From ba4fcea499c74515925f2bc6a414ba64fff7754c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 13:26:01 +0100
Subject: gnu: r-desolve: Update description.

* gnu/packages/cran.scm (r-desolve)[description]: Use texinfo syntax.
---
 gnu/packages/cran.scm | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ad8c6ebe67..c2f0e156bd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15940,16 +15940,17 @@ programming problems.")
      `(("gfortran" ,gfortran)))
     (home-page "https://desolve.r-forge.r-project.org/")
     (synopsis "Solvers for initial value problems of differential equations")
-    (description "This package provides functions that solve initial
-value problems of a system of first-order ordinary differential equations (ODE),
-of partial differential equations (PDE), of differential algebraic equations
-(DAE), and of delay differential equations.  The functions provide an interface
-to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
-to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
-the Runge-Kutta family with fixed or variable time steps.  The package contains
-routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
-differential equations (PDE) that have been converted to ODEs by numerical
-differencing.")
+    (description "This package provides functions that solve initial value
+problems of a system of first-order @dfn{ordinary differential
+equations} (ODE), of @dfn{partial differential equations} (PDE), of
+@dfn{differential algebraic equations} (DAE), and of delay differential
+equations.  The functions provide an interface to the FORTRAN functions
+@code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
+collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
+C-implementation of solvers of the Runge-Kutta family with fixed or variable
+time steps.  The package contains routines designed for solving ODEs resulting
+from 1-D, 2-D and 3-D partial differential equations that have been converted
+to ODEs by numerical differencing.")
     (license license:gpl2+)))
 
 (define-public r-pracma
-- 
cgit v1.2.3


From e44c4cd73cfb256c97a0f14f8b3731b35b024dd8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 13:30:58 +0100
Subject: gnu: Add r-bio3d.

* gnu/packages/cran.scm (r-bio3d): 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 c2f0e156bd..1c3d40d76c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16013,3 +16013,34 @@ graphics directly in the terminal window.  This package provides a basic
 plotting function (and equivalents of curve, density, acf and barplot) as well
 as a boxplot function.")
     (license license:lgpl3+)))
+
+(define-public r-bio3d
+  (package
+    (name "r-bio3d")
+    (version "2.4-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bio3d" version))
+       (sha256
+        (base32
+         "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
+    (properties `((upstream-name . "bio3d")))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "http://thegrantlab.org/bio3d/")
+    (synopsis "Biological structure analysis")
+    (description
+     "This package provides utilities to process, organize and explore protein
+structure, sequence and dynamics data.  Features include the ability to read
+and write structure, sequence and dynamic trajectory data, perform sequence
+and structure database searches, data summaries, atom selection, alignment,
+superposition, rigid core identification, clustering, torsion analysis,
+distance matrix analysis, structure and sequence conservation analysis, normal
+mode analysis, principal component analysis of heterogeneous structure data,
+and correlation network analysis from normal mode and molecular dynamics data.
+In addition, various utility functions are provided to enable the statistical
+and graphical power of the R environment to work with biological sequence and
+structural data.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From db07641a676cf057597fb2e08bac7e391cb846d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 13:31:20 +0100
Subject: gnu: Add r-bios2cor.

* gnu/packages/cran.scm (r-bios2cor): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1c3d40d76c..d6013d3b9f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16044,3 +16044,36 @@ In addition, various utility functions are provided to enable the statistical
 and graphical power of the R environment to work with biological sequence and
 structural data.")
     (license license:gpl2+)))
+
+(define-public r-bios2cor
+  (package
+    (name "r-bios2cor")
+    (version "2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Bios2cor" version))
+       (sha256
+        (base32
+         "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
+    (properties `((upstream-name . "Bios2cor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bigmemory" ,r-bigmemory)
+       ("r-bio3d" ,r-bio3d)
+       ("r-circular" ,r-circular)
+       ("r-igraph" ,r-igraph)))
+    (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
+    (synopsis "From biological sequences and simulations to correlation analysis")
+    (description
+     "This package provides utilities for computation and analysis of
+correlation/covariation in multiple sequence alignments and in side chain
+motions during molecular dynamics simulations.  Features include the
+computation of correlation/covariation scores using a variety of scoring
+functions between either sequence positions in alignments or side chain
+dihedral angles in molecular dynamics simulations and utilities to analyze the
+correlation/covariation matrix through a variety of tools including network
+representation and principal components analysis.  In addition, several
+utility functions are based on the R graphical environment to provide friendly
+tools for help in data interpretation.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 59beb0d23feaa046646bfcc84acb121d10fb2fb0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 13:49:24 +0100
Subject: gnu: Add r-networkd3.

* gnu/packages/cran.scm (r-networkd3): New variable.
---
 gnu/packages/cran.scm | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d6013d3b9f..984b8b8858 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16077,3 +16077,69 @@ representation and principal components analysis.  In addition, several
 utility functions are based on the R graphical environment to provide friendly
 tools for help in data interpretation.")
     (license license:gpl2+)))
+
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-networkd3
+  (package
+    (name "r-networkd3")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "networkD3" version))
+       (sha256
+        (base32
+         "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
+       (snippet
+        '(begin
+           (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
+           #t))))
+    (properties `((upstream-name . "networkD3")))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'process-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst/htmlwidgets/lib/"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "d3.v4.js")
+                         "d3-4.5.0/d3.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ;; NOTE: Make sure that this version of d3 is still valid when
+       ;; upgrading the package.
+       ("d3.v4.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://d3js.org/d3.v4.js")
+           (sha256
+            (base32
+             "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+    (propagated-inputs
+     `(("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)))
+    (home-page "https://cran.r-project.org/package=networkD3")
+    (synopsis "D3 JavaScript network graphs from R")
+    (description
+     "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
+graphs from R.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 303c7d1dff7e0a2f91591489c83fb0dfa15ca8a8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 13:57:37 +0100
Subject: gnu: Add r-aasea.

* gnu/packages/cran.scm (r-aasea): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 984b8b8858..3b7cb48038 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16143,3 +16143,35 @@ tools for help in data interpretation.")
      "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
 graphs from R.")
     (license license:gpl3+)))
+
+(define-public r-aasea
+  (package
+    (name "r-aasea")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aaSEA" version))
+       (sha256
+        (base32
+         "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
+    (properties `((upstream-name . "aaSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bios2cor" ,r-bios2cor)
+       ("r-dt" ,r-dt)
+       ("r-hmisc" ,r-hmisc)
+       ("r-magrittr" ,r-magrittr)
+       ("r-networkd3" ,r-networkd3)
+       ("r-plotly" ,r-plotly)
+       ("r-seqinr" ,r-seqinr)
+       ("r-shiny" ,r-shiny)
+       ("r-shinydashboard" ,r-shinydashboard)))
+    (home-page "https://cran.r-project.org/web/packages/aaSEA/")
+    (synopsis "Amino acid substitution effect analyzer")
+    (description
+     "Given a protein multiple sequence alignment, it is a daunting task to
+assess the effects of substitutions along sequence length.  The aaSEA package
+is intended to help researchers to rapidly analyze property changes caused by
+single, multiple and correlated amino acid substitutions in proteins.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From c20a81eed1b22b4cec136f78925bcc4d2be2393f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 15:22:10 +0100
Subject: gnu: Add r-fastmap.

* gnu/packages/cran.scm (r-fastmap): 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 3b7cb48038..de66afcabc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -729,6 +729,30 @@ objects in HTML format.")
 and vice-versa.")
     (license license:gpl2+)))
 
+(define-public r-fastmap
+  (package
+    (name "r-fastmap")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fastmap" version))
+       (sha256
+        (base32
+         "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
+    (properties `((upstream-name . "fastmap")))
+    (build-system r-build-system)
+    (home-page "https://r-lib.github.io/fastmap/")
+    (synopsis "Fast implementation of a key-value store")
+    (description
+     "This package provides a fast implementation of a key-value store.
+Environments are commonly used as key-value stores, but every time a new key
+is used, it is added to R's global symbol table, causing a small amount of
+memory leakage.  This can be problematic in cases where many different keys
+are used.  Fastmap avoids this memory leak issue by implementing the map using
+data structures in C++.")
+    (license license:expat)))
+
 (define-public r-shiny
   (package
     (name "r-shiny")
-- 
cgit v1.2.3


From 6e6fa954af3515c093821362450dc4e94db65ead Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 15:22:30 +0100
Subject: gnu: r-shiny: Update to 1.4.0.

* gnu/packages/cran.scm (r-shiny): Update to 1.4.0.
[arguments]: Update list of JavaScript files to replace.
[propagated-inputs]: Add r-fastmap.
---
 gnu/packages/cran.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de66afcabc..ad7cff55a5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -756,7 +756,7 @@ data structures in C++.")
 (define-public r-shiny
   (package
     (name "r-shiny")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method git-fetch)
@@ -766,7 +766,7 @@ data structures in C++.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
+         "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
     (build-system r-build-system)
     (arguments
      `(#:modules ((guix build r-build-system)
@@ -795,7 +795,7 @@ data structures in C++.")
                                               "/share/javascript/html5shiv.min.js"))
                  (replace-file "json2-min.js"
                                (string-append (assoc-ref inputs "js-json2")
-                                              "/share/javascript/json2.min.js"))
+                                              "/share/javascript/json2-min.js"))
                  (replace-file "strftime/strftime-min.js"
                                (string-append (assoc-ref inputs "js-strftime")
                                               "/share/javascript/strftime.min.js"))
@@ -826,10 +826,15 @@ data structures in C++.")
                              ("shiny.js" .
                               "shiny.min.js")
                              ("jquery.js" .
-                              "jquery.min.js")))))
+                              "jquery.min.js")
+                             ("legacy/jquery.js" .
+                              "legacy/jquery.min.js")
+                             ("showdown/src/showdown.js" .
+                              "showdown/compressed/showdown.js")))))
              #t)))))
     (propagated-inputs
      `(("r-crayon" ,r-crayon)
+       ("r-fastmap" ,r-fastmap)
        ("r-httpuv" ,r-httpuv)
        ("r-mime" ,r-mime)
        ("r-jsonlite" ,r-jsonlite)
-- 
cgit v1.2.3


From 595d9502238947e276eb49c63b74b519537a81d5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 15:14:01 +0100
Subject: gnu: Add r-abacus.

* gnu/packages/cran.scm (r-abacus): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ad7cff55a5..d06d1d2d5d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16204,3 +16204,28 @@ assess the effects of substitutions along sequence length.  The aaSEA package
 is intended to help researchers to rapidly analyze property changes caused by
 single, multiple and correlated amino acid substitutions in proteins.")
     (license license:gpl3)))
+
+(define-public r-abacus
+  (package
+    (name "r-abacus")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ABACUS" version))
+       (sha256
+        (base32
+         "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
+    (properties `((upstream-name . "ABACUS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
+    (synopsis "Apps-based activities for communicating and understanding statistics")
+    (description
+     "This package provides a set of Shiny apps for effective communication
+and understanding in statistics.  The current version includes properties of
+normal distribution, properties of sampling distribution, one-sample z and t
+tests, two samples independent (unpaired) t test and analysis of variance.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 8fed766a7d3988ec39861c546507b945da9c84d9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:38:43 +0100
Subject: gnu: Add r-abc-rap.

* gnu/packages/cran.scm (r-abc-rap): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d06d1d2d5d..8916e50f10 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16229,3 +16229,24 @@ and understanding in statistics.  The current version includes properties of
 normal distribution, properties of sampling distribution, one-sample z and t
 tests, two samples independent (unpaired) t test and analysis of variance.")
     (license license:gpl3)))
+
+(define-public r-abc-rap
+  (package
+    (name "r-abc-rap")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ABC.RAP" version))
+       (sha256
+        (base32
+         "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
+    (properties `((upstream-name . "ABC.RAP")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
+    (synopsis "Array-based CpG region analysis pipeline")
+    (description
+     "This package aims to identify candidate genes that are differentially
+methylated between cases and controls.  It applies Student's t-test and delta
+beta analysis to identify candidate genes containing multiple CpG sites.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 647ff4a98b422028c162fb4f861ad9d323a4cadf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:40:40 +0100
Subject: gnu: Add r-abcadm.

* gnu/packages/cran.scm (r-abcadm): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8916e50f10..b7555f959c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16250,3 +16250,28 @@ tests, two samples independent (unpaired) t test and analysis of variance.")
 methylated between cases and controls.  It applies Student's t-test and delta
 beta analysis to identify candidate genes containing multiple CpG sites.")
     (license license:gpl3)))
+
+(define-public r-abcadm
+  (package
+    (name "r-abcadm")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abcADM" version))
+       (sha256
+        (base32
+         "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
+    (properties `((upstream-name . "abcADM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/abcADM/")
+    (synopsis "Fit accumulated damage models and estimate reliability using ABC")
+    (description
+     "This package provides tools to estimate parameters of accumulated
+damage (load duration) models based on failure time data under a Bayesian
+framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
+long-term reliability under stochastic load profiles.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 72e5c6e95f1b16b08a8d69680833f7ce15b8e50f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:42:35 +0100
Subject: gnu: Add r-rglpk.

