From 53cc59a1d86cb31fc2505ead2bf9f80b13743ecf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:15:30 +0100
Subject: gnu: r-ape: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c4cf394e6e..adcc178592 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,32 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
+(define-public r-ape
+  (package
+    (name "r-ape")
+    (version "5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ape" version))
+       (sha256
+        (base32
+         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-nlme" ,r-nlme)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://ape-package.ird.fr/")
+    (synopsis "Analyses of phylogenetics and evolution")
+    (description
+     "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+    (license license:gpl2+)))
+
 (define-public r-colorspace
   (package
     (name "r-colorspace")
-- 
cgit 1.4.1


From 35b0c051c51d0d582a7ba9664c2270aae7b45f6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:03 +0100
Subject: gnu: Add r-signal.

* gnu/packages/cran.scm (r-signal): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index adcc178592..c096a9d037 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2951,3 +2951,26 @@ created.  Experimental designs may be blocked or blocked designs created from
 a candidate list, using several criteria.  The blocking can be done when whole
 and within plot factors interact.")
     (license license:gpl2+)))
+
+(define-public r-signal
+  (package
+    (name "r-signal")
+    (version "0.7-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "signal" version))
+       (sha256
+        (base32
+         "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/signal/")
+    (synopsis "Signal processing")
+    (description
+     "This package provides a set of signal processing functions originally
+written for Matlab and GNU Octave.  It includes filter generation utilities,
+filtering functions, resampling routines, and visualization of filter models.
+It also includes interpolation functions.")
+    (license license:gpl2)))
-- 
cgit 1.4.1


From db80dd4a1d7e2371bc3c300f48b84a817adb3550 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:11 +0100
Subject: gnu: Add r-psych.

* gnu/packages/cran.scm (r-psych): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c096a9d037..84b7b244d9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2974,3 +2974,34 @@ written for Matlab and GNU Octave.  It includes filter generation utilities,
 filtering functions, resampling routines, and visualization of filter models.
 It also includes interpolation functions.")
     (license license:gpl2)))
+
+(define-public r-psych
+  (package
+    (name "r-psych")
+    (version "1.7.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "psych" version))
+       (sha256
+        (base32
+         "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreign" ,r-foreign)
+       ("r-lattice" ,r-lattice)
+       ("r-mnormt" ,r-mnormt)
+       ("r-nlme" ,r-nlme)))
+    (home-page "http://cran.r-project.org/web/packages/psych")
+    (synopsis "Procedures for psychological, psychometric, and personality research")
+    (description
+     "This package provides a general purpose toolbox for personality,
+psychometric theory and experimental psychology.  The functions are primarily
+for multivariate analysis and scale construction using factor analysis,
+principal component analysis, cluster analysis and reliability analysis,
+although others provide basic descriptive statistics.  It provides functions
+for analyzing data at multiple levels within and between group statistics,
+including correlations and factor analysis; functions for simulating and
+testing particular item and test structures are included.  Several functions
+serve as a useful front end for structural equation modeling.")
+    (license license:gpl2+)))
-- 
cgit 1.4.1


From 3dab50d92aedeb276d7997ccf9b37535ada58454 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:19 +0100
Subject: gnu: Add r-gsubfn.

* gnu/packages/cran.scm (r-gsubfn): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 84b7b244d9..ae7b442f64 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3005,3 +3005,29 @@ including correlations and factor analysis; functions for simulating and
 testing particular item and test structures are included.  Several functions
 serve as a useful front end for structural equation modeling.")
     (license license:gpl2+)))
+
+(define-public r-gsubfn
+  (package
+    (name "r-gsubfn")
+    (version "0.6-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gsubfn" version))
+       (sha256
+        (base32
+         "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-proto" ,r-proto)))
+    (home-page "http://gsubfn.googlecode.com")
+    (synopsis "Utilities for strings and function arguments.")
+    (description
+     "This package provides @code{gsubfn} which is like @code{gsub} but can
+take a replacement function or certain other objects instead of the
+replacement string.  Matches and back references are input to the replacement
+function and replaced by the function output.  @code{gsubfn} can be used to
+split strings based on content rather than delimiters and for quasi-perl-style
+string interpolation.  The package also has facilities for translating
+formulas to functions and allowing such formulas in function calls instead of
+functions.")
+    (license license:gpl2+)))
-- 
cgit 1.4.1


From 3a563a410ab8791dfc2a51aae4cd79c1fce1458d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:29 +0100
Subject: gnu: Add r-sqldf.

