more
+control over dimensions and appearance.")
+ (license license:gpl2+)))
+
(define-public r-labeling
(package
(name "r-labeling")
@@ -361,13 +386,13 @@ Munsell colour system.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "0.12.5")
+ (version "0.12.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "1vw0zbd6zhqixqg7h8ahn1dr1hb492365x419nrp2lhvr60r8i0k"))))
+ (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ Integration")
@@ -382,17 +407,39 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation(\"Rcpp\")' for details on these last two.")
(license license:gpl2+)))
+(define-public r-matrix
+ (package
+ (name "r-matrix")
+ (version "1.2-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Matrix" version))
+ (sha256
+ (base32
+ "18x3mdq5cdhbk1lw5cj7vbr41lk8w9p4i5kzh8wslgq6p3d9ac3c"))))
+ (properties `((upstream-name . "Matrix")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)))
+ (home-page "http://Matrix.R-forge.R-project.org/")
+ (synopsis "Sparse and dense matrix classes and methods")
+ (description
+ "This package provides classes and methods for dense and sparse matrices
+and operations on them using LAPACK and SuiteSparse.")
+ (license license:gpl2+)))
+
(define-public r-mgcv
(package
(name "r-mgcv")
- (version "1.8-12")
+ (version "1.8-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
(base32
- "1khzy36nn6xbnzqfc2953ng0sv8w91mns1ymhibaqn1150x1qid0"))))
+ "0ly9x23q6kd7aqrsb8qjsj8jc597h3068iaqjmkkdv56r5dln29f"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/mgcv")
(synopsis "Mixed generalised additive model computation")
@@ -406,14 +453,14 @@ distributions beyond the exponential family.")
(define-public r-permute
(package
(name "r-permute")
- (version "0.9-0")
+ (version "0.9-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "permute" version))
(sha256
(base32
- "0w68cqw6s4pixix8bh1qzsy1pm64jqh1cjznw74h82ygp8sj7p73"))))
+ "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
(build-system r-build-system)
;; Tests do not run correctly, but running them properly would entail a
;; circular dependency with vegan.
@@ -429,13 +476,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.")
(define-public r-plyr
(package
(name "r-plyr")
- (version "1.8.3")
+ (version "1.8.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "plyr" version))
(sha256
- (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
+ (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
(build-system r-build-system)
(native-inputs `(("r-rcpp" ,r-rcpp)))
(home-page "http://had.co.nz/plyr")
@@ -485,17 +532,40 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
;; Includes code licensed under bsd-4
(license license:asl2.0)))
+(define-public r-sendmailr
+ (package
+ (name "r-sendmailr")
+ (version "1.2-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sendmailR" version))
+ (sha256
+ (base32
+ "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
+ (properties `((upstream-name . "sendmailR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-base64enc" ,r-base64enc)))
+ (home-page
+ "http://cran.r-project.org/web/packages/sendmailR")
+ (synopsis "Send email using R")
+ (description
+ "This package contains a simple SMTP client which provides a portable
+solution for sending email, including attachments, from within R.")
+ (license license:gpl2+)))
+
(define-public r-stringi
(package
(name "r-stringi")
- (version "1.0-1")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
- "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77"))))
+ "0rg14hga1g2havd3imhk04iyh1dnisnmxf7yhiiwhs7y72hphc94"))))
(build-system r-build-system)
(inputs `(("icu4c" ,icu4c)))
(native-inputs `(("pkg-config" ,pkg-config)))
@@ -514,13 +584,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.")
(define-public r-stringr
(package
(name "r-stringr")
- (version "1.0.0")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringr" version))
(sha256
- (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
+ (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
@@ -685,13 +755,13 @@ wrong.")
(define-public r-lazyeval
(package
(name "r-lazyeval")
- (version "0.1.10")
+ (version "0.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "lazyeval" version))
(sha256
(base32
- "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
+ "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk"))))
(build-system r-build-system)
(home-page "https://github.com/hadley/lazyeval")
(synopsis "Lazy (non-standard) evaluation in R")
@@ -703,13 +773,13 @@ evaluation (NSE) in R.")
(define-public r-dbi
(package
(name "r-dbi")
- (version "0.4-1")
+ (version "0.5-1")
(source (origin
(method url-fetch)
(uri (cran-uri "DBI" version))
(sha256
(base32
- "13n6ibmrma42qmq17qgkyjsc0ciwqf17sd7lw7w26pwpyjd4mwgg"))))
+ "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi"))))
(build-system r-build-system)
(home-page "https://github.com/rstats-db/DBI")
(synopsis "R database interface")
@@ -802,13 +872,13 @@ supported via Andre Simon's highlight package.")