* gnu/packages/cran.scm (r-rglpk): 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 b7555f959c..d6891ce6c3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16275,3 +16275,29 @@ damage (load duration) models based on failure time data under a Bayesian
 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
 long-term reliability under stochastic load profiles.")
     (license license:gpl3)))
+
+(define-public r-rglpk
+  (package
+    (name "r-rglpk")
+    (version "0.6-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Rglpk" version))
+       (sha256
+        (base32
+         "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
+    (properties `((upstream-name . "Rglpk")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-slam" ,r-slam)))
+    (inputs
+     `(("glpk" ,glpk)))
+    (home-page "http://R-Forge.R-project.org/projects/rglp/")
+    (synopsis "R interface to the GNU Linear Programming Kit")
+    (description
+     "This package provides an R interface to the GNU Linear Programming Kit,
+software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
+integer linear programming} (MILP) and other related problems.")
+    ;; Either license
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 84822497c2b7854ab16c35599c11edba3fa84b7a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:43:02 +0100
Subject: gnu: Add r-abcdefba.

* gnu/packages/cran.scm (r-abcdefba): 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 d6891ce6c3..c3b9a56c81 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16301,3 +16301,29 @@ software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
 integer linear programming} (MILP) and other related problems.")
     ;; Either license
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-abcdefba
+  (package
+    (name "r-abcdefba")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abcdeFBA" version))
+       (sha256
+        (base32
+         "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
+    (properties `((upstream-name . "abcdeFBA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-corrplot" ,r-corrplot)
+       ("r-lattice" ,r-lattice)
+       ("r-rgl" ,r-rgl)
+       ("r-rglpk" ,r-rglpk)))
+    (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
+    (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
+    (description
+     "This package provides functions for Constraint Based Simulation using
+Flux Balance Analysis and informative analysis of the data generated during
+simulation.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From ae07172c659796f07d9ad878c33be6a7c79ec6ee Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:45:50 +0100
Subject: gnu: Add r-abcrlda.

* gnu/packages/cran.scm (r-abcrlda): 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 c3b9a56c81..6432af9392 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16327,3 +16327,26 @@ integer linear programming} (MILP) and other related problems.")
 Flux Balance Analysis and informative analysis of the data generated during
 simulation.")
     (license license:gpl2)))
+
+(define-public r-abcrlda
+  (package
+    (name "r-abcrlda")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abcrlda" version))
+       (sha256
+        (base32
+         "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
+    (properties `((upstream-name . "abcrlda")))
+    (build-system r-build-system)
+    (home-page "https://ieeexplore.ieee.org/document/8720003/")
+    (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
+    (description
+     "This package offers methods to perform @dfn{asymptotically
+bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
+cost-sensitive binary classification.  The bias-correction is an estimate of
+the bias term added to regularized discriminant analysis that minimizes the
+overall risk.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 3e33377767b9b2cd3a37724cae364c317698317d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 16:47:10 +0100
Subject: gnu: Add r-abemus.

* gnu/packages/cran.scm (r-abemus): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6432af9392..21a51a6d9f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16350,3 +16350,28 @@ cost-sensitive binary classification.  The bias-correction is an estimate of
 the bias term added to regularized discriminant analysis that minimizes the
 overall risk.")
     (license license:gpl3)))
+
+(define-public r-abemus
+  (package
+    (name "r-abemus")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abemus" version))
+       (sha256
+        (base32
+         "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
+    (properties `((upstream-name . "abemus")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)))
+    (home-page "https://cran.r-project.org/web/packages/abemus/")
+    (synopsis "Adaptive base error model in ultra-deep sequencing data")
+    (description
+     "This package provides an implementation of @dfn{Adaptive Base Error
+Model in Ultra-deep Sequencing data} (ABEMUS), which combines
+platform-specific genetic knowledge and empirical signal to readily detect and
+quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
+cell free DNA} (cfDNA).")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 8990fc1584ce2270063774e098ebf2ac8090c32d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:26:01 +0100
Subject: gnu: Add r-rintrojs.

* gnu/packages/cran.scm (r-rintrojs): New variable.
---
 gnu/packages/cran.scm | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 21a51a6d9f..d4bfcfaaa0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16375,3 +16375,65 @@ platform-specific genetic knowledge and empirical signal to readily detect and
 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
 cell free DNA} (cfDNA).")
     (license license:gpl3)))
+
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-rintrojs
+  (package
+    (name "r-rintrojs")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rintrojs" version))
+       (sha256
+        (base32
+         "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
+    (properties `((upstream-name . "rintrojs")))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'process-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst/javascript/introjs/"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "intro.js")
+                         "intro.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ("intro.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
+           (sha256
+            (base32
+             "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
+    (propagated-inputs
+     `(("r-jsonlite" ,r-jsonlite)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://github.com/carlganz/rintrojs")
+    (synopsis "Wrapper for the Intro.js library")
+    (description
+     "This package provides a wrapper for the @url{http://www.introjs.com,
+Intro.js} library.  This package makes it easy to include step-by-step
+introductions, and clickable hints in a Shiny application.  It supports both
+static introductions in the UI, and programmatic introductions from the
+server-side.")
+    (license license:agpl3+)))
-- 
cgit v1.2.3


From 322e8d85798f32bc0a4f5bf30d4896931046780d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:26:59 +0100
Subject: gnu: Add r-sysfonts.

* gnu/packages/cran.scm (r-sysfonts): 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 d4bfcfaaa0..2838dcb37a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16437,3 +16437,29 @@ introductions, and clickable hints in a Shiny application.  It supports both
 static introductions in the UI, and programmatic introductions from the
 server-side.")
     (license license:agpl3+)))
+
+(define-public r-sysfonts
+  (package
+    (name "r-sysfonts")
+    (version "0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sysfonts" version))
+       (sha256
+        (base32
+         "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
+    (properties `((upstream-name . "sysfonts")))
+    (build-system r-build-system)
+    (inputs
+     `(("freetype" ,freetype)
+       ("libpng" ,libpng)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/yixuan/sysfonts")
+    (synopsis "Loading fonts into R")
+    (description
+     "This is a package to simplify loading of system fonts and Google Fonts
+into R, in order to support other packages.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 369e1bb6a89695280b4a47acdd3ac9eb4f935085 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:28:36 +0100
Subject: gnu: Add r-showtextdb.

* gnu/packages/cran.scm (r-showtextdb): 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 2838dcb37a..c4f1586f64 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16463,3 +16463,25 @@ server-side.")
      "This is a package to simplify loading of system fonts and Google Fonts
 into R, in order to support other packages.")
     (license license:gpl2)))
+
+(define-public r-showtextdb
+  (package
+    (name "r-showtextdb")
+    (version "2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "showtextdb" version))
+       (sha256
+        (base32
+         "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
+    (properties `((upstream-name . "showtextdb")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-sysfonts" ,r-sysfonts)))
+    (home-page "https://cran.r-project.org/web/packages/showtextdb/")
+    (synopsis "Font files for the 'showtext' package")
+    (description
+     "This package provides font files that can be used by the @code{showtext}
+package.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From d7937243bad6ffb204b98521c8cdda0f7864bf5a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:28:53 +0100
Subject: gnu: Add r-showtext.

* gnu/packages/cran.scm (r-showtext): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c4f1586f64..cddf78951d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16485,3 +16485,35 @@ into R, in order to support other packages.")
      "This package provides font files that can be used by the @code{showtext}
 package.")
     (license license:asl2.0)))
+
+(define-public r-showtext
+  (package
+    (name "r-showtext")
+    (version "0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "showtext" version))
+       (sha256
+        (base32
+         "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
+    (properties `((upstream-name . "showtext")))
+    (build-system r-build-system)
+    (inputs
+     `(("freetype" ,freetype)
+       ("libpng" ,libpng)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-showtextdb" ,r-showtextdb)
+       ("r-sysfonts" ,r-sysfonts)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/yixuan/showtext")
+    (synopsis "Using fonts more easily in R graphs")
+    (description
+     "This package aims to make it easy to use various types of
+fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
+most output formats of R graphics including PNG, PDF and SVG.  Text glyphs
+will be converted into polygons or raster images, hence after the plot has
+been created, it no longer relies on the font files.  No external software
+such as Ghostscript is needed to use this package.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From 2ecd4e3bfdd6fe2d2ca3acbf50d6917af905fee0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:29:58 +0100
Subject: gnu: Add r-emojifont.

* gnu/packages/cran.scm (r-emojifont): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cddf78951d..2101489577 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16517,3 +16517,28 @@ will be converted into polygons or raster images, hence after the plot has
 been created, it no longer relies on the font files.  No external software
 such as Ghostscript is needed to use this package.")
     (license license:asl2.0)))
+
+(define-public r-emojifont
+  (package
+    (name "r-emojifont")
+    (version "0.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "emojifont" version))
+       (sha256
+        (base32
+         "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
+    (properties `((upstream-name . "emojifont")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-proto" ,r-proto)
+       ("r-showtext" ,r-showtext)
+       ("r-sysfonts" ,r-sysfonts)))
+    (home-page "https://guangchuangyu.github.io/emojifont")
+    (synopsis "Emoji and Font Awesome in R graphics")
+    (description
+     "This package enables the use of emoji and the Font Awesome glyphs in
+both base and ggplot2 graphics.")
+    (license license:artistic2.0)))
-- 
cgit v1.2.3


From a99c4c7584fc7e16df0fe3f55d640fa8e1bbed03 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:30:32 +0100
Subject: gnu: Add r-abstractr.

* gnu/packages/cran.scm (r-abstractr): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2101489577..2b318e6090 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16542,3 +16542,32 @@ such as Ghostscript is needed to use this package.")
      "This package enables the use of emoji and the Font Awesome glyphs in
 both base and ggplot2 graphics.")
     (license license:artistic2.0)))
+
+(define-public r-abstractr
+  (package
+    (name "r-abstractr")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abstractr" version))
+       (sha256
+        (base32
+         "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
+    (properties `((upstream-name . "abstractr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colourpicker" ,r-colourpicker)
+       ("r-emojifont" ,r-emojifont)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-rintrojs" ,r-rintrojs)
+       ("r-shiny" ,r-shiny)
+       ("r-shinythemes" ,r-shinythemes)))
+    (home-page "https://matt-kumar.shinyapps.io/portfolio")
+    (synopsis "R-Shiny application for creating visual abstracts")
+    (description
+     "This package provides an R Shiny application to create visual abstracts
+for original research.  A variety of user defined options and formatting are
+included.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From bd74d7e6fc0e4b0c282a3a202b3dbfb4858368d0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:31:07 +0100
Subject: gnu: Add r-abtest.

* gnu/packages/cran.scm (r-abtest): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2b318e6090..f931aa67e3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16571,3 +16571,33 @@ both base and ggplot2 graphics.")
 for original research.  A variety of user defined options and formatting are
 included.")
     (license license:gpl3)))
+
+(define-public r-abtest
+  (package
+    (name "r-abtest")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abtest" version))
+       (sha256
+        (base32
+         "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
+    (properties `((upstream-name . "abtest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-plotrix" ,r-plotrix)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-sn" ,r-sn)
+       ("r-truncnorm" ,r-truncnorm)
+       ("r-vgam" ,r-vgam)))
+    (home-page "https://cran.r-project.org/web/packages/abtest/")
+    (synopsis "Bayesian A/B testing")
+    (description
+     "This package provides functions for Bayesian A/B testing including prior
+elicitation options based on Kass and Vaidyanathan (1992)
+@url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 0379a167612f40e525251f4c1b92c9150405af7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:41:48 +0100
Subject: gnu: Add r-accept.

* gnu/packages/cran.scm (r-accept): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f931aa67e3..385b97adfc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16601,3 +16601,32 @@ included.")
 elicitation options based on Kass and Vaidyanathan (1992)
 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
     (license license:gpl2+)))
+
+(define-public r-accept
+  (package
+    (name "r-accept")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accept" version))
+       (sha256
+        (base32
+         "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
+    (properties `((upstream-name . "accept")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-extrafont" ,r-extrafont)
+       ("r-mass" ,r-mass)
+       ("r-plotly" ,r-plotly)
+       ("r-stringr" ,r-stringr)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://cran.r-project.org/web/packages/accept/")
+    (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
+    (description
+     "This package allows clinicians to predict the rate and severity of
+future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
+Disease} (COPD) patients, based on the clinical prediction model published in
+Adibi et al. (2019) @url{doi:10.1101/651901}.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From bba4ec62e36a6071d978cdb2e5d267f9bc2068c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:42:45 +0100
Subject: gnu: Add r-smpracticals.