* gnu/packages/cran.scm (r-sqldf): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ae7b442f64..c8a4216767 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3031,3 +3031,34 @@ string interpolation.  The package also has facilities for translating
 formulas to functions and allowing such formulas in function calls instead of
 functions.")
     (license license:gpl2+)))
+
+(define-public r-sqldf
+  (package
+    (name "r-sqldf")
+    (version "0.4-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sqldf" version))
+       (sha256
+        (base32
+         "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-chron" ,r-chron)
+       ("r-dbi" ,r-dbi)
+       ("r-gsubfn" ,r-gsubfn)
+       ("r-proto" ,r-proto)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://github.com/ggrothendieck/sqldf")
+    (synopsis "Manipulate R data frames using SQL")
+    (description
+     "The @code{sqldf} function is typically passed a single argument which is
+an SQL select statement where the table names are ordinary R data frame names.
+@code{sqldf} transparently sets up a database, imports the data frames into
+that database, performs the SQL statement and returns the result using a
+heuristic to determine which class to assign to each column of the returned
+data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
+used to read filtered files into R even if the original files are larger than
+R itself can handle.")
+    (license license:gpl2)))
-- 
cgit 1.4.1


From 94e46cabc1222b82f1cef091fd955b839f2493d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:36 +0100
Subject: gnu: Add r-abind.

* gnu/packages/cran.scm (r-abind): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c8a4216767..e7e49fd519 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3062,3 +3062,25 @@ data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
 used to read filtered files into R even if the original files are larger than
 R itself can handle.")
     (license license:gpl2)))
+
+(define-public r-abind
+  (package
+    (name "r-abind")
+    (version "1.4-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abind" version))
+       (sha256
+        (base32
+         "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/abind/")
+    (synopsis "Combine multidimensional arrays")
+    (description
+     "This package provides tools to combine multidimensional arrays into a
+single array.  This is a generalization of @code{cbind} and @code{rbind}.  It
+works with vectors, matrices, and higher-dimensional arrays.  It also provides
+the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
+extracting and replacing data in arrays.")
+    (license license:lgpl2.0+)))
-- 
cgit 1.4.1


From fc784b6672eb8d21e1cb52dda1fd32c1bc4ae9a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:44 +0100
Subject: gnu: Add r-prroc.

* gnu/packages/cran.scm (r-prroc): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e7e49fd519..4b63c0f644 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3084,3 +3084,27 @@ works with vectors, matrices, and higher-dimensional arrays.  It also provides
 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
 extracting and replacing data in arrays.")
     (license license:lgpl2.0+)))
+
+(define-public r-prroc
+  (package
+    (name "r-prroc")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PRROC" version))
+       (sha256
+        (base32
+         "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc"))))
+    (properties `((upstream-name . "PRROC")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/PRROC/")
+    (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
+    (description
+     "This package computes the areas under the @dfn{precision-recall} (PR)
+and ROC curve for weighted (e.g. soft-labeled) and unweighted data.  In
+contrast to other implementations, the interpolation between points of the PR
+curve is done by a non-linear piecewise function.  In addition to the areas
+under the curves, the curves themselves can also be computed and plotted by a
+specific S3-method.")
+    (license license:gpl3)))
-- 
cgit 1.4.1


From 661bb51e668a239372dbc4df582b73ca356e38bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:15 +0100
Subject: gnu: Add r-vim.