(define-public r-mime
(package
(name "r-mime")
- (version "0.4")
+ (version "0.5")
(source (origin
(method url-fetch)
(uri (cran-uri "mime" version))
(sha256
(base32
- "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p"))))
+ "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
(build-system r-build-system)
(home-page "https://github.com/yihui/mime")
(synopsis "R package to map filenames to MIME types")
@@ -864,13 +934,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.13")
+ (version "1.14")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "0v69846myi4fbjp8wiik4295fhba67s3i6ccysghm6x031i2f26q"))))
+ "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
@@ -995,13 +1065,13 @@ you call it again with the same arguments it returns the pre-computed value.")
(define-public r-crayon
(package
(name "r-crayon")
- (version "1.3.1")
+ (version "1.3.2")
(source (origin
(method url-fetch)
(uri (cran-uri "crayon" version))
(sha256
(base32
- "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm"))))
+ "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws"))))
(build-system r-build-system)
(propagated-inputs
`(("r-memoise" ,r-memoise)))
@@ -1061,13 +1131,13 @@ flexible and easy to set up.")
(define-public r-r6
(package
(name "r-r6")
- (version "2.1.2")
+ (version "2.1.3")
(source (origin
(method url-fetch)
(uri (cran-uri "R6" version))
(sha256
(base32
- "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv"))))
+ "19qrkgxvssyi51fm80h93sabzz0n2vgqgv1w8xjqbsap0nx379vy"))))
(build-system r-build-system)
(home-page "https://github.com/wch/R6/")
(synopsis "Classes with reference semantics in R")
@@ -1080,23 +1150,47 @@ private members, and they support inheritance, even when the classes are
defined in different packages.")
(license license:expat)))
+(define-public r-tibble
+ (package
+ (name "r-tibble")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tibble" version))
+ (sha256
+ (base32
+ "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-lazyeval" ,r-lazyeval)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/hadley/tibble")
+ (synopsis "Simple data frames")
+ (description
+ "This package provides a @code{tbl_df} class that offers better checking
+and printing capabilities than traditional data frames.")
+ (license license:expat)))
+
(define-public r-dplyr
(package
(name "r-dplyr")
- (version "0.4.3")
+ (version "0.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
- "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc"))))
+ "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-r6" ,r-r6)
("r-magrittr" ,r-magrittr)
("r-lazyeval" ,r-lazyeval)
- ("r-dbi" ,r-dbi)))
+ ("r-dbi" ,r-dbi)
+ ("r-tibble" ,r-tibble)))
(native-inputs
`(("r-rcpp" ,r-rcpp)
("r-bh" ,r-bh)))
@@ -1431,14 +1525,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
(define-public r-xml2
(package
(name "r-xml2")
- (version "0.1.2")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
- "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c"))))
+ "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr"))))
(build-system r-build-system)
(inputs
`(("libxml2" ,libxml2)))
@@ -1455,14 +1549,14 @@ files in R. It is built on top of the libxml2 C library.")
(define-public r-multitaper
(package
(name "r-multitaper")
- (version "1.0-11")
+ (version "1.0-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "multitaper" version))
(sha256
(base32
- "1s0lmjzpyd7zmc2p1ywv5fm7qkq357p70b76gw9wjlms6d81j1n4"))))
+ "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -1481,13 +1575,13 @@ jackknifed confidence intervals are available for most estimates.")
(define-public r-rversions
(package
(name "r-rversions")
- (version "1.0.2")
+ (version "1.0.3")
(source (origin
(method url-fetch)
(uri (cran-uri "rversions" version))
(sha256
(base32
- "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68"))))
+ "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@@ -1518,6 +1612,126 @@ previous R versions and their release dates.")
limited to R.")
(license license:gpl3+)))
+(define-public r-backports
+ (package
+ (name "r-backports")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "backports" version))
+ (sha256
+ (base32
+ "0s04mbb7imqc00jl37i081y4yf7qdimk687dyrkvb20nixvjvjyh"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/backports")
+ (synopsis "Reimplementations of functions introduced since R 3.0.0")
+ (description
+ "Provides implementations of functions which have been introduced in R
+since version 3.0.0. The backports are conditionally exported which results
+in R resolving the function names to the version shipped with R (if available)
+and uses the implemented backports as fallback. This way package developers
+can make use of the new functions without worrying about the minimum required
+R version.")