* gnu/packages/cran.scm (r-smpracticals): New variable.
---
 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 385b97adfc..2de143ca13 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16630,3 +16630,30 @@ future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
 Disease} (COPD) patients, based on the clinical prediction model published in
 Adibi et al. (2019) @url{doi:10.1101/651901}.")
     (license license:gpl3)))
+
+(define-public r-smpracticals
+  (package
+    (name "r-smpracticals")
+    (version "1.4-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SMPracticals" version))
+       (sha256
+        (base32
+         "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
+    (properties `((upstream-name . "SMPracticals")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ellipse" ,r-ellipse)
+       ("r-mass" ,r-mass)
+       ("r-nlme" ,r-nlme)
+       ("r-survival" ,r-survival)))
+    (home-page "http://statwww.epfl.ch/davison/SM/")
+    (synopsis "Practicals for use with Davison (2003) Statistical Models")
+    (description
+     "This package contains the datasets and a few functions for use with the
+practicals outlined in Appendix A of the book Statistical Models (Davison,
+2003, Cambridge University Press).  The practicals themselves can be found at
+@url{http://statwww.epfl.ch/davison/SM/}.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5a5431e406fb75fef1d80a937e1b4ed605ed30fa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:48:12 +0100
Subject: gnu: Add r-fgui.

* gnu/packages/cran.scm (r-fgui): New variable.
---
 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 2de143ca13..ea9994915d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16657,3 +16657,30 @@ practicals outlined in Appendix A of the book Statistical Models (Davison,
 2003, Cambridge University Press).  The practicals themselves can be found at
 @url{http://statwww.epfl.ch/davison/SM/}.")
     (license license:gpl2+)))
+
+(define-public r-fgui
+  (package
+    (name "r-fgui")
+    (version "1.0-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fgui" version))
+       (sha256
+        (base32
+         "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
+    (properties `((upstream-name . "fgui")))
+    (build-system r-build-system)
+    (home-page
+     "https://sites.google.com/site/thomashoffmannproject/software/fgui")
+    (synopsis "Create GUI for R functions")
+    (description
+     "Rapidly create a GUI for a function you created by automatically
+creating widgets for arguments of the function.  This package automatically
+parses help routines for context-sensitive help to these arguments.  The
+interface is essentially a wrapper to some Tcl/Tk routines to both simplify
+and facilitate GUI creation.  More advanced Tcl/Tk routines/GUI objects can be
+incorporated into the interface for greater customization for the more
+experienced.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))
-- 
cgit v1.2.3


From f9d9c83183c02a6d50fa0b277ec69a897def73bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:48:33 +0100
Subject: gnu: Add r-tcltk2.

* gnu/packages/cran.scm (r-tcltk2): 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 ea9994915d..82403e5b42 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -73,6 +73,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xorg))
@@ -16684,3 +16685,26 @@ incorporated into the interface for greater customization for the more
 experienced.")
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-tcltk2
+  (package
+    (name "r-tcltk2")
+    (version "1.2-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tcltk2" version))
+       (sha256
+        (base32
+         "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
+    (properties `((upstream-name . "tcltk2")))
+    (build-system r-build-system)
+    (inputs
+     `(("tcl" ,tcl)
+       ("tk" ,tk)))
+    (home-page "http://www.sciviews.org/SciViews-R")
+    (synopsis "Tcl/Tk additions")
+    (description
+     "This package provides a series of additional Tcl commands and Tk widgets
+with style and various functions to supplement the tcltk package")
+    (license license:lgpl3)))
-- 
cgit v1.2.3


From c5b86d3a18fc671ee645dc8bfdaaced1a995ab2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:49:05 +0100
Subject: gnu: Add r-accrual.

* gnu/packages/cran.scm (r-accrual): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 82403e5b42..0186fe7a52 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16708,3 +16708,33 @@ experienced.")
      "This package provides a series of additional Tcl commands and Tk widgets
 with style and various functions to supplement the tcltk package")
     (license license:lgpl3)))
+
+(define-public r-accrual
+  (package
+    (name "r-accrual")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accrual" version))
+       (sha256
+        (base32
+         "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
+    (properties `((upstream-name . "accrual")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fgui" ,r-fgui)
+       ("r-smpracticals" ,r-smpracticals)
+       ("r-tcltk2" ,r-tcltk2)))
+    (home-page "https://cran.r-project.org/web/packages/accrual/")
+    (synopsis "Bayesian accrual prediction")
+    (description
+     "Subject recruitment for medical research is challenging.  Slow patient
+accrual leads to delay in research.  Accrual monitoring during the process of
+recruitment is critical.  Researchers need reliable tools to manage the
+accrual rate.  This package provides an implementation of a Bayesian method
+that integrates researcher's experience on previous trials and data from the
+current study, providing reliable prediction on accrual rate for clinical
+studies.  It provides functions for Bayesian accrual prediction which can be
+easily used by statisticians and clinical researchers.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 592d423ca5d751d4dc6beb6b7500228ec6103937 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:49:29 +0100
Subject: gnu: Add r-accrued.

* gnu/packages/cran.scm (r-accrued): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0186fe7a52..7547b176fc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16738,3 +16738,23 @@ current study, providing reliable prediction on accrual rate for clinical
 studies.  It provides functions for Bayesian accrual prediction which can be
 easily used by statisticians and clinical researchers.")
     (license license:gpl2)))
+
+(define-public r-accrued
+  (package
+    (name "r-accrued")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accrued" version))
+       (sha256
+        (base32
+         "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
+    (properties `((upstream-name . "accrued")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/accrued/")
+    (synopsis "Data quality visualization tools for partially accruing data")
+    (description
+     "This is a package for visualizing data quality of partially accruing
+data.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 7e2e46cbe2dd2fe9f90f61dfffdd89e66172ce8e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:49:53 +0100
Subject: gnu: Add r-mda.

* gnu/packages/cran.scm (r-mda): 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 7547b176fc..dcbad9cb12 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16758,3 +16758,25 @@ easily used by statisticians and clinical researchers.")
      "This is a package for visualizing data quality of partially accruing
 data.")
     (license license:gpl3)))
+
+(define-public r-mda
+  (package
+    (name "r-mda")
+    (version "0.4-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mda" version))
+       (sha256
+        (base32
+         "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
+    (properties `((upstream-name . "mda")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-class" ,r-class)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/mda/")
+    (synopsis "Mixture and flexible discriminant analysis")
+    (description
+     "This is a package for mixture and flexible discriminant analysis,
+@dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From c909b710a4ee5021268fc0abbaf324771d6dd63c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:50:09 +0100
Subject: gnu: Add r-elasticnet.

* gnu/packages/cran.scm (r-elasticnet): 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 dcbad9cb12..a92a487059 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16780,3 +16780,26 @@ data.")
      "This is a package for mixture and flexible discriminant analysis,
 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
     (license license:gpl2)))
+
+(define-public r-elasticnet
+  (package
+    (name "r-elasticnet")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "elasticnet" version))
+       (sha256
+        (base32
+         "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
+    (properties `((upstream-name . "elasticnet")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lars" ,r-lars)))
+    (home-page "http://www.stat.umn.edu/~hzou")
+    (synopsis "Elastic-Net for sparse estimation and sparse PCA")
+    (description
+     "This package provides functions for fitting the entire solution path of
+the Elastic-Net and also provides functions for estimating sparse Principal
+Components.  The Lasso solution paths can be computed by the same function.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 7199d2a5fcd4db00314086947285bbe3f5ea8fc3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:50:26 +0100
Subject: gnu: Add r-sparselda.

* gnu/packages/cran.scm (r-sparselda): 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 a92a487059..5c0d44ebf7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16803,3 +16803,27 @@ data.")
 the Elastic-Net and also provides functions for estimating sparse Principal
 Components.  The Lasso solution paths can be computed by the same function.")
     (license license:gpl2+)))
+
+(define-public r-sparselda
+  (package
+    (name "r-sparselda")
+    (version "0.1-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sparseLDA" version))
+       (sha256
+        (base32
+         "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
+    (properties `((upstream-name . "sparseLDA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-elasticnet" ,r-elasticnet)
+       ("r-mass" ,r-mass)
+       ("r-mda" ,r-mda)))
+    (home-page "http://www.imm.dtu.dk/~lhc")
+    (synopsis "Sparse discriminant analysis")
+    (description
+     "This package performs sparse linear discriminant analysis for Gaussians
+and mixture of Gaussian models.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From b8d52fe2771220742bf7e55700d0a91e05d8536c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:50:49 +0100
Subject: gnu: Add r-accsda.

* gnu/packages/cran.scm (r-accsda): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c0d44ebf7..5c530a6a36 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16827,3 +16827,36 @@ Components.  The Lasso solution paths can be computed by the same function.")
      "This package performs sparse linear discriminant analysis for Gaussians
 and mixture of Gaussian models.")
     (license license:gpl2+)))
+
+(define-public r-accsda
+  (package
+    (name "r-accsda")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accSDA" version))
+       (sha256
+        (base32
+         "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
+    (properties `((upstream-name . "accSDA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ggthemes" ,r-ggthemes)
+       ("r-gridextra" ,r-gridextra)
+       ("r-mass" ,r-mass)
+       ("r-rarpack" ,r-rarpack)
+       ("r-sparselda" ,r-sparselda)))
+    (home-page "https://github.com/gumeo/accSDA/wiki")
+    (synopsis "Accelerated sparse discriminant analysis")
+    (description
+     "This package provides an implementation of sparse linear discriminant
+analysis, which is a supervised classification method for multiple classes.
+Various novel optimization approaches to this problem are implemented
+including @dfn{alternating direction method of multipliers} (ADMM),
+@dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
+Functions for performing cross validation are also supplied along with basic
+prediction and plotting functions.  @dfn{Sparse zero variance
+discriminant} (SZVD) analysis is also included in the package.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From b441dac7af3f6fbf8b0a7def117abc0181b52f33 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:51:11 +0100
Subject: gnu: Add r-ace2fastq.

* gnu/packages/cran.scm (r-ace2fastq): 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 5c530a6a36..4b4d1996b7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16860,3 +16860,29 @@ Functions for performing cross validation are also supplied along with basic
 prediction and plotting functions.  @dfn{Sparse zero variance
 discriminant} (SZVD) analysis is also included in the package.")
     (license license:gpl2+)))
+
+(define-public r-ace2fastq
+  (package
+    (name "r-ace2fastq")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ace2fastq" version))
+       (sha256
+        (base32
+         "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
+    (properties `((upstream-name . "ace2fastq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-stringr" ,r-stringr)))
+    (home-page "https://github.com/c5sire/ace2fastq")
+    (synopsis "ACE file to FASTQ converter")
+    (description
+     "The ACE file format is used in genomics to store contigs from sequencing
+machines.  This tools converts it into FASTQ format.  Both formats contain the
+sequence characters and their corresponding quality information.  Unlike the
+FASTQ file, the ACE file stores the quality values numerically.  The
+conversion algorithm uses the standard Sanger formula.  The package
+facilitates insertion into pipelines, and content inspection.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From ca1bc50cad56b45e3db9c42bb9ac3fde288986c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:51:44 +0100
Subject: gnu: Add r-rngwell.

* gnu/packages/cran.scm (r-rngwell): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4b4d1996b7..e823b82e0e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16886,3 +16886,24 @@ FASTQ file, the ACE file stores the quality values numerically.  The
 conversion algorithm uses the standard Sanger formula.  The package
 facilitates insertion into pipelines, and content inspection.")
     (license license:gpl3)))
+
+(define-public r-rngwell
+  (package
+    (name "r-rngwell")
+    (version "0.10-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rngWELL" version))
+       (sha256
+        (base32
+         "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
+    (properties `((upstream-name . "rngWELL")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/rngWELL/")
+    (synopsis "Toolbox for WELL random number generators")
+    (description
+     "This is a dedicated package to WELL pseudo random generators, which were
+introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
+on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From e6bf147293e8cf36aa4090e5b4aa5d653201c9a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:52:39 +0100
Subject: gnu: Add r-randtoolbox.

* gnu/packages/cran.scm (r-randtoolbox): New variable.
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e823b82e0e..ed47472583 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16907,3 +16907,40 @@ facilitates insertion into pipelines, and content inspection.")
 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
     (license license:bsd-3)))
+
+(define-public r-randtoolbox
+  (package
+    (name "r-randtoolbox")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "randtoolbox" version))
+       (sha256
+        (base32
+         "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
+    (properties `((upstream-name . "randtoolbox")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rngwell" ,r-rngwell)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
+    (synopsis "Toolbox for pseudo and quasi random number generation")
+    (description
+     "This package provides
+
+@enumerate
+@item pseudo random generators, such as general linear
+congruential generators, multiple recursive generators and generalized
+feedback shift register (SF-Mersenne Twister algorithm and WELL
+generators)
+
+@item quasi random generators, such as the Torus algorithm, the Sobol
+sequence, the Halton sequence (including the Van der Corput sequence), and
+
+@item some generator tests: the gap test, the serial test, the poker test.
+@end enumerate
+
+See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 390bc8726bbd9625557f1cd02b3853995de34b8f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:53:00 +0100
Subject: gnu: Add r-lhs.

