From 58612fd2c869995fd18ed915d4d240b173079e73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 14:55:01 +0100 Subject: gnu: Add r-rematch. * gnu/packages/statistics.scm (r-rematch): New variable. --- gnu/packages/statistics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 700a8957cc..612ea530d8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3272,6 +3272,26 @@ 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-rpart (package (name "r-rpart") -- cgit v1.2.3 From d427e03eee99461ade0df4837bc2e7c20c397f10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 14:56:05 +0100 Subject: gnu: Add r-cellranger. * gnu/packages/statistics.scm (r-cellranger): New variable. --- gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 612ea530d8..cec304db66 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3292,6 +3292,28 @@ 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-rpart (package (name "r-rpart") -- cgit v1.2.3 From 9f5435d96391cd8438ba6ce6142b20753360b025 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 14:57:06 +0100 Subject: gnu: Add r-googlesheets. * gnu/packages/statistics.scm (r-googlesheets): New variable. --- gnu/packages/statistics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cec304db66..0ba33165d6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3314,6 +3314,34 @@ character vector.") @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-rpart (package (name "r-rpart") -- cgit v1.2.3 From e7d16ad1616878f28b9e0eb403be845d3892a4aa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 14:58:40 +0100 Subject: gnu: Add r-spams. * gnu/packages/statistics.scm (r-spams): New variable. --- gnu/packages/statistics.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0ba33165d6..dcf6dbe626 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3342,6 +3342,58 @@ character vector.") 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 " 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") -- cgit v1.2.3 From c9a6671490c4f415cdd17691fc6585baff892db7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:06:32 +0100 Subject: gnu: Add r-dynamictreecut. * gnu/packages/statistics.scm (r-dynamictreecut): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dcf6dbe626..c48620895c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3497,6 +3497,27 @@ 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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From c4708783eec4cf0d312b6401949b15e76407b724 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:08:22 +0100 Subject: gnu: Add r-preprocesscore. * gnu/packages/statistics.scm (r-preprocesscore): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c48620895c..d2ca35ef6b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3518,6 +3518,27 @@ framework, with additional code inspection and report generation tools.") 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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 1bd46f55207f5940131e37678bdd10ccff1dd56d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:15:27 +0100 Subject: gnu: Add r-fastcluster. * gnu/packages/statistics.scm (r-fastcluster): New variable. --- gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d2ca35ef6b..3c2bd0c03c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3539,6 +3539,31 @@ hierarchical clustering dendrograms.") routines.") (license license:lgpl2.0+))) +(define-public r-fastcluster + (package + (name "r-fastcluster") + (version "1.1.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastcluster" version)) + (sha256 + (base32 + "0rlbxhh894znf10x0xgkv9dzpibgq9jw5aqpgviccdnxc2c5hwid")))) + (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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 6335bf1c805940f2c3ea9b16f477084c2cf0eb52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:16:53 +0100 Subject: gnu: Add r-sfsmisc. * gnu/packages/statistics.scm (r-sfsmisc): New variable. --- gnu/packages/statistics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3c2bd0c03c..0c5425860c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3564,6 +3564,25 @@ 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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 1571f90e3520b3b606078cdb1e92291a638da15f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:19:01 +0100 Subject: gnu: Add r-gtools. * gnu/packages/statistics.scm (r-gtools): New variable. --- gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0c5425860c..8027aed617 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3583,6 +3583,28 @@ existing packages provide.") 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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 6034cd905e610e2ed5d7d40b30953917b8619535 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:38:41 +0100 Subject: gnu: Add r-gdata. * gnu/packages/statistics.scm (r-gdata): New variable. --- gnu/packages/statistics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8027aed617..dc519b46a2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3605,6 +3605,46 @@ 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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 0cfe0570f2d6c88bd811fa4739075bfe2f223324 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:39:24 +0100 Subject: gnu: Add r-gplots. * gnu/packages/statistics.scm (r-gplots): New variable. --- gnu/packages/statistics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dc519b46a2..f014f16a97 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3645,6 +3645,46 @@ including: @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-kernsmooth (package (name "r-kernsmooth") -- cgit v1.2.3 From 419a8a186f87308e6092067ad01b4f80199dd629 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:41:17 +0100 Subject: gnu: Add r-rocr. * gnu/packages/statistics.scm (r-rocr): New variable. --- gnu/packages/statistics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/statistics.scm') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f014f16a97..c2d46f29d4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3685,6 +3685,36 @@ including: @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") -- cgit v1.2.3