+ (license license:gpl2+)))
+
+(define-public r-checkmate
+ (package
+ (name "r-checkmate")
+ (version "1.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "checkmate" version))
+ (sha256
+ (base32
+ "1nqyi58jl33af82y8kw8iy9xbna2080y1khhy90kf6lim6q74024"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-backports" ,r-backports)))
+ (home-page "https://github.com/mllg/checkmate")
+ (synopsis "Fast and versatile argument checks")
+ (description
+ "This package provides tests and assertions to perform frequent argument
+checks. A substantial part of the package was written in C to minimize any
+worries about execution time overhead.")
+ (license license:bsd-3)))
+
+(define-public r-bbmisc
+ (package
+ (name "r-bbmisc")
+ (version "1.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "BBmisc" version))
+ (sha256
+ (base32
+ "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl"))))
+ (properties `((upstream-name . "BBmisc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)))
+ (home-page "https://github.com/berndbischl/BBmisc")
+ (synopsis "Miscellaneous functions for R package development")
+ (description
+ "This package provides miscellaneous helper functions for the development
+of R packages.")
+ (license license:bsd-3)))
+
+(define-public r-fail
+ (package
+ (name "r-fail")
+ (version "1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fail" version))
+ (sha256
+ (base32
+ "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmisc" ,r-bbmisc)
+ ("r-checkmate" ,r-checkmate)))
+ (home-page "https://github.com/mllg/fail")
+ (synopsis "File abstraction interface layer (FAIL)")
+ (description
+ "This package provides a more comfortable interface to work with R data
+or source files in a key-value fashion.")
+ (license license:bsd-3)))
+
+(define-public r-batchjobs
+ (package
+ (name "r-batchjobs")
+ (version "1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "BatchJobs" version))
+ (sha256
+ (base32
+ "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0"))))
+ (properties `((upstream-name . "BatchJobs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmisc" ,r-bbmisc)
+ ("r-brew" ,r-brew)
+ ("r-checkmate" ,r-checkmate)
+ ("r-dbi" ,r-dbi)
+ ("r-digest" ,r-digest)
+ ("r-fail" ,r-fail)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-sendmailr" ,r-sendmailr)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/tudo-r/BatchJobs")
+ (synopsis "Batch computing with R")
+ (description
+ "This package provides @code{Map}, @code{Reduce} and @code{Filter}
+variants to generate jobs on batch computing systems like PBS/Torque, LSF,
+SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
+ (license license:bsd-2)))
+
(define-public r-brew
(package
(name "r-brew")
@@ -1564,14 +1778,14 @@ collation, and NAMESPACE files.")
(define-public r-openssl
(package
(name "r-openssl")
- (version "0.9.3")
+ (version "0.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "0ldqam7d9fyxwhr651ld6lsh05lg4v2y8ajxwzq9ywzjmfb3vlpz"))))
+ "0rpb3xdzab453yjddr8ryad53ll27zss8abnj30aqa2lzbg4jwyb"))))
(build-system r-build-system)
(inputs
`(("openssl" ,openssl)))
@@ -1593,13 +1807,13 @@ integers.")
(define-public r-httr
(package
(name "r-httr")
- (version "1.1.0")
+ (version "1.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "httr" version))
(sha256
(base32
- "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p"))))
+ "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@@ -1647,13 +1861,13 @@ pure C implementation of the Git core methods.")
(define-public r-rstudioapi
(package
(name "r-rstudioapi")
- (version "0.5")
+ (version "0.6")
(source (origin
(method url-fetch)
(uri (cran-uri "rstudioapi" version))
(sha256
(base32
- "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym"))))
+ "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/rstudioapi")
(synopsis "Safely access the RStudio API")
@@ -1665,13 +1879,13 @@ informative error messages when it's not available.")
(define-public r-devtools
(package
(name "r-devtools")
- (version "1.11.1")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
- "0ik3l3q62sspdph613f9ik5yz36s8q5nrc50dqgn3pxzvpwpdj2i"))))
+ "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@@ -1695,13 +1909,13 @@ tools to simplify the devolpment of R packages.")
(define-public r-withr
(package
(name "r-withr")
- (version "1.0.1")
+ (version "1.0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "withr" version))
(sha256
(base32
- "0zbj3rd7dc0ycknmay7y7rm1qvnh9n05jw93gjggz46j2zfmy93y"))))
+ "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493"))))
(build-system r-build-system)
(home-page "https://github.com/jimhester/withr")
(synopsis "Run code with temporarily modified global state")
@@ -1711,20 +1925,42 @@ in which global state has been temporarily modified. Many of these functions
were originally a part of the r-devtools package.")