* gnu/packages/cran.scm (r-lhs): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ed47472583..1a09342180 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16944,3 +16944,24 @@ sequence, the Halton sequence (including the Van der Corput sequence), and
 
 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
     (license license:bsd-3)))
+
+(define-public r-lhs
+  (package
+    (name "r-lhs")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lhs" version))
+       (sha256
+        (base32
+         "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
+    (properties `((upstream-name . "lhs")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/bertcarnell/lhs")
+    (synopsis "Latin Hypercube Samples")
+    (description
+     "This package provides a number of methods for creating and augmenting
+Latin Hypercube Samples.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 1442ca73402ba7904830204e59aa2d76bd85af46 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:53:16 +0100
Subject: gnu: Add r-acebayes.

* gnu/packages/cran.scm (r-acebayes): 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 1a09342180..91f842e8f4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16965,3 +16965,34 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
      "This package provides a number of methods for creating and augmenting
 Latin Hypercube Samples.")
     (license license:gpl3)))
+
+(define-public r-acebayes
+  (package
+    (name "r-acebayes")
+    (version "1.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acebayes" version))
+       (sha256
+        (base32
+         "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
+    (properties `((upstream-name . "acebayes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-compare" ,r-compare)
+       ("r-lhs" ,r-lhs)
+       ("r-randtoolbox" ,r-randtoolbox)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/acebayes/")
+    (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
+    (description
+     "Finding an optimal Bayesian experimental design involves maximizing an
+objective function given by the expectation of some appropriately chosen
+utility function with respect to the joint distribution of unknown
+quantities (including responses).  This objective function is usually not
+available in closed form and the design space can be continuous and of high
+dimensionality.  This package uses @dfn{Approximate Coordinate Exchange} (ACE)
+to maximise an approximation to the expectation of the utility function.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 43a70edc291de476d705805230f61458de992f70 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:56:16 +0100
Subject: gnu: Add r-acet.

* gnu/packages/cran.scm (r-acet): 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 91f842e8f4..8c7fe23667 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16996,3 +16996,29 @@ available in closed form and the design space can be continuous and of high
 dimensionality.  This package uses @dfn{Approximate Coordinate Exchange} (ACE)
 to maximise an approximation to the expectation of the utility function.")
     (license license:gpl2)))
+
+(define-public r-acet
+  (package
+    (name "r-acet")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACEt" version))
+       (sha256
+        (base32
+         "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
+    (properties `((upstream-name . "ACEt")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-mass" ,r-mass)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/ACEt/")
+    (synopsis "Estimating dynamic heritability and twin model comparison")
+    (description
+     "This package supports twin models that are able to estimate the dynamic
+behaviour of the variance components in the classical twin models with respect
+to age using B-splines and P-splines.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From a8a7ba9acb5108f710a89e6e79c686ee5979c209 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:56:39 +0100
Subject: gnu: Add r-acfmperiod.

* gnu/packages/cran.scm (r-acfmperiod): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8c7fe23667..ece356e7cd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17022,3 +17022,32 @@ to maximise an approximation to the expectation of the utility function.")
 behaviour of the variance components in the classical twin models with respect
 to age using B-splines and P-splines.")
     (license license:gpl2+)))
+
+(define-public r-acfmperiod
+  (package
+    (name "r-acfmperiod")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acfMPeriod" version))
+       (sha256
+        (base32
+         "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
+    (properties `((upstream-name . "acfMPeriod")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
+    (synopsis "Estimation of the ACF from the M-periodogram")
+    (description
+     "This package support non-robust and robust computations of the sample
+autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
+univariate and multivariate processes.  The methodology consists in reversing
+the diagonalization procedure involving the periodogram or the
+cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
+ACOVF or the ACF as discussed in Fuller (1995)
+@url{doi:10.1002/9780470316917}.  The robust version is obtained by fitting
+robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
+discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 3b89a8af7a8cf873b8712aecce7ac1335adb9856 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:56:55 +0100
Subject: gnu: Add r-gamlss-data.

* gnu/packages/cran.scm (r-gamlss-data): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ece356e7cd..280810f929 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17051,3 +17051,24 @@ ACOVF or the ACF as discussed in Fuller (1995)
 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
     (license license:gpl2+)))
+
+(define-public r-gamlss-data
+  (package
+    (name "r-gamlss-data")
+    (version "5.1-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gamlss.data" version))
+       (sha256
+        (base32
+         "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
+    (properties `((upstream-name . "gamlss.data")))
+    (build-system r-build-system)
+    (home-page "http://www.gamlss.org/")
+    (synopsis "GAMLSS data")
+    (description
+     "This package provides data used as examples to demonstrate GAMLSS
+models.")
+    ;; Either version of the license
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 6cc356c3535cd5b16b7a6929903d62beded8e732 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:59:02 +0100
Subject: gnu: Add r-gamlss.

* gnu/packages/cran.scm (r-gamlss): 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 280810f929..ed705145c7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17072,3 +17072,34 @@ discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
 models.")
     ;; Either version of the license
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-gamlss
+  (package
+    (name "r-gamlss")
+    (version "5.1-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gamlss" version))
+       (sha256
+        (base32
+         "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc"))))
+    (properties `((upstream-name . "gamlss")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gamlss-data" ,r-gamlss-data)
+       ("r-gamlss-dist" ,r-gamlss-dist)
+       ("r-mass" ,r-mass)
+       ("r-nlme" ,r-nlme)
+       ("r-survival" ,r-survival)))
+    (home-page "http://www.gamlss.org/")
+    (synopsis "Generalized additive models for location scale and shape")
+    (description
+     "This package provides functions for fitting the generalized additive
+models for location scale and shape introduced by Rigby and
+Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}.  The models
+use a distributional regression approach where all the parameters of the
+conditional distribution of the response variable are modelled using
+explanatory variables.")
+    ;; Either version of the license
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 220557a7f3e9468682dda5f4b3efe1e2e9203920 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 18:59:33 +0100
Subject: gnu: Add r-acid.

* gnu/packages/cran.scm (r-acid): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ed705145c7..c2ea959234 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17103,3 +17103,32 @@ conditional distribution of the response variable are modelled using
 explanatory variables.")
     ;; Either version of the license
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-acid
+  (package
+    (name "r-acid")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acid" version))
+       (sha256
+        (base32
+         "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
+    (properties `((upstream-name . "acid")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gamlss" ,r-gamlss)
+       ("r-gamlss-dist" ,r-gamlss-dist)
+       ("r-hmisc" ,r-hmisc)))
+    (home-page "https://cran.r-project.org/web/packages/acid/")
+    (synopsis "Analysing conditional income distributions")
+    (description
+     "This package provides functions for the analysis of income distributions
+for subgroups of the population as defined by a set of variables like age,
+gender, region, etc.  This entails a Kolmogorov-Smirnov test for a mixture
+distribution as well as functions for moments, inequality measures, entropy
+measures and polarisation measures of income distributions.  This package thus
+aides the analysis of income inequality by offering tools for the exploratory
+analysis of income distributions at the disaggregated level.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 542590c5a3714a06bd364b54763fcfd78826c245 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 19:10:05 +0100
Subject: gnu: Add r-acm4r.

* gnu/packages/cran.scm (r-acm4r): 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 c2ea959234..b491484508 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17132,3 +17132,27 @@ measures and polarisation measures of income distributions.  This package thus
 aides the analysis of income inequality by offering tools for the exploratory
 analysis of income distributions at the disaggregated level.")
     (license license:gpl3)))
+
+(define-public r-acm4r
+  (package
+    (name "r-acm4r")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acm4r" version))
+       (sha256
+        (base32
+         "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
+    (properties `((upstream-name . "acm4r")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/acm4r/")
+    (synopsis "Align-and-count method comparisons of RFLP data")
+    (description
+     "This is a package to compare sequence fragment lengths or molecular
+weights from pairs of lanes.  The number of matching bands in the
+@dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
+the align-and-count method.")
+    ;; Any version of the GPL
+    (license (list license:gpl2+ license:gpl3+))))
-- 
cgit v1.2.3


From fa82997feac8636464bcf92571236105e1719999 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 19:10:33 +0100
Subject: gnu: Add r-filematrix.

* gnu/packages/cran.scm (r-filematrix): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b491484508..ddbd8dec25 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17156,3 +17156,33 @@ weights from pairs of lanes.  The number of matching bands in the
 the align-and-count method.")
     ;; Any version of the GPL
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-filematrix
+  (package
+    (name "r-filematrix")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "filematrix" version))
+       (sha256
+        (base32
+         "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
+    (properties `((upstream-name . "filematrix")))
+    (build-system r-build-system)
+    ;; These inputs are needed for vignettes
+    (native-inputs
+     `(("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
+    (home-page "https://github.com/andreyshabalin/filematrix")
+    (synopsis "File-backed matrix class with convenient read and write access")
+    (description
+     "This package provides an interface for working with large matrices
+stored in files, not in computer memory.  It supports multiple non-character
+data types (double, integer, logical and raw) of various sizes (e.g.  8 and 4
+byte real values).  Access to parts of the matrix is done by indexing, exactly
+as with usual R matrices.  It supports very large matrices; the package has
+been tested on multi-terabyte matrices.  It allows for more than 2^32 rows or
+columns, ad allows for quick addition of extra columns to a filematrix.")
+    (license license:lgpl3)))
-- 
cgit v1.2.3


From 73f055df34b1d174544e0232b5aaf1d735f90d9e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 19:24:31 +0100
Subject: gnu: Add r-acmeeqtl.

* gnu/packages/cran.scm (r-acmeeqtl): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ddbd8dec25..943a1b629f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17186,3 +17186,28 @@ as with usual R matrices.  It supports very large matrices; the package has
 been tested on multi-terabyte matrices.  It allows for more than 2^32 rows or
 columns, ad allows for quick addition of extra columns to a filematrix.")
     (license license:lgpl3)))
+
+(define-public r-acmeeqtl
+  (package
+    (name "r-acmeeqtl")
+    (version "1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACMEeqtl" version))
+       (sha256
+        (base32
+         "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
+    (properties `((upstream-name . "ACMEeqtl")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-filematrix" ,r-filematrix)))
+    (home-page "https://github.com/andreyshabalin/ACMEeqtl")
+    (synopsis "Estimation of interpretable eQTL effect sizes")
+    (description
+     "This package provides a non-linear model, termed ACME, that reflects a
+parsimonious biological model for allelic contributions of cis-acting eQTLs.
+With non-linear least-squares algorithm the maximum likelihood parameters can
+be estimated.  The ACME model provides interpretable effect size estimates and
+p-values with well controlled Type-I error.")
+    (license license:lgpl3)))
-- 
cgit v1.2.3


From 2dc8723abd724d2fac491511a27102c6e5b8e61c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 19:25:07 +0100
Subject: gnu: Add r-acmer.

* gnu/packages/cran.scm (r-acmer): New variable.
---
 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 943a1b629f..ce34315b03 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17211,3 +17211,30 @@ With non-linear least-squares algorithm the maximum likelihood parameters can
 be estimated.  The ACME model provides interpretable effect size estimates and
 p-values with well controlled Type-I error.")
     (license license:lgpl3)))
+
+(define-public r-acmer
+  (package
+    (name "r-acmer")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acmeR" version))
+       (sha256
+        (base32
+         "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
+    (properties `((upstream-name . "acmeR")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-foreign" ,r-foreign)))
+    (home-page "https://cran.r-project.org/web/packages/acmeR/")
+    (synopsis "ACME estimator of bird and bat mortality by wind turbines")
+    (description
+     "This package provides an implementation of the ACME estimator, described
+in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
+Mortality at Wind Turbines.  Unlike most other models, this estimator supports
+decreasing-hazard Weibull model for persistence; decreasing search proficiency
+as carcasses age; variable bleed-through at successive searches; and interval
+mortality estimates.  The package provides, based on search data, functions
+for estimating the mortality inflation factor in Frequentist and Bayesian
+settings.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 1c2e3d7d316573b3fd51d2a37af19a27df20be97 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 19:26:05 +0100
Subject: gnu: Add r-r-huge.

* gnu/packages/cran.scm (r-r-huge): 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 ce34315b03..413211f363 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17238,3 +17238,29 @@ mortality estimates.  The package provides, based on search data, functions
 for estimating the mortality inflation factor in Frequentist and Bayesian
 settings.")
     (license license:expat)))
+
+(define-public r-r-huge
+  (package
+    (name "r-r-huge")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "R.huge" version))
+       (sha256
+        (base32
+         "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
+    (properties `((upstream-name . "R.huge")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://github.com/HenrikBengtsson/R.huge")
+    (synopsis "Methods for accessing huge amounts of data")
+    (description
+     "This is a deprecated package for accessing huge amounts of data.
+  Cross-platform alternatives are the following packages: bigmemory (CRAN),
+ff (CRAN), or BufferedMatrix (Bioconductor).  The main usage of it was inside
+the @code{aroma.affymetrix} package.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From 2fe1e66c4d2cab9922a6c98680c8d71bfc05654c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:01:20 +0100
Subject: gnu: Add r-r-filesets.

