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-rw-r--r--gnu/packages/statistics.scm374
1 files changed, 351 insertions, 23 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 700a8957cc..36f1889efa 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1394,13 +1394,7 @@ 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 +1410,10 @@ 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 +1444,13 @@ 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)
@@ -1487,10 +1478,7 @@ 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
@@ -3272,6 +3260,128 @@ 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")
@@ -3375,6 +3485,224 @@ 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 "1.1.20")
+ (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-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")