(license license:gpl2+)))
+(define-public r-hms
+ (package
+ (name "r-hms")
+ (version "0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hms" version))
+ (sha256
+ (base32
+ "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/rstats-db/hms")
+ (synopsis "Pretty time of day")
+ (description
+ "This package implements an S3 class for storing and formatting
+time-of-day values, based on the @code{difftime} class.")
+ (license license:gpl3+)))
+
(define-public r-readr
(package
(name "r-readr")
- (version "0.2.2")
+ (version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "readr" version))
(sha256
(base32
- "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m"))))
+ "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
("r-rcpp" ,r-rcpp)
+ ("r-hms" ,r-hms)
+ ("r-tibble" ,r-tibble)
+ ("r-r6" ,r-r6)
("r-bh" ,r-bh)))
(home-page "https://github.com/hadley/readr")
(synopsis "Read tabular data")
@@ -1736,13 +1972,13 @@ disk (or a connection).")
(define-public r-plotrix
(package
(name "r-plotrix")
- (version "3.6-2")
+ (version "3.6-3")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
- "1jn1k3skmlgyvpijj6vlcn5m2zgrsdh00g1fq8n5dqs1pkl1sqrw"))))
+ "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@@ -1771,13 +2007,13 @@ scaling functions for R.")
(define-public r-lattice
(package
(name "r-lattice")
- (version "0.20-33")
+ (version "0.20-34")
(source (origin
(method url-fetch)
(uri (cran-uri "lattice" version))
(sha256
(base32
- "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg"))))
+ "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
(build-system r-build-system)
(home-page "http://lattice.r-forge.r-project.org/")
(synopsis "High-level data visualization system")
@@ -1815,13 +2051,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.6.700.6.0")
+ (version "0.7.400.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "0x736cjg1pbvn8c6h91c88qmmz4pddvvqg88k9c9kwhn24fjrra0"))
+ "0g2658iy43higy1cay00ljibgnwh0zv5gcwvbhckjs48y8z1a2pb"))
(modules '((guix build utils)))
;; Remove bundled armadillo sources
(snippet
@@ -1899,19 +2135,35 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "0.9.6")
+ (version "1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "09ajq5miqzz46q0i9svvbh93dbi7xbjn4702d6z3scdz272gx7l2"))))
+ "0c7gs9c8xdjfxviw0syh13pf3vys2b2ssixmnyqbji64xdscn7pz"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; See https://github.com/rstudio/rmarkdown/pull/800
+ ;; The resource files are in the store and have mode 444. After
+ ;; copying the files R fails to remove them again because it doesn't
+ ;; have write access to them.
+ (add-after 'unpack 'copy-files-without-mode
+ (lambda _
+ (substitute* "R/render.R"
+ (("file.copy\\(from = from," prefix)
+ (string-append prefix
+ " copy.mode = FALSE, ")))
+ #t)))))
(propagated-inputs
`(("r-catools" ,r-catools)
("r-htmltools" ,r-htmltools)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-base64enc" ,r-base64enc)
("r-knitr" ,r-knitr)
("r-yaml" ,r-yaml)
("ghc-pandoc" ,ghc-pandoc)))
@@ -2074,13 +2326,13 @@ plotted and compared with the asymptotic curve.")
(define-public r-lambda-r
(package
(name "r-lambda-r")
- (version "1.1.7")
+ (version "1.1.9")
(source (origin
(method url-fetch)
(uri (cran-uri "lambda.r" version))
(sha256
(base32
- "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa"))))
+ "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14"))))
(properties `((upstream-name . "lambda.r")))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/lambda.r")
@@ -2117,13 +2369,13 @@ options defined in other packages.")
(define-public r-futile-logger
(package
(name "r-futile-logger")
- (version "1.4.1")
+ (version "1.4.3")
(source (origin
(method url-fetch)
(uri (cran-uri "futile.logger" version))
(sha256
(base32
- "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51"))))
+ "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
(properties `((upstream-name . "futile.logger")))
(build-system r-build-system)
(propagated-inputs
@@ -2138,6 +2390,26 @@ convenient and easy to use replacement for @code{cat} and @code{print}
statements.")