* gnu/packages/cran.scm (r-r-filesets): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 413211f363..495ef13628 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17264,3 +17264,35 @@ settings.")
 ff (CRAN), or BufferedMatrix (Bioconductor).  The main usage of it was inside
 the @code{aroma.affymetrix} package.")
     (license license:lgpl2.1+)))
+
+(define-public r-r-filesets
+  (package
+    (name "r-r-filesets")
+    (version "2.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "R.filesets" version))
+       (sha256
+        (base32
+         "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
+    (properties `((upstream-name . "R.filesets")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-r-cache" ,r-r-cache)
+       ("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://github.com/HenrikBengtsson/R.filesets")
+    (synopsis "Easy handling of and access to files")
+    (description
+     "This package provides classes and methods to locate, setup, subset,
+navigate and iterate file sets, i.e. sets of files located in one or more
+directories on the file system.  The API is designed such that these classes
+can be extended via inheritance to provide a richer API for special file
+formats.  Moreover, a specific name format is defined such that filenames and
+directories can be considered to have full names which consists of a name
+followed by comma-separated tags.  This adds additional flexibility to
+identify file sets and individual files.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From 217cd2e3ee6b04ed2ac0ab4548106f8708367aa5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:02:28 +0100
Subject: gnu: Add r-r-devices.

* gnu/packages/cran.scm (r-r-devices): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 495ef13628..ec001ab383 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17296,3 +17296,33 @@ directories can be considered to have full names which consists of a name
 followed by comma-separated tags.  This adds additional flexibility to
 identify file sets and individual files.")
     (license license:lgpl2.1+)))
+
+(define-public r-r-devices
+  (package
+    (name "r-r-devices")
+    (version "2.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "R.devices" version))
+       (sha256
+        (base32
+         "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
+    (properties `((upstream-name . "R.devices")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://github.com/HenrikBengtsson/R.devices")
+    (synopsis "Unified handling of graphics devices")
+    (description
+     "This package provides functions for creating plots and image files in a
+unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
+Default device options as well as scales and aspect ratios are controlled in a
+uniform way across all device types.  Switching output format requires minimal
+changes in code.  This package is ideal for large-scale batch processing,
+because it will never leave open graphics devices or incomplete image files
+behind, even on errors or user interrupts.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From eff3e8a471e4ca7a449f6acd338a4db0c4c95a0e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:03:13 +0100
Subject: gnu: Add r-acnr.

* gnu/packages/cran.scm (r-acnr): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ec001ab383..207bb13bcd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17326,3 +17326,24 @@ changes in code.  This package is ideal for large-scale batch processing,
 because it will never leave open graphics devices or incomplete image files
 behind, even on errors or user interrupts.")
     (license license:lgpl2.1+)))
+
+(define-public r-acnr
+  (package
+    (name "r-acnr")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acnr" version))
+       (sha256
+        (base32
+         "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
+    (properties `((upstream-name . "acnr")))
+    (build-system r-build-system)
+    (home-page "https://github.com/mpierrejean/acnr")
+    (synopsis "Annotated copy-number regions")
+    (description
+     "This package provides SNP array data from different types of copy-number
+regions.  These regions were identified manually by the authors of the package
+and may be used to generate realistic data sets with known truth.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From 5d887a03551a24228a4cf5519bcd27a5ae6a123b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:03:31 +0100
Subject: gnu: Add r-acopula.

* gnu/packages/cran.scm (r-acopula): 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 207bb13bcd..6f2eb07951 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17347,3 +17347,29 @@ behind, even on errors or user interrupts.")
 regions.  These regions were identified manually by the authors of the package
 and may be used to generate realistic data sets with known truth.")
     (license license:lgpl2.1+)))
+
+(define-public r-acopula
+  (package
+    (name "r-acopula")
+    (version "0.9.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acopula" version))
+       (sha256
+        (base32
+         "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
+    (properties `((upstream-name . "acopula")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/acopula/")
+    (synopsis "Modelling dependence with multivariate Archimax copulas")
+    (description
+     "Archimax copulas are a mixture of Archimedean and EV copulas.  This
+package provides definitions of several parametric families of generator and
+dependence function, computes CDF and PDF, estimates parameters, tests for
+goodness of fit, generates random sample and checks copula properties for
+custom constructs.  In the 2-dimensional case explicit formulas for density
+are used, contrary to higher dimensions when all derivatives are linearly
+approximated.  Several non-archimax families (normal, FGM, Plackett) are
+provided as well.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From cb350053dab549e9bbd85aec651e3662a9f68062 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:05:18 +0100
Subject: gnu: Add r-tuner.

* gnu/packages/cran.scm (r-tuner): 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 6f2eb07951..b1217ad992 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17373,3 +17373,27 @@ are used, contrary to higher dimensions when all derivatives are linearly
 approximated.  Several non-archimax families (normal, FGM, Plackett) are
 provided as well.")
     (license license:gpl2)))
+
+(define-public r-tuner
+  (package
+    (name "r-tuner")
+    (version "1.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tuneR" version))
+       (sha256
+        (base32
+         "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
+    (properties `((upstream-name . "tuneR")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-signal" ,r-signal)))
+    (home-page "https://cran.r-project.org/web/packages/tuneR/")
+    (synopsis "Analysis of music and speech")
+    (description
+     "This is a package for the analysis of music and speech.  Analyze music
+and speech, extract features like MFCCs, handle wave files and their
+representation in various ways, read MP3, read MIDI, perform steps of a
+transcription, ...")
+    ;; Either of these versions.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 19172e12ef990f9c7527a90fe24ab3e38a348974 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:05:27 +0100
Subject: gnu: Add r-seewave.

* gnu/packages/cran.scm (r-seewave): 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 b1217ad992..0f0ecb6829 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17397,3 +17397,29 @@ representation in various ways, read MP3, read MIDI, perform steps of a
 transcription, ...")
     ;; Either of these versions.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-seewave
+  (package
+    (name "r-seewave")
+    (version "2.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "seewave" version))
+       (sha256
+        (base32
+         "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
+    (properties `((upstream-name . "seewave")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-tuner" ,r-tuner)))
+    (home-page "http://rug.mnhn.fr/seewave")
+    (synopsis "Sound analysis and synthesis")
+    (description
+     "This package provides functions for analysing, manipulating, displaying,
+editing and synthesizing time waves (particularly sound).  This package
+processes time analysis (oscillograms and envelopes), spectral content,
+resonance quality factor, entropy, cross correlation and autocorrelation,
+zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
+and 3D spectrograms and many other analyses.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From c12227d9719898dd1bd405ef0141747bd90e53b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:08:25 +0100
Subject: gnu: Add r-acousticndlcoder.

* gnu/packages/cran.scm (r-acousticndlcoder): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0f0ecb6829..a07cfbe153 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17423,3 +17423,32 @@ resonance quality factor, entropy, cross correlation and autocorrelation,
 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
 and 3D spectrograms and many other analyses.")
     (license license:gpl2+)))
+
+(define-public r-acousticndlcoder
+  (package
+    (name "r-acousticndlcoder")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AcousticNDLCodeR" version))
+       (sha256
+        (base32
+         "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
+    (properties
+     `((upstream-name . "AcousticNDLCodeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-seewave" ,r-seewave)
+       ("r-tuner" ,r-tuner)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
+    (synopsis "Coding sound files for use with NDL")
+    (description
+     "Make acoustic cues to use with the R package @code{ndl}.
+The package implements functions used in the PLoS ONE paper \"Words from
+spontaneous conversational speech can be recognized with human-like accuracy
+by an error-driven learning algorithm that discriminates between meanings
+straight from smart acoustic features, bypassing the phoneme as recognition
+unit.\" @url{doi:10.1371/journal.pone.0174623}")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 56cba940c3e56d0c811652e638408d098894ae8e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:08:51 +0100
Subject: gnu: Add r-acp.

* gnu/packages/cran.scm (r-acp): 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 a07cfbe153..d09bc22e19 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17452,3 +17452,27 @@ by an error-driven learning algorithm that discriminates between meanings
 straight from smart acoustic features, bypassing the phoneme as recognition
 unit.\" @url{doi:10.1371/journal.pone.0174623}")
     (license license:gpl2+)))
+
+(define-public r-acp
+  (package
+    (name "r-acp")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acp" version))
+       (sha256
+        (base32
+         "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
+    (properties `((upstream-name . "acp")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-quantmod" ,r-quantmod)
+       ("r-tseries" ,r-tseries)))
+    (home-page "https://cran.r-project.org/web/packages/acp/")
+    (synopsis "Autoregressive conditional Poisson")
+    (description
+     "This package supports the analysis of count data exhibiting
+autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
+model (ACP(p,q)) proposed by Heinen (2003).")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From f18c0544f6dd48aee582d95a0d6400939fa8b441 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:09:24 +0100
Subject: gnu: Add r-ada.

* gnu/packages/cran.scm (r-ada): 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 d09bc22e19..d7b8e866d6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17476,3 +17476,27 @@ unit.\" @url{doi:10.1371/journal.pone.0174623}")
 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
 model (ACP(p,q)) proposed by Heinen (2003).")
     (license license:gpl2)))
+
+(define-public r-ada
+  (package
+    (name "r-ada")
+    (version "2.0-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ada" version))
+       (sha256
+        (base32
+         "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
+    (properties `((upstream-name . "ada")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rpart" ,r-rpart)))
+    (home-page "https://cran.r-project.org/web/packages/ada/")
+    (synopsis "Stochastic boosting")
+    (description
+     "This package provides a straightforward, well-documented, and broad
+boosting routine for classification, ideally suited for small to
+moderate-sized data sets.  It performs discrete, real, and gentle boost under
+both exponential and logistic loss on a given data set.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))
-- 
cgit v1.2.3


From 270529f633e3636bc10cc00ae5081093bb2e95cb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:09:40 +0100
Subject: gnu: Add r-genalg.

* gnu/packages/cran.scm (r-genalg): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d7b8e866d6..9edf9eaf7f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17500,3 +17500,23 @@ moderate-sized data sets.  It performs discrete, real, and gentle boost under
 both exponential and logistic loss on a given data set.")
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-genalg
+  (package
+    (name "r-genalg")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "genalg" version))
+       (sha256
+        (base32
+         "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
+    (properties `((upstream-name . "genalg")))
+    (build-system r-build-system)
+    (home-page "https://github.com/egonw/genalg")
+    (synopsis "R based genetic algorithm")
+    (description
+     "This package provides an R based genetic algorithm for binary and
+floating point chromosomes.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 6afc037e74a2bc92adde2ffecb2c3722f9113b6b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:09:52 +0100
Subject: gnu: Add r-kernelfactory.

* gnu/packages/cran.scm (r-kernelfactory): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9edf9eaf7f..1b03627a8a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17520,3 +17520,28 @@ both exponential and logistic loss on a given data set.")
      "This package provides an R based genetic algorithm for binary and
 floating point chromosomes.")
     (license license:gpl2)))
+
+(define-public r-kernelfactory
+  (package
+    (name "r-kernelfactory")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "kernelFactory" version))
+       (sha256
+        (base32
+         "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
+    (properties `((upstream-name . "kernelFactory")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-auc" ,r-auc)
+       ("r-genalg" ,r-genalg)
+       ("r-kernlab" ,r-kernlab)
+       ("r-randomforest" ,r-randomforest)))
+    (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
+    (synopsis "Ensemble of kernel machines")
+    (description
+     "Kernel factory is an ensemble method where each base classifier (random
+forest) is fit on the kernel matrix of a subset of the training data.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 6c2dcba99df361cdbb3f1b1beeff5b3cf34330b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:10:09 +0100
Subject: gnu: Add r-dummies.

* gnu/packages/cran.scm (r-dummies): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1b03627a8a..3a332a428e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17545,3 +17545,23 @@ floating point chromosomes.")
      "Kernel factory is an ensemble method where each base classifier (random
 forest) is fit on the kernel matrix of a subset of the training data.")
     (license license:gpl2+)))
+
+(define-public r-dummies
+  (package
+    (name "r-dummies")
+    (version "1.5.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dummies" version))
+       (sha256
+        (base32
+         "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
+    (properties `((upstream-name . "dummies")))
+    (build-system r-build-system)
+    (home-page "http://www.decisionpatterns.com")
+    (synopsis "Create dummy/indicator variables flexibly and efficiently")
+    (description
+     "This package lets you expand factors, characters and other eligible
+classes into dummy/indicator variables.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 3bc2c210431720d75c3a0eb786d4b4ff14a19061 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:10:23 +0100
Subject: gnu: Add r-acrm.