* gnu/packages/cran.scm (r-vim): New variable.
---
 gnu/packages/cran.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4b63c0f644..efb612e34f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3108,3 +3108,41 @@ curve is done by a non-linear piecewise function.  In addition to the areas
 under the curves, the curves themselves can also be computed and plotted by a
 specific S3-method.")
     (license license:gpl3)))
+
+(define-public r-vim
+  (package
+    (name "r-vim")
+    (version "4.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "VIM" version))
+       (sha256
+        (base32
+         "1vjcs5wvjv94ln01d94h9rs4j50d3ky4n26mm3prgh13raylrmnd"))))
+    (properties `((upstream-name . "VIM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-colorspace" ,r-colorspace)
+       ("r-data-table" ,r-data-table)
+       ("r-e1071" ,r-e1071)
+       ("r-laeken" ,r-laeken)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-robustbase" ,r-robustbase)
+       ("r-sp" ,r-sp)
+       ("r-vcd" ,r-vcd)))
+    (home-page "https://github.com/alexkowa/VIM")
+    (synopsis "Visualization and imputation of missing values")
+    (description
+     "This package provides tools for the visualization of missing and/or
+imputed values are introduced, which can be used for exploring the data and
+the structure of the missing and/or imputed values.  Depending on this
+structure of the missing values, the corresponding methods may help to
+identify the mechanism generating the missing values and allows to explore the
+data including missing values.  In addition, the quality of imputation can be
+visually explored using various univariate, bivariate, multiple and
+multivariate plot methods.")
+    (license license:gpl2+)))
-- 
cgit 1.4.1


From d10b0952ce6be1c4f172b21622184e59bb3e1020 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:44 +0100
Subject: gnu: Add r-fnn.

* gnu/packages/cran.scm (r-fnn): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index efb612e34f..81b791d346 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3146,3 +3146,26 @@ data including missing values.  In addition, the quality of imputation can be
 visually explored using various univariate, bivariate, multiple and
 multivariate plot methods.")
     (license license:gpl2+)))
+
+(define-public r-fnn
+  (package
+    (name "r-fnn")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FNN" version))
+       (sha256
+        (base32
+         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+    (properties `((upstream-name . "FNN")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (synopsis "Fast nearest neighbor search algorithms and applications")
+    (description
+     "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms.  Related applications including KNN classification,
+regression and information measures are implemented.")
+    ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
+    ;; later can be used.
+    (license license:gpl2+)))
-- 
cgit 1.4.1


From be815dbdda155e1e920667a1c34bf264cb20f5b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:53 +0100
Subject: gnu: Add r-smoother.

* gnu/packages/cran.scm (r-smoother): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 81b791d346..4e3a036044 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3169,3 +3169,26 @@ regression and information measures are implemented.")
     ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
     ;; later can be used.
     (license license:gpl2+)))
+
+(define-public r-smoother
+  (package
+    (name "r-smoother")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "smoother" version))
+       (sha256
+        (base32
+         "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ttr" ,r-ttr)))
+    (home-page "http://cran.r-project.org/web/packages/smoother")
+    (synopsis "Functions relating to the smoothing of numerical data")
+    (description
+     "This package provides a collection of methods for smoothing numerical
+data, commencing with a port of the Matlab gaussian window smoothing function.
+In addition, several functions typically used in smoothing of financial data
+are included.")
+    (license license:gpl2)))
-- 
cgit 1.4.1


From 1b5905fe689716e73ad7defc1bf8c6a13966f3c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:38:41 +0100
Subject: gnu: r-fnn: Remove duplicate definition.

* gnu/packages/cran.scm (r-fnn)[home-page]: Use HTTPS.
* gnu/packages/statistics.scm (r-fnn): Remove.
---
 gnu/packages/cran.scm       |  2 +-
 gnu/packages/statistics.scm | 21 ---------------------
 2 files changed, 1 insertion(+), 22 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4e3a036044..9b690833ce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3160,7 +3160,7 @@ multivariate plot methods.")
          "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
     (properties `((upstream-name . "FNN")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (home-page "https://cran.r-project.org/web/packages/FNN")
     (synopsis "Fast nearest neighbor search algorithms and applications")
     (description
      "This package provides cover-tree and kd-tree fast k-nearest neighbor
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7722cb3aa0..1324abd1f5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4906,27 +4906,6 @@ functions apply.  The implementation can easily be added to functions where
 showing the progress is useful e.g. bootstrap.")
     (license license:gpl2)))
 
