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-rw-r--r--gnu/packages/statistics.scm203
1 files changed, 197 insertions, 6 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index db1a6871ad..133ce41c43 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1,12 +1,12 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; 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>
+;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -116,7 +116,9 @@ be output in text, PostScript, PDF or HTML.")
`(#:make-flags
(list (string-append "LDFLAGS=-Wl,-rpath="
(assoc-ref %outputs "out")
- "/lib/R/lib"))
+ "/lib/R/lib")
+ ;; This affects the embedded timestamp of only the core packages.
+ "PKG_BUILT_STAMP=1970-01-01")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-uname
@@ -126,8 +128,13 @@ be output in text, PostScript, PDF or HTML.")
(substitute* "src/scripts/R.sh.in"
(("uname") uname-bin)))
#t))
- (add-before
- 'configure 'set-default-pager
+ (add-after 'unpack 'build-recommended-packages-reproducibly
+ (lambda _
+ (substitute* "src/library/Recommended/Makefile.in"
+ (("INSTALL_OPTS =.*" line)
+ (string-append line " --built-timestamp=1970-01-01")))
+ #t))
+ (add-before 'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
;; making "help()" print nothing at all.
(lambda _ (setenv "PAGER" "cat") #t))
@@ -727,7 +734,8 @@ legends.")
("r-lazyeval" ,r-lazyeval)
("r-tibble" ,r-tibble)
("r-reshape2" ,r-reshape2)
- ("r-scales" ,r-scales)))
+ ("r-scales" ,r-scales)
+ ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
(home-page "http://ggplot2.org")
(synopsis "An implementation of the grammar of graphics")
(description
@@ -4004,3 +4012,186 @@ 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))))
+
+(define-public r-rann
+ (package
+ (name "r-rann")
+ (version "2.5")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "RANN" version))
+ (sha256
+ (base32
+ "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7"))))
+ (properties
+ `((upstream-name . "RANN")))
+ (build-system r-build-system)
+ (home-page "https://github.com/jefferis/RANN")
+ (synopsis "Fast nearest neighbour search")
+ (description
+ "This package finds the k nearest neighbours for every point in a given
+dataset in O(N log N) time using Arya and Mount's ANN library. Provides
+approximate, exact searches, fixed radius searches, bd and kb trees.")
+ (license license:gpl3+)))
+
+(define-public r-fivethirtyeight
+ (package
+ (name "r-fivethirtyeight")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://mran.microsoft.com/src/contrib/"
+ "fivethirtyeight_" version ".tar.gz"))
+ (sha256
+ (base32
+ "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-dplyr" ,r-dplyr)
+ ("r-readr" ,r-readr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
+ (synopsis "Data and code behind the stories at FiveThirtyEight")
+ (description "This R package provides access to the code and data sets
+published by the statistics blog FiveThirtyEight.")
+ (license license:expat)))
+
+(define-public r-compquadform
+ (package
+ (name "r-compquadform")
+ (version "1.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "CompQuadForm" version))
+ (sha256
+ (base32
+ "0bsgbdblxpv57mbwnf51xyiydp2bqyxkg4zzwqki85cv5xqlrq1n"))))
+ (properties `((upstream-name . "CompQuadForm")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/CompQuadForm")
+ (synopsis "Distribution function of quadratic forms in normal variables")
+ (description
+ "This package provides functions to compute the distribution function of
+quadratic forms in normal variables using Imhof's method, Davies's algorithm,
+Farebrother's algorithm or Liu et al.'s algorithm.")
+ (license license:gpl2+)))
+
+(define-public r-cowplot
+ (package
+ (name "r-cowplot")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "cowplot" version))
+ (sha256
+ (base32
+ "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-gtable" ,r-gtable)
+ ("r-plyr" ,r-plyr)))
+ (home-page "https://github.com/wilkelab/cowplot")
+ (synopsis "Streamlined plot theme and plot annotations for ggplot2")
+ (description
+ "This package provides some helpful extensions and modifications to the
+ggplot2 package to combine multiple ggplot2 plots into one and label them with
+letters, as is often required for scientific publications.")
+ (license license:gpl2)))
+
+(define-public r-mixtools
+ (package
+ (name "r-mixtools")
+ (version "1.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mixtools" version))
+ (sha256
+ (base32
+ "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-segmented" ,r-segmented)))
+ (home-page "http://cran.r-project.org/web/packages/mixtools")
+ (synopsis "Tools for analyzing finite mixture models")
+ (description
+ "This package provides a collection of R functions for analyzing finite
+mixture models.")
+ (license license:gpl2+)))
+
+(define-public r-lars
+ (package
+ (name "r-lars")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lars" version))
+ (sha256
+ (base32
+ "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
+ (synopsis "Least angle regression software")
+ (description
+ "Least Angle Regression (\"LAR\") is a model selection algorithm; a
+useful and less greedy version of traditional forward selection methods. A
+simple modification of the LAR algorithm implements Tibshirani's Lasso; the
+Lasso modification of LARS calculates the entire Lasso path of coefficients
+for a given problem at the cost of a single least squares fit. Another LARS
+modification efficiently implements epsilon Forward Stagewise linear
+regression.")
+ (license license:gpl2)))
+
+(define-public r-fastica
+ (package
+ (name "r-fastica")
+ (version "1.2-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fastICA" version))
+ (sha256
+ (base32
+ "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r"))))
+ (properties `((upstream-name . "fastICA")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/fastICA")
+ (synopsis "FastICA algorithms to perform ICA and projection pursuit")
+ (description
+ "This package provides an implementation of the FastICA algorithm to
+perform @dfn{independent component analysis} (ICA) and projection pursuit.")
+ ;; Any GPL version.
+ (license license:gpl3+)))
+
+(define-public r-randomforest
+ (package
+ (name "r-randomforest")
+ (version "4.6-12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "randomForest" version))
+ (sha256
+ (base32
+ "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
+ (properties `((upstream-name . "randomForest")))
+ (build-system r-build-system)
+ (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (synopsis "Breiman and Cutler's random forests for classification and regression")
+ (description
+"This package provides the Breiman and Cutler's random forests algorithm, based on a
+forest of trees using random inputs, for classification and regression.")
+ (license license:gpl2+)))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-10 07:03:58 +0000