* gnu/packages/cran.scm (r-acrm): 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 3a332a428e..d3db6b0ca4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17565,3 +17565,29 @@ forest) is fit on the kernel matrix of a subset of the training data.")
      "This package lets you expand factors, characters and other eligible
 classes into dummy/indicator variables.")
     (license license:gpl2+)))
+
+(define-public r-acrm
+  (package
+    (name "r-acrm")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aCRM" version))
+       (sha256
+        (base32
+         "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
+    (properties `((upstream-name . "aCRM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ada" ,r-ada)
+       ("r-dummies" ,r-dummies)
+       ("r-kernelfactory" ,r-kernelfactory)
+       ("r-randomforest" ,r-randomforest)))
+    (home-page "https://cran.r-project.org/web/packages/aCRM/")
+    (synopsis "Convenience functions for analytical customer relationship management")
+    (description
+     "This package provides convenience functions for data preparation and
+modeling often used in @dfn{analytical customer relationship
+management} (aCRM).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From c3f5989c8f92de1693610c5237e0794991d7534d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:11:26 +0100
Subject: gnu: Add r-treeclust.

* gnu/packages/cran.scm (r-treeclust): 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 d3db6b0ca4..6dd36c36ce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17591,3 +17591,27 @@ classes into dummy/indicator variables.")
 modeling often used in @dfn{analytical customer relationship
 management} (aCRM).")
     (license license:gpl2+)))
+
+(define-public r-treeclust
+  (package
+    (name "r-treeclust")
+    (version "1.1-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "treeClust" version))
+       (sha256
+        (base32
+         "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
+    (properties `((upstream-name . "treeClust")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-rpart" ,r-rpart)))
+    (home-page "https://cran.r-project.org/web/packages/treeClust/")
+    (synopsis "Cluster distances through trees")
+    (description
+     "This package provides tools to create a measure of inter-point
+dissimilarity useful for clustering mixed data, and, optionally, perform the
+clustering.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 4b44bfb6ec86fd51bc7d3bac31adcb6731592578 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:11:55 +0100
Subject: gnu: Add r-acrosstic.

* gnu/packages/cran.scm (r-acrosstic): 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 6dd36c36ce..ebff9de29c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17615,3 +17615,27 @@ management} (aCRM).")
 dissimilarity useful for clustering mixed data, and, optionally, perform the
 clustering.")
     (license license:gpl2+)))
+
+(define-public r-acrosstic
+  (package
+    (name "r-acrosstic")
+    (version "1.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AcrossTic" version))
+       (sha256
+        (base32
+         "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
+    (properties `((upstream-name . "AcrossTic")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lpsolve" ,r-lpsolve)
+       ("r-treeclust" ,r-treeclust)))
+    (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
+    (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
+    (description
+     "This is a package for constructing minimum-cost regular spanning
+subgraph as part of a non-parametric two-sample test for equality of
+distribution.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From d015db6f57888c5573dfb276121971cb7d44f4b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:12:12 +0100
Subject: gnu: Add r-acrt.

* gnu/packages/cran.scm (r-acrt): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ebff9de29c..6c0bc01df0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17639,3 +17639,28 @@ clustering.")
 subgraph as part of a non-parametric two-sample test for equality of
 distribution.")
     (license license:gpl2+)))
+
+(define-public r-acrt
+  (package
+    (name "r-acrt")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acrt" version))
+       (sha256
+        (base32
+         "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
+    (properties `((upstream-name . "acrt")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-sandwich" ,r-sandwich)))
+    (home-page "https://cran.r-project.org/web/packages/acrt/")
+    (synopsis "Autocorrelation robust testing")
+    (description
+     "This package provides functions for testing affine hypotheses on the
+regression coefficient vector in regression models with autocorrelated
+errors.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 49e9a9aea2131f39c44689aebf02a87887cc0f87 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 13 Dec 2019 23:12:24 +0100
Subject: gnu: Add r-acs.

* gnu/packages/cran.scm (r-acs): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6c0bc01df0..76bae8ec93 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17664,3 +17664,36 @@ distribution.")
 regression coefficient vector in regression models with autocorrelated
 errors.")
     (license license:gpl2)))
+
+(define-public r-acs
+  (package
+    (name "r-acs")
+    (version "2.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acs" version))
+       (sha256
+        (base32
+         "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
+    (properties `((upstream-name . "acs")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-httr" ,r-httr)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-stringr" ,r-stringr)
+       ("r-xml" ,r-xml)))
+    (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
+    (synopsis "Work with data from the US Census")
+    (description
+     "This package provides a general toolkit for downloading, managing,
+analyzing, and presenting data from the
+@url{https://www.census.gov/data/developers/data-sets.html, U.S.  Census},
+including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
+American Community Survey (ACS).  Confidence intervals provided with ACS data
+are converted to standard errors to be bundled with estimates in complex
+@code{acs} objects.  The package provides new methods to conduct standard
+operations on @code{acs} objects and present/plot data in statistically
+appropriate ways.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 07d958fe0edb21df38541cc3a9eabf0ae1ab9f84 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 09:22:21 +0100
Subject: gnu: Add r-acss-data.

* gnu/packages/cran.scm (r-acss-data): New variable.
---
 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 76bae8ec93..37f8e8d877 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17697,3 +17697,30 @@ are converted to standard errors to be bundled with estimates in complex
 operations on @code{acs} objects and present/plot data in statistically
 appropriate ways.")
     (license license:gpl3)))
+
+(define-public r-acss-data
+  (package
+    (name "r-acss-data")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acss.data" version))
+       (sha256
+        (base32
+         "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
+    (properties `((upstream-name . "acss.data")))
+    (build-system r-build-system)
+    (home-page "http://complexitycalculator.com/methodology.html")
+    (synopsis "Data for algorithmic complexity of short strings")
+    (description
+     "This is a data only package providing the algorithmic complexity of
+short strings, computed using the coding theorem method.  For a given set of
+symbols in a string, all possible or a large number of random samples of
+Turing machines with a given number of states (e.g., 5) and number of symbols
+corresponding to the number of symbols in the strings were simulated until
+they reached a halting state or failed to end.  This package contains data on
+4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
+4, 5, 6, and 9 symbols.  The complexity of the string corresponds to the
+distribution of the halting states.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 0ea0b2dd46014fdfef14614d582d60ce29c65a1f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 09:22:36 +0100
Subject: gnu: Add r-acss.

* gnu/packages/cran.scm (r-acss): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 37f8e8d877..b588d6e9f0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17724,3 +17724,32 @@ they reached a halting state or failed to end.  This package contains data on
 4, 5, 6, and 9 symbols.  The complexity of the string corresponds to the
 distribution of the halting states.")
     (license license:gpl2+)))
+
+(define-public r-acss
+  (package
+    (name "r-acss")
+    (version "0.2-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acss" version))
+       (sha256
+        (base32
+         "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
+    (properties `((upstream-name . "acss")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-acss-data" ,r-acss-data)
+       ("r-zoo" ,r-zoo)))
+    (home-page "http://complexitycalculator.com/methodology.html")
+    (synopsis "Algorithmic complexity for short strings")
+    (description
+     "The main purpose of this package is to provide the algorithmic
+complexity for short strings, an approximation of the Kolmogorov Complexity of
+a short string using the coding theorem method.  While the database containing
+the complexity is provided in the data only package @code{acss.data}, this
+package provides functions accessing the data such as @code{prob_random}
+returning the posterior probability that a given string was produced by a
+random process.  In addition, two traditional (but problematic) measures of
+complexity are also provided: entropy and change complexity.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From ffecbcbf517b78f31e2289ea067e9825a76a489b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:07:08 +0100
Subject: gnu: Add r-acswr.

* gnu/packages/cran.scm (r-acswr): 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 b588d6e9f0..6059acdddd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17753,3 +17753,25 @@ returning the posterior probability that a given string was produced by a
 random process.  In addition, two traditional (but problematic) measures of
 complexity are also provided: entropy and change complexity.")
     (license license:gpl2+)))
+
+(define-public r-acswr
+  (package
+    (name "r-acswr")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACSWR" version))
+       (sha256
+        (base32
+         "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
+    (properties `((upstream-name . "ACSWR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/ACSWR/")
+    (synopsis "Companion package for the book \"A Course in Statistics with R\"")
+    (description
+     "This is a companion package for the book \"A Course in Statistics with
+R\" (ISBN 978-1-119-15272-9.)")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 6f0a5ab09819d1237d7434f1565db3016d785c8a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:07:18 +0100
Subject: gnu: Add r-alabama.

* gnu/packages/cran.scm (r-alabama): 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 6059acdddd..22e994059b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17775,3 +17775,26 @@ complexity are also provided: entropy and change complexity.")
      "This is a companion package for the book \"A Course in Statistics with
 R\" (ISBN 978-1-119-15272-9.)")
     (license license:gpl2)))
+
+(define-public r-alabama
+  (package
+    (name "r-alabama")
+    (version "2015.3-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "alabama" version))
+       (sha256
+        (base32
+         "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
+    (properties `((upstream-name . "alabama")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-numderiv" ,r-numderiv)))
+    (home-page "https://cran.r-project.org/web/packages/alabama/")
+    (synopsis "Constrained nonlinear optimization")
+    (description
+     "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
+Algorithm; it is used for optimizing smooth nonlinear objective functions with
+constraints.  Linear or nonlinear equality and inequality constraints are
+allowed.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 70c0dbe73fa099cd7bebccb3bffba3dfe3c3137b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:07:26 +0100
Subject: gnu: Add r-gdina.

* gnu/packages/cran.scm (r-gdina): New variable.
---
 gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 22e994059b..cb68994565 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17798,3 +17798,43 @@ Algorithm; it is used for optimizing smooth nonlinear objective functions with
 constraints.  Linear or nonlinear equality and inequality constraints are
 allowed.")
     (license license:gpl2+)))
+
+(define-public r-gdina
+  (package
+    (name "r-gdina")
+    (version "2.7.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GDINA" version))
+       (sha256
+        (base32
+         "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx"))))
+    (properties `((upstream-name . "GDINA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-alabama" ,r-alabama)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-mass" ,r-mass)
+       ("r-nloptr" ,r-nloptr)
+       ("r-numderiv" ,r-numderiv)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rsolnp" ,r-rsolnp)
+       ("r-shiny" ,r-shiny)
+       ("r-shinydashboard" ,r-shinydashboard)))
+    (home-page "https://github.com/Wenchao-Ma/GDINA")
+    (synopsis "Generalized DINA model framework")
+    (description
+     "This package provides a set of psychometric tools for cognitive
+diagnosis modeling based on the generalized deterministic inputs, noisy and
+gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
+and its extensions, including the sequential G-DINA model by Ma and de la
+Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
+polytomous G-DINA model by Chen and de la Torre
+@url{doi:10.1177/0146621613479818} for polytomous attributes.  Joint attribute
+distribution can be independent, saturated, higher-order, loglinear smoothed
+or structured.  Q-matrix validation, item and model fit statistics, model
+comparison at test and item level and differential item functioning can also
+be conducted.  A graphical user interface is also provided.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From d024207e7bfaba0453e34de48510378ddd2dff4d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:07:48 +0100
Subject: gnu: Add r-actcd.

* gnu/packages/cran.scm (r-actcd): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cb68994565..dd30ba3fbe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17838,3 +17838,33 @@ or structured.  Q-matrix validation, item and model fit statistics, model
 comparison at test and item level and differential item functioning can also
 be conducted.  A graphical user interface is also provided.")
     (license license:gpl3)))
+
+(define-public r-actcd
+  (package
+    (name "r-actcd")
+    (version "1.2-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACTCD" version))
+       (sha256
+        (base32
+         "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
+    (properties `((upstream-name . "ACTCD")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdina" ,r-gdina)
+       ("r-r-methodss3" ,r-r-methodss3)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/ACTCD/")
+    (synopsis "Asymptotic classification theory for cognitive diagnosis")
+    (description
+     "This is a package supporting cluster analysis for cognitive diagnosis
+based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
+@url{doi:10.1007/s11336-009-9125-0}).  Given the sample statistic of
+sum-scores, cluster analysis techniques can be used to classify examinees into
+latent classes based on their attribute patterns.  In addition to the
+algorithms used to classify data, three labeling approaches are proposed to
+label clusters so that examinees' attribute profiles can be obtained.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 6790adf338a1e3606d451135cec244f737c96156 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:10:38 +0100
Subject: gnu: Add r-ineq.

* gnu/packages/cran.scm (r-ineq): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index dd30ba3fbe..f01df24bb2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17868,3 +17868,24 @@ latent classes based on their attribute patterns.  In addition to the
 algorithms used to classify data, three labeling approaches are proposed to
 label clusters so that examinees' attribute profiles can be obtained.")
     (license license:gpl2+)))
+
+(define-public r-ineq
+  (package
+    (name "r-ineq")
+    (version "0.2-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ineq" version))
+       (sha256
+        (base32
+         "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
+    (properties `((upstream-name . "ineq")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ineq/")
+    (synopsis "Measuring inequality, concentration, and poverty")
+    (description
+     "This package provides tools for measuring inequality, concentration, and
+poverty measures.  It provides both empirical and theoretical Lorenz curves.")
+    ;; Either of these two versions.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From c090b9977c22854c23a5e3f6c5352263c67713f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:10:56 +0100
Subject: gnu: Add r-actfrag.