-(define-public r-fnn
-  (package
-    (name "r-fnn")
-    (version "1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "FNN" version))
-       (sha256
-        (base32
-         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
-    (properties `((upstream-name . "FNN")))
-    (build-system r-build-system)
-    (home-page "https://cran.r-project.org/web/packages/FNN")
-    (synopsis "Fast nearest neighbor search algorithms and applications")
-    (description
-     "This package provides cover-tree and kd-tree fast k-nearest neighbor
-search algorithms and related applications including KNN classification,
-regression and information measures.")
-    (license license:gpl2+)))
-
 (define-public r-minqa
   (package
     (name "r-minqa")
-- 
cgit 1.4.1


From 0efd09acd402e1d333e21df35fe64cb9ee8d6811 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Mar 2018 19:57:35 +0100
Subject: gnu: Add r-riverplot.

* gnu/packages/cran.scm (r-riverplot): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9b690833ce..b7126518c1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3192,3 +3192,25 @@ data, commencing with a port of the Matlab gaussian window smoothing function.
 In addition, several functions typically used in smoothing of financial data
 are included.")
     (license license:gpl2)))
+
+(define-public r-riverplot
+  (package
+    (name "r-riverplot")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "riverplot" version))
+       (sha256
+        (base32
+         "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
+    (build-system r-build-system)
+    (home-page "https://logfc.wordpress.com")
+    (synopsis "Sankey or ribbon plots")
+    (description
+     "Sankey plots are a type of diagram that is convenient to illustrate how
+flow of information, resources etc. separates and joins, much like observing
+how rivers split and merge.  For example, they can be used to compare
+different clusterings.  This package provides an implementation of Sankey
+plots for R.")
+    (license license:gpl2+)))
-- 
cgit 1.4.1


From 5ade82bbb8c768861d8dc6f12d07b661e6f92f73 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 15 Mar 2018 04:03:27 +0100
Subject: gnu: r-scatterplot3d: Update to 0.3-41.

* gnu/packages/cran.scm (r-scatterplot3d): Update to 0.3-41.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b7126518c1..9b045c122f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1809,14 +1809,14 @@ statistics, etc.")
 (define-public r-scatterplot3d
   (package
     (name "r-scatterplot3d")
-    (version "0.3-40")
+    (version "0.3-41")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterplot3d" version))
        (sha256
         (base32
-         "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2"))))
+         "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
     (synopsis "3D scatter plot")
-- 
cgit 1.4.1


From d062957a8797d1bd6cc44bdc94259051f42afaab Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 15 Mar 2018 20:29:14 +0100
Subject: gnu: Use HTTPS for r-project.org home pages.