(license license:lgpl3+)))
+(define-public r-segmented
+ (package
+ (name "r-segmented")
+ (version "0.5-1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "segmented" version))
+ (sha256
+ (base32
+ "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/segmented")
+ (synopsis "Regression models with breakpoints estimation")
+ (description
+ "Given a regression model, segmented updates the model by adding one or
+more segmented (i.e., piecewise-linear) relationships. Several variables with
+multiple breakpoints are allowed.")
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-snow
(package
(name "r-snow")
@@ -2162,13 +2434,13 @@ worker processes and collect and return the results on the master.")
(define-public r-sparsem
(package
(name "r-sparsem")
- (version "1.7")
+ (version "1.72")
(source (origin
(method url-fetch)
(uri (cran-uri "SparseM" version))
(sha256
(base32
- "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz"))))
+ "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka"))))
(properties
`((upstream-name . "SparseM")))
(inputs
@@ -2297,13 +2569,13 @@ using the multicore functionality of the parallel package.")
(define-public r-dt
(package
(name "r-dt")
- (version "0.1")
+ (version "0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
- "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj"))))
+ "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
(properties
`((upstream-name . "DT")))
(build-system r-build-system)
@@ -2349,14 +2621,14 @@ flexible than the orphaned \"base64\" package.")
(define-public r-irlba
(package
(name "r-irlba")
- (version "2.0.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "irlba" version))
(sha256
(base32
- "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m"))))
+ "0yb8b8g6f3cb0f56r702fn2px8nf5rx8cyy2scq36xai9w7f25jj"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/irlba")
(synopsis "Methods for eigendecomposition of large matrices")
@@ -2463,6 +2735,50 @@ for reproducibility. Notably, convenient default methods greatly facilitate
the way current RNG settings can be changed.")
(license license:gpl3+)))
+(define-public r-rtsne
+ (package
+ (name "r-rtsne")
+ (version "0.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Rtsne" version))
+ (sha256
+ (base32
+ "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy"))))
+ (properties `((upstream-name . "Rtsne")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/jkrijthe/Rtsne")
+ (synopsis "T-distributed stochastic neighbor embedding")
+ (description
+ "This package provides an R wrapper around the fast T-distributed
+Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
+ ;; The declared license for this package is BSD-3, but it also includes
+ ;; code licensed under BSD-4.
+ (license (list license:bsd-3 license:bsd-4))))
+
+(define-public r-e1071
+ (package
+ (name "r-e1071")
+ (version "1.6-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "e1071" version))
+ (sha256
+ (base32
+ "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/e1071")
+ (synopsis "Miscellaneous functions for probability theory")
+ (description
+ "This package provides functions for latent class analysis, short time
+Fourier transform, fuzzy clustering, support vector machines, shortest path
+computation, bagged clustering, naive Bayes classifier, and more.")
+ (license license:gpl2+)))
+
(define-public r-nmf
(package
(name "r-nmf")
@@ -2729,14 +3045,14 @@ most common form of color blindness.")
(define-public r-tidyr
(package
(name "r-tidyr")
- (version "0.4.1")
+ (version "0.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
- "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h"))))
+ "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -2834,6 +3150,63 @@ noncentral hypergeometric distribution (also called extended hypergeometric
distribution).")
(license license:gpl3+)))
+(define-public r-rpart
+ (package
+ (name "r-rpart")
+ (version "4.1-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rpart" version))
+ (sha256
+ (base32
+ "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/rpart")
+ (synopsis "Recursive partitioning and regression trees")
+ (description
+ "This package provides recursive partitioning functions for
+classification, regression and survival trees.")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-hmisc
+ (package
+ (name "r-hmisc")
+ (version "3.17-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Hmisc" version))
+ (sha256
+ (base32
+ "1hr2kycpm0h3li9gnlbx9pl6h13das7g2wqfk6cip1kx6lv00ypw"))))
+ (properties `((upstream-name . "Hmisc")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("r-acepack" ,r-acepack)
+ ("r-cluster" ,r-cluster)
+ ("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)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-nnet" ,r-nnet)
+ ("r-rpart" ,r-rpart)))
+ (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
+ (synopsis "Miscellaneous data analysis and graphics functions")
+ (description
+ "This package contains many functions useful for data analysis,
+high-level graphics, utility operations, functions for computing sample size
+and power, importing and annotating datasets, imputing missing values,
+advanced table making, variable clustering, character string manipulation,
+conversion of R objects to LaTeX code, and recoding variables.")
+ (license license:gpl2+)))
+
(define-public r-runit
(package
(name "r-runit")
generated by cgit v1.2.3 (git 2.25.4) at 2024-11-08 01:06:37 +0000