* gnu/packages/cran.scm (r-actfrag): New variable.
---
 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 f01df24bb2..c36328c896 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17889,3 +17889,30 @@ label clusters so that examinees' attribute profiles can be obtained.")
 poverty measures.  It provides both empirical and theoretical Lorenz curves.")
     ;; Either of these two versions.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-actfrag
+  (package
+    (name "r-actfrag")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ActFrag" version))
+       (sha256
+        (base32
+         "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d"))))
+    (properties `((upstream-name . "ActFrag")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-accelerometry" ,r-accelerometry)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ineq" ,r-ineq)
+       ("r-survival" ,r-survival)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/junruidi/ActFrag")
+    (synopsis "Activity fragmentation metrics extraction")
+    (description
+     "This package provides functions to extract commonly used fragmentation
+metrics to quantify time accumulation strategies based on minute level
+actigraphy-measured activity counts data.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 77a5bf938febc580d972e02c89fe27a691a53445 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:11:09 +0100
Subject: gnu: Add r-fda.

* gnu/packages/cran.scm (r-fda): 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 c36328c896..a1a64c0ec2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17916,3 +17916,27 @@ poverty measures.  It provides both empirical and theoretical Lorenz curves.")
 metrics to quantify time accumulation strategies based on minute level
 actigraphy-measured activity counts data.")
     (license license:gpl3)))
+
+(define-public r-fda
+  (package
+    (name "r-fda")
+    (version "2.4.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fda" version))
+       (sha256
+        (base32
+         "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2"))))
+    (properties `((upstream-name . "fda")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)))
+    (home-page "http://www.functionaldata.org")
+    (synopsis "Functional data analysis")
+    (description
+     "These functions were developed to support functional data analysis as
+described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
+Analysis.  The package includes data sets and script files working many
+examples.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 402dae07b5a8baa5d99d6d8e39b3917d0706b9b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:52:27 +0100
Subject: gnu: Add r-actigraphy.

* gnu/packages/cran.scm (r-actigraphy): 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 a1a64c0ec2..6efd1a66c2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17940,3 +17940,26 @@ described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
 Analysis.  The package includes data sets and script files working many
 examples.")
     (license license:gpl2+)))
+
+(define-public r-actigraphy
+  (package
+    (name "r-actigraphy")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Actigraphy" version))
+       (sha256
+        (base32
+         "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"))))
+    (properties `((upstream-name . "Actigraphy")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fda" ,r-fda)
+       ("r-sdmtools" ,r-sdmtools)))
+    (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
+    (synopsis "Actigraphy data analysis")
+    (description
+     "This package provides tools for functional linear modeling and analysis
+of actigraphy data.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From 7f960d81fb8685e707b6805e1ac00da63f39407c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:54:34 +0100
Subject: gnu: Add r-activedriver.

* gnu/packages/cran.scm (r-activedriver): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6efd1a66c2..00ce9ad934 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17963,3 +17963,31 @@ examples.")
      "This package provides tools for functional linear modeling and analysis
 of actigraphy data.")
     (license license:asl2.0)))
+
+(define-public r-activedriver
+  (package
+    (name "r-activedriver")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ActiveDriver" version))
+       (sha256
+        (base32
+         "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
+    (properties `((upstream-name . "ActiveDriver")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
+    (synopsis "Tools for finding cancer driver proteins")
+    (description
+     "This package provides a mutation analysis tool that discovers cancer
+driver genes with frequent mutations in protein signalling sites such as
+post-translational modifications (phosphorylation, ubiquitination, etc).  The
+Poisson generalized linear regression model identifies genes where cancer
+mutations in signalling sites are more frequent than expected from the
+sequence of the entire gene.  Integration of mutations with signalling
+information helps find new driver genes and propose candidate mechanisms to
+known drivers.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 89d4f154b982a83ded18cbae801fd41f56cbada8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:54:49 +0100
Subject: gnu: Add r-activitycounts.

* gnu/packages/cran.scm (r-activitycounts): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 00ce9ad934..259fa1d3e9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17991,3 +17991,35 @@ sequence of the entire gene.  Integration of mutations with signalling
 information helps find new driver genes and propose candidate mechanisms to
 known drivers.")
     (license license:gpl2+)))
+
+(define-public r-activitycounts
+  (package
+    (name "r-activitycounts")
+    (version "0.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "activityCounts" version))
+       (sha256
+        (base32
+         "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
+    (properties
+     `((upstream-name . "activityCounts")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lubridate" ,r-lubridate)
+       ("r-magrittr" ,r-magrittr)
+       ("r-seewave" ,r-seewave)
+       ("r-signal" ,r-signal)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/walkabillylab/activityCounts")
+    (synopsis "Generate ActiLife counts")
+    (description
+     "ActiLife generates activity counts from data collected by Actigraph
+accelerometers.  Actigraph is one of the most common research-grade
+accelerometers.  There is considerable research validating and developing
+algorithms for human activity using ActiLife counts.  Unfortunately, ActiLife
+counts are proprietary and difficult to implement if researchers use different
+accelerometer brands.  The code creates ActiLife counts from raw acceleration
+data for different accelerometer brands.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 6f94a3e5f599d2fb1a70ed8297576b39658ebed2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:55:01 +0100
Subject: gnu: Add r-activityindex.

* gnu/packages/cran.scm (r-activityindex): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 259fa1d3e9..4ff97d350c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18023,3 +18023,28 @@ counts are proprietary and difficult to implement if researchers use different
 accelerometer brands.  The code creates ActiLife counts from raw acceleration
 data for different accelerometer brands.")
     (license license:gpl3)))
+
+(define-public r-activityindex
+  (package
+    (name "r-activityindex")
+    (version "0.3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ActivityIndex" version))
+       (sha256
+        (base32
+         "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
+    (properties `((upstream-name . "ActivityIndex")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
+    (synopsis "Activity Index calculation using raw accelerometry data")
+    (description
+     "This is a package to read raw accelerometry from GT3X+ accelerometry
+data and plain table data to calculate the Activity Index from Bai et
+al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From bbaab253966522abb74d8b3937d69f158de360f9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:55:14 +0100
Subject: gnu: Add r-activpal.

* gnu/packages/cran.scm (r-activpal): 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 4ff97d350c..2c83e70563 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18048,3 +18048,34 @@ data for different accelerometer brands.")
 data and plain table data to calculate the Activity Index from Bai et
 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
     (license license:gpl3)))
+
+(define-public r-activpal
+  (package
+    (name "r-activpal")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "activPAL" version))
+       (sha256
+        (base32
+         "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
+    (properties `((upstream-name . "activPAL")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-devtools" ,r-devtools)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lubridate" ,r-lubridate)
+       ("r-magrittr" ,r-magrittr)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://cran.r-project.org/web/packages/activPAL")
+    (synopsis "Processing and chart generation from activPAL events files")
+    (description
+     "This package contains functions to generate pre-defined summary
+statistics from activPAL events files.  The package also contains functions to
+produce informative graphics that visualize physical activity behaviour and
+trends.  This includes generating graphs that align physical activity
+behaviour with additional time based observations described by other data
+sets, such as sleep diaries and continuous glucose monitoring data.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From a5d4dc7efb2b1bf01fe7bbbf18d91f8b6c63e7aa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:56:03 +0100
Subject: gnu: Add r-activpalprocessing.

* gnu/packages/cran.scm (r-activpalprocessing): 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 2c83e70563..7020725983 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18079,3 +18079,27 @@ trends.  This includes generating graphs that align physical activity
 behaviour with additional time based observations described by other data
 sets, such as sleep diaries and continuous glucose monitoring data.")
     (license license:gpl3)))
+
+(define-public r-activpalprocessing
+  (package
+    (name "r-activpalprocessing")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "activpalProcessing" version))
+       (sha256
+        (base32
+         "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
+    (properties
+     `((upstream-name . "activpalProcessing")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-chron" ,r-chron)))
+    (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
+    (synopsis "Process activPAL events files")
+    (description
+     "This package performs estimation of physical activity and sedentary
+behavior variables from activPAL events files.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 5f08fa64f023192c1aef0b34afb00b17bdd591de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:56:22 +0100
Subject: gnu: Add r-actogrammr.

* gnu/packages/cran.scm (r-actogrammr): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7020725983..ba322ee220 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18103,3 +18103,32 @@ sets, such as sleep diaries and continuous glucose monitoring data.")
 behavior variables from activPAL events files.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-actogrammr
+  (package
+    (name "r-actogrammr")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "actogrammr" version))
+       (sha256
+        (base32
+         "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
+    (properties `((upstream-name . "actogrammr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lubridate" ,r-lubridate)
+       ("r-readr" ,r-readr)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://cran.r-project.org/web/packages/actogrammr/")
+    (synopsis "Read in activity data and plot actograms")
+    (description
+     "Read in activity measurements from standard file formats used by
+circadian rhythm researchers, currently only ClockLab format, and process and
+plot the data.  The central type of plot is the actogram, as first described
+in \"Activity and distribution of certain wild mice in relation to biotic
+communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 1830e0383b808a1a1b943f714335cf36efc38795 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:56:41 +0100
Subject: gnu: Add r-expint.

* gnu/packages/cran.scm (r-expint): 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 ba322ee220..7bb4726fd1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18132,3 +18132,26 @@ plot the data.  The central type of plot is the actogram, as first described
 in \"Activity and distribution of certain wild mice in relation to biotic
 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
     (license license:gpl3)))
+
+(define-public r-expint
+  (package
+    (name "r-expint")
+    (version "0.1-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "expint" version))
+       (sha256
+        (base32
+         "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
+    (properties `((upstream-name . "expint")))
+    (build-system r-build-system)
+    (home-page "https://gitlab.com/vigou3/expint")
+    (synopsis "Exponential integral and incomplete Gamma function")
+    (description
+     "This package provides the exponential integrals @code{E_1(x)},
+@code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
+function @code{G(a, x)} defined for negative values of its first argument.
+The package also gives easy access to the underlying C routines through an
+API; see the package vignette for details.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 7faa05377eda6b7ec5d9292da435f1534285f3dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:56:56 +0100
Subject: gnu: Add r-actuar.

* gnu/packages/cran.scm (r-actuar): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7bb4726fd1..1f0ebea2c1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18155,3 +18155,31 @@ function @code{G(a, x)} defined for negative values of its first argument.
 The package also gives easy access to the underlying C routines through an
 API; see the package vignette for details.")
     (license license:gpl2+)))
+
+(define-public r-actuar
+  (package
+    (name "r-actuar")
+    (version "2.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "actuar" version))
+       (sha256
+        (base32
+         "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
+    (properties `((upstream-name . "actuar")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-expint" ,r-expint)))
+    (home-page "https://gitlab.com/vigou3/actuar")
+    (synopsis "Actuarial functions and heavy tailed distributions")
+    (description
+     "This package provides functions and data sets for actuarial science:
+modeling of loss distributions; risk theory and ruin theory; simulation of
+compound models, discrete mixtures and compound hierarchical models;
+credibility theory.  It boasts support for many additional probability
+distributions to model insurance loss amounts and loss frequency: 19
+continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
+distribution; zero-truncated and zero-modified extensions of the standard
+discrete distributions.  It also supports phase-type distributions commonly
+used to compute ruin probabilities.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 6968aa2fe71a5f5ee63b453d43d3b6d00b1b0f22 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:57:13 +0100
Subject: gnu: Add r-bmp.

* gnu/packages/cran.scm (r-bmp): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1f0ebea2c1..58d9a7f69f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18183,3 +18183,23 @@ distribution; zero-truncated and zero-modified extensions of the standard
 discrete distributions.  It also supports phase-type distributions commonly
 used to compute ruin probabilities.")
     (license license:gpl2+)))
+
+(define-public r-bmp
+  (package
+    (name "r-bmp")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bmp" version))
+       (sha256
+        (base32
+         "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
+    (properties `((upstream-name . "bmp")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/bmp/")
+    (synopsis "Read Bitmap (BMP) images")
+    (description
+     "This package provides pure R tools to read BMP format images.  It is
+currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 7dd1fbf9ee14dd534bbd7ce2b629d1a2f6333341 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 10:57:29 +0100
Subject: gnu: Add r-readbitmap.

* gnu/packages/cran.scm (r-readbitmap): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 58d9a7f69f..1699abb85d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18203,3 +18203,32 @@ used to compute ruin probabilities.")
      "This package provides pure R tools to read BMP format images.  It is
 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
     (license license:gpl2+)))
+
+(define-public r-readbitmap
+  (package
+    (name "r-readbitmap")
+    (version "0.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "readbitmap" version))
+       (sha256
+        (base32
+         "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
+    (properties `((upstream-name . "readbitmap")))
+    (build-system r-build-system)
+    (inputs
+     `(("libjpeg" ,libjpeg)
+       ("libpng" ,libpng)))
+    (propagated-inputs
+     `(("r-bmp" ,r-bmp)
+       ("r-jpeg" ,r-jpeg)
+       ("r-png" ,r-png)
+       ("r-tiff" ,r-tiff)))
+    (home-page "https://github.com/jefferis/readbitmap")
+    (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
+    (description
+     "This package provides tools to identify and read BMP, JPEG, PNG, and
+TIFF format bitmap images.  Identification defaults to the use of the magic
+number embedded in the file rather than the file extension.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5e2ad376848845ce114e97b24901a90a222ef939 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:28:11 +0100
Subject: gnu: Add r-imager.