* gnu/packages/cran.scm (r-performanceanalytics, r-qap, r-gclus, r-leaps)
(r-splus2r, r-ifultools, r-sapa, r-quantmod, r-tseries, r-wmtsa, r-fractal)
(r-urca, r-trend, r-expm, r-complexplus, r-powerplus, r-signal, r-abind)
(r-prroc)[home-page]: Use HTTPS.
* gnu/packages/emacs.scm (emacs-ess)[home-page]: Likewise.
* gnu/packages/graph.scm (r-diffusionmap)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-minimal, r-quantreg)[home-page]: Likewise.
---
 gnu/packages/cran.scm       | 38 +++++++++++++++++++-------------------
 gnu/packages/emacs.scm      |  2 +-
 gnu/packages/graph.scm      |  2 +-
 gnu/packages/statistics.scm |  4 ++--
 4 files changed, 23 insertions(+), 23 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9b045c122f..717fa7fdfa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1679,7 +1679,7 @@ simplifying cross-class interoperability.")
      `(("r-quadprog" ,r-quadprog)
        ("r-xts" ,r-xts)
        ("r-zoo" ,r-zoo)))
-    (home-page "http://r-forge.r-project.org/projects/returnanalytics/")
+    (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
     (synopsis "Econometric tools for performance and risk analysis")
     (description "This is a collection of econometric functions for
 performance and risk analysis.  This package aims to aid practitioners and
@@ -1996,7 +1996,7 @@ traveling salesman problem).")
          "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/qap/")
+    (home-page "https://cran.r-project.org/web/packages/qap/")
     (synopsis "Heuristics for the quadratic assignment problem (QAP)")
     (description "This package implements heuristics for the @dfn{quadratic
 assignment problem} (QAP).  Currently only a simulated annealing heuristic is
@@ -2016,7 +2016,7 @@ available.")
          "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-cluster" ,r-cluster)))
-    (home-page "http://cran.r-project.org/web/packages/gclus/")
+    (home-page "https://cran.r-project.org/web/packages/gclus/")
     (synopsis "Clustering graphics")
     (description "This package orders panels in scatterplot matrices and
 parallel coordinate displays by some merit index.  It contains various indices
@@ -2355,7 +2355,7 @@ rules with R.")
          "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/leaps/")
+    (home-page "https://cran.r-project.org/web/packages/leaps/")
     (synopsis "Regression subset selection")
     (description
      "This package provides tools for regression subset selection, including
@@ -2376,7 +2376,7 @@ exhaustive search.")
     (properties `((upstream-name . "splus2R")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/splus2R/")
+    (home-page "https://cran.r-project.org/web/packages/splus2R/")
     (synopsis "Supplemental S-PLUS functionality in R")
     (description
      "Currently there are many functions in S-PLUS that are missing in R.  To
@@ -2399,7 +2399,7 @@ provides some missing S-PLUS functionality in R.")
     (propagated-inputs
      `(("r-mass" ,r-mass)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/ifultools/")
+    (home-page "https://cran.r-project.org/web/packages/ifultools/")
     (synopsis "Insightful research tools")
     (description "This package provides C code used by the wmtsa, fractal, and
 sapa R packages.")
@@ -2420,7 +2420,7 @@ sapa R packages.")
     (propagated-inputs
      `(("r-ifultools" ,r-ifultools)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/sapa/")
+    (home-page "https://cran.r-project.org/web/packages/sapa/")
     (synopsis "Spectral analysis for physical applications")
     (description "This package provides software for the book Spectral
 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
@@ -2444,7 +2444,7 @@ Cambridge University Press, 1993.")
        ("r-ttr" ,r-ttr)
        ("r-xts" ,r-xts)
        ("r-zoo" ,r-zoo)))
-    (home-page "http://cran.r-project.org/web/packages/quantmod/")
+    (home-page "https://cran.r-project.org/web/packages/quantmod/")
     (synopsis "Quantitative financial modelling framework")
     (description "This package provides a quantitative financial modelling
 framework to allow users to specify, build, trade, and analyse quantitative
@@ -2469,7 +2469,7 @@ financial trading strategies.")
        ("r-zoo" ,r-zoo)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/tseries/")
+    (home-page "https://cran.r-project.org/web/packages/tseries/")
     (synopsis "Time series analysis and computational finance")
     (description
      "This package provides functions relating to time series analysis and
@@ -2492,7 +2492,7 @@ computational finance.")
      `(("r-ifultools" ,r-ifultools)
        ("r-mass" ,r-mass)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/wmtsa/")
+    (home-page "https://cran.r-project.org/web/packages/wmtsa/")
     (synopsis "Wavelet methods for time series analysis")
     (description
      "This package provides software to accompany the book \"Wavelet Methods
@@ -2568,7 +2568,7 @@ multivariate distributions.")
        ("r-scatterplot3d" ,r-scatterplot3d)
        ("r-splus2r" ,r-splus2r)
        ("r-wmtsa" ,r-wmtsa)))
-    (home-page "http://cran.r-project.org/web/packages/fractal/")
+    (home-page "https://cran.r-project.org/web/packages/fractal/")
     (synopsis "Fractal time series modeling and analysis")
     (description
      "This package provides tools for stochastic fractal and deterministic
@@ -2589,7 +2589,7 @@ chaotic time series analysis.")
     (build-system r-build-system)
     (propagated-inputs `(("r-nlme" ,r-nlme)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/urca/")
+    (home-page "https://cran.r-project.org/web/packages/urca/")
     (synopsis "Unit root and cointegration tests for time series data")
     (description
      "This package provides unit root and cointegration tests encountered in
@@ -2637,7 +2637,7 @@ interface.")
      `(("r-extradistr" ,r-extradistr)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/trend/")
+    (home-page "https://cran.r-project.org/web/packages/trend/")
     (synopsis "Non-parametric trend tests and change-point detection")
     (description
      "The analysis of environmental data often requires the detection of
@@ -2666,7 +2666,7 @@ sample Robust Rank-Order Distributional Test.")
     (build-system r-build-system)
     (propagated-inputs `(("r-matrix" ,r-matrix)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://r-forge.r-project.org/projects/expm/")
+    (home-page "https://r-forge.r-project.org/projects/expm/")
     (synopsis "Tools for matrix exponentials and related quantities")
     (description
      "This package provides tools for the computation of the matrix
@@ -2688,7 +2688,7 @@ exponential, logarithm, square root, and related quantities.")
     (propagated-inputs
      `(("r-expm" ,r-expm)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://cran.r-project.org/web/packages/complexplus/")
+    (home-page "https://cran.r-project.org/web/packages/complexplus/")
     (synopsis "Functions of complex or real variables")
     (description
      "This package extends several functions to the complex domain, including
@@ -2759,7 +2759,7 @@ ordered factor data types.")
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
        ("r-phontools" ,r-phontools)))
-    (home-page "http://cran.r-project.org/web/packages/powerplus/")
+    (home-page "https://cran.r-project.org/web/packages/powerplus/")
     (synopsis "Exponentiation operations")
     (description
      "This package provides tools for the computation of matrix and scalar
@@ -2966,7 +2966,7 @@ and within plot factors interact.")
     (build-system r-build-system)
     (propagated-inputs `(("r-mass" ,r-mass)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/signal/")
+    (home-page "https://cran.r-project.org/web/packages/signal/")
     (synopsis "Signal processing")
     (description
      "This package provides a set of signal processing functions originally
@@ -3075,7 +3075,7 @@ R itself can handle.")
         (base32
          "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/abind/")
+    (home-page "https://cran.r-project.org/web/packages/abind/")
     (synopsis "Combine multidimensional arrays")
     (description
      "This package provides tools to combine multidimensional arrays into a
@@ -3098,7 +3098,7 @@ extracting and replacing data in arrays.")
          "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc"))))
     (properties `((upstream-name . "PRROC")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/PRROC/")
+    (home-page "https://cran.r-project.org/web/packages/PRROC/")
     (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
     (description
      "This package computes the areas under the @dfn{precision-recall} (PR)
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index a6c674dfb2..da366441bd 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3773,7 +3773,7 @@ programming language.")
                                         texlive-latex-seminar
                                         texlive-latex-hyperref
                                         texlive-tex-texinfo)))))
-    (home-page "http://ess.r-project.org/")
+    (home-page "https://ess.r-project.org/")
     (synopsis "Emacs mode for statistical analysis programs")
     (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
 Emacs.  It is designed to support editing of scripts and interaction with
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 6a5e0e753f..38924e42b2 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -142,7 +142,7 @@ more.")
      `(("r-igraph" ,r-igraph)
        ("r-matrix" ,r-matrix)
        ("r-scatterplot3d" ,r-scatterplot3d)))
-    (home-page "http://www.r-project.org")
+    (home-page "https://www.r-project.org")
     (synopsis "Diffusion map")
     (description "This package implements the diffusion map method of data
 parametrization, including creation and visualization of diffusion maps,
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 78afb77a8b..8afccb0737 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -271,7 +271,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
      (list (search-path-specification
             (variable "R_LIBS_SITE")
             (files (list "site-library/")))))
-    (home-page "http://www.r-project.org/")
+    (home-page "https://www.r-project.org/")
     (synopsis "Environment for statistical computing and graphics")
     (description
      "R is a language and environment for statistical computing and graphics.
@@ -5018,7 +5018,7 @@ using modular prediction and response module classes.")
      `(("r-matrix" ,r-matrix)
        ("r-matrixmodels" ,r-matrixmodels)
        ("r-sparsem" ,r-sparsem)))
-    (home-page "http://www.r-project.org")
+    (home-page "https://www.r-project.org")
     (synopsis "Quantile regression")
     (description
      "This package provides an estimation and inference methods for models
-- 
cgit 1.4.1