* gnu/packages/cran.scm (r-imager): New variable.
---
 gnu/packages/cran.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1699abb85d..f5eaf88c1b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18232,3 +18232,45 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
 TIFF format bitmap images.  Identification defaults to the use of the magic
 number embedded in the file rather than the file extension.")
     (license license:gpl2+)))
+
+(define-public r-imager
+  (package
+    (name "r-imager")
+    (version "0.41.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "imager" version))
+       (sha256
+        (base32
+         "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v"))))
+    (properties `((upstream-name . "imager")))
+    (build-system r-build-system)
+    (inputs
+     `(("fftw" ,fftw)
+       ("libtiff" ,libtiff)
+       ("libx11" ,libx11)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-cairo" ,r-cairo)
+       ("r-downloader" ,r-downloader)
+       ("r-igraph" ,r-igraph)
+       ("r-jpeg" ,r-jpeg)
+       ("r-magrittr" ,r-magrittr)
+       ("r-plyr" ,r-plyr)
+       ("r-png" ,r-png)
+       ("r-purrr" ,r-purrr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readbitmap" ,r-readbitmap)
+       ("r-stringr" ,r-stringr)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (home-page "http://dahtah.github.io/imager")
+    (synopsis "Image processing library")
+    (description
+     "This is a package for fast image processing for images in up to 4
+dimensions (two spatial dimensions, one time/depth dimension, one color
+dimension).  It provides most traditional image processing tools (filtering,
+morphology, transformations, etc.) as well as various functions for easily
+analyzing image data using R.  The package wraps @url{http://cimg.eu, CImg}, a
+simple, modern C++ library for image processing.")
+    (license license:lgpl3)))
-- 
cgit v1.2.3


From 154555e42fafbbeb45ebc44a2f4de19b41adc2cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:28:35 +0100
Subject: gnu: Add r-acuityview.

* gnu/packages/cran.scm (r-acuityview): 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 f5eaf88c1b..64b6ed9c10 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18274,3 +18274,27 @@ morphology, transformations, etc.) as well as various functions for easily
 analyzing image data using R.  The package wraps @url{http://cimg.eu, CImg}, a
 simple, modern C++ library for image processing.")
     (license license:lgpl3)))
+
+(define-public r-acuityview
+  (package
+    (name "r-acuityview")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AcuityView" version))
+       (sha256
+        (base32
+         "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
+    (properties `((upstream-name . "AcuityView")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fftwtools" ,r-fftwtools)
+       ("r-imager" ,r-imager)
+       ("r-plotrix" ,r-plotrix)))
+    (home-page "https://cran.r-project.org/web/packages/AcuityView/")
+    (synopsis "Display scenes as seen by an animal with less acute vision")
+    (description
+     "This package provides a simple method for representing a visual scene as
+it may be seen by an animal with less acute vision.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 2a1fd51864826dd983194a16a49a9e0220f02454 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:28:50 +0100
Subject: gnu: Add r-adabag.

* gnu/packages/cran.scm (r-adabag): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 64b6ed9c10..6b64e797ea 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18298,3 +18298,31 @@ simple, modern C++ library for image processing.")
      "This package provides a simple method for representing a visual scene as
 it may be seen by an animal with less acute vision.")
     (license license:gpl2+)))
+
+(define-public r-adabag
+  (package
+    (name "r-adabag")
+    (version "4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "adabag" version))
+       (sha256
+        (base32
+         "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
+    (properties `((upstream-name . "adabag")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-caret" ,r-caret)
+       ("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-rpart" ,r-rpart)))
+    (home-page "https://cran.r-project.org/web/packages/adabag/")
+    (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
+    (description
+     "This package implements Freund and Schapire's Adaboost.M1 algorithm and
+Breiman's Bagging algorithm using classification trees as individual
+classifiers.  Once these classifiers have been trained, they can be used to
+predict on new data.  Also, cross validation estimation of the error can be
+done.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 0b13a75716136aac6ffee5f1f10bec77393a1ca7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:29:24 +0100
Subject: gnu: Add r-adagio.

* gnu/packages/cran.scm (r-adagio): 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 6b64e797ea..bebf4acbe4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18326,3 +18326,26 @@ classifiers.  Once these classifiers have been trained, they can be used to
 predict on new data.  Also, cross validation estimation of the error can be
 done.")
     (license license:gpl2+)))
+
+(define-public r-adagio
+  (package
+    (name "r-adagio")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "adagio" version))
+       (sha256
+        (base32
+         "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
+    (properties `((upstream-name . "adagio")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/adagio/")
+    (synopsis "Discrete and global optimization routines")
+    (description
+     "This package provides methods and algorithms for discrete optimization,
+e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
+Hooke-Jeeves minimization, and some (evolutionary) global optimization
+functions.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 09e9ad334ac15ddea7e440cb1737f2c687f5c43a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:29:40 +0100
Subject: gnu: Add r-univoutl.

* gnu/packages/cran.scm (r-univoutl): 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 bebf4acbe4..855a3c956e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18349,3 +18349,29 @@ e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
 Hooke-Jeeves minimization, and some (evolutionary) global optimization
 functions.")
     (license license:gpl3+)))
+
+(define-public r-univoutl
+  (package
+    (name "r-univoutl")
+    (version "0.1-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "univOutl" version))
+       (sha256
+        (base32
+         "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
+    (properties `((upstream-name . "univOutl")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-hmisc" ,r-hmisc)
+       ("r-robustbase" ,r-robustbase)))
+    (home-page "https://github.com/marcellodo/univOutl")
+    (synopsis "Detection of univariate outliers")
+    (description
+     "This package provides well-known outlier detection techniques in the
+univariate case.  Methods to deal with skewed distribution are included too.
+The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
+historical data is implemented as well.  When available, survey weights can be
+used in outliers detection.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5458490ebb2aa5fbb5d72ce8468791669bc634ca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 11:29:56 +0100
Subject: gnu: Add r-tolerance.

* gnu/packages/cran.scm (r-tolerance): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 855a3c956e..cc0f876d85 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18375,3 +18375,33 @@ The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
 historical data is implemented as well.  When available, survey weights can be
 used in outliers detection.")
     (license license:gpl2+)))
+
+(define-public r-tolerance
+  (package
+    (name "r-tolerance")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tolerance" version))
+       (sha256
+        (base32
+         "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"))))
+    (properties `((upstream-name . "tolerance")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rgl" ,r-rgl)))
+    (home-page "https://cran.r-project.org/web/packages/tolerance/")
+    (synopsis "Statistical tolerance intervals and regions")
+    (description
+     "This package provides functions for estimating tolerance
+limits (intervals) for various univariate distributions (binomial, Cauchy,
+discrete Pareto, exponential, two-parameter exponential, extreme value,
+hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
+normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
+Bayesian normal tolerance limits, multivariate normal tolerance regions,
+nonparametric tolerance intervals, tolerance bands for regression
+settings (linear regression, nonlinear regression, nonparametric regression,
+and multivariate regression), and analysis of variance tolerance intervals.
+Visualizations are also available for most of these settings.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 94ecf71344bc55fa2610d45f391a21befdfb54f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:30:50 +0100
Subject: gnu: Add r-additivitytests.

* gnu/packages/cran.scm (r-additivitytests): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cc0f876d85..0aa20b8e6e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18405,3 +18405,24 @@ settings (linear regression, nonlinear regression, nonparametric regression,
 and multivariate regression), and analysis of variance tolerance intervals.
 Visualizations are also available for most of these settings.")
     (license license:gpl2+)))
+
+(define-public r-additivitytests
+  (package
+    (name "r-additivitytests")
+    (version "1.1-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "additivityTests" version))
+       (sha256
+        (base32
+         "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
+    (properties
+     `((upstream-name . "additivityTests")))
+    (build-system r-build-system)
+    (home-page "https://github.com/simecek/additivityTests")
+    (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
+    (description
+     "This package provides an implementation of the Tukey, Mandel,
+Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 9906cb80de8e2bcfc55507d6c6f00fc3a89000b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:31:21 +0100
Subject: gnu: Add r-flexclust.

* gnu/packages/cran.scm (r-flexclust): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0aa20b8e6e..3cd12d185c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18426,3 +18426,32 @@ Visualizations are also available for most of these settings.")
      "This package provides an implementation of the Tukey, Mandel,
 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
     (license license:gpl3)))
+
+(define-public r-flexclust
+  (package
+    (name "r-flexclust")
+    (version "1.4-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "flexclust" version))
+       (sha256
+        (base32
+         "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
+    (properties `((upstream-name . "flexclust")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-class" ,r-class)
+       ("r-lattice" ,r-lattice)
+       ("r-modeltools" ,r-modeltools)))
+    (home-page "https://cran.r-project.org/web/packages/flexclust/")
+    (synopsis "Flexible cluster algorithms")
+    (description
+     "The main function @code{kcca} implements a general framework for
+k-centroids cluster analysis supporting arbitrary distance measures and
+centroid computation.  Further cluster methods include hard competitive
+learning, neural gas, and QT clustering.  There are numerous visualization
+methods for cluster results (neighborhood graphs, convex cluster hulls,
+barcharts of centroids, ...), and bootstrap methods for the analysis of
+cluster stability.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 86a760cc67170331abcb1f0bdf73af4716effad5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:31:40 +0100
Subject: gnu: Add r-biclust.

* gnu/packages/cran.scm (r-biclust): 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 3cd12d185c..354837823b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18455,3 +18455,34 @@ methods for cluster results (neighborhood graphs, convex cluster hulls,
 barcharts of centroids, ...), and bootstrap methods for the analysis of
 cluster stability.")
     (license license:gpl2)))
+
+(define-public r-biclust
+  (package
+    (name "r-biclust")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "biclust" version))
+       (sha256
+        (base32
+         "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0"))))
+    (properties `((upstream-name . "biclust")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-additivitytests" ,r-additivitytests)
+       ("r-colorspace" ,r-colorspace)
+       ("r-flexclust" ,r-flexclust)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://cran.r-project.org/web/packages/biclust/")
+    (synopsis "BiCluster algorithms")
+    (description
+     "The main function @code{biclust()} provides several algorithms to find
+biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
+In addition, the package provides methods for data
+preprocessing (normalization and discretization), visualization, and
+validation of bicluster solutions.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 9cd3ae8620ed27fb54da1face9ec1a4265746602 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:32:02 +0100
Subject: gnu: Add r-icge.

* gnu/packages/cran.scm (r-icge): 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 354837823b..8482f274b6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18486,3 +18486,27 @@ In addition, the package provides methods for data
 preprocessing (normalization and discretization), visualization, and
 validation of bicluster solutions.")
     (license license:gpl3)))
+
+(define-public r-icge
+  (package
+    (name "r-icge")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ICGE" version))
+       (sha256
+        (base32
+         "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
+    (properties `((upstream-name . "ICGE")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/ICGE/")
+    (synopsis "Cluster estimation and identification of atypical units")
+    (description
+     "ICGE is a package that helps to estimate the number of real clusters in
+data as well as to identify atypical units.  The underlying methods are based
+on distances rather than on unit x variables.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 9fd2d4fdb17ad70b8e94a388546eab59642faecd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:32:19 +0100
Subject: gnu: Add r-depth.

* gnu/packages/cran.scm (r-depth): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8482f274b6..7688e90f23 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18510,3 +18510,32 @@ validation of bicluster solutions.")
 data as well as to identify atypical units.  The underlying methods are based
 on distances rather than on unit x variables.")
     (license license:gpl2+)))
+
+(define-public r-depth
+  (package
+    (name "r-depth")
+    (version "2.1-1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "depth" version))
+       (sha256
+        (base32
+         "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
+    (properties `((upstream-name . "depth")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-circular" ,r-circular)
+       ("r-rgl" ,r-rgl)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/depth/")
+    (synopsis "Nonparametric depth functions for multivariate analysis")
+    (description
+     "This package provides tools for depth functions methodology applied to
+multivariate analysis.  Besides allowing calculation of depth values and
+depth-based location estimators, the package includes functions or drawing
+contour plots and perspective plots of depth functions.  Euclidian and
+spherical depths are supported.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From ccc2c19b02ef2a5b71ea67719a0d57b34e2622b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:32:39 +0100
Subject: gnu: Add r-archetypes.

* gnu/packages/cran.scm (r-archetypes): 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 7688e90f23..dbaf4f88af 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18539,3 +18539,27 @@ depth-based location estimators, the package includes functions or drawing
 contour plots and perspective plots of depth functions.  Euclidian and
 spherical depths are supported.")
     (license license:gpl2)))
+
+(define-public r-archetypes
+  (package
+    (name "r-archetypes")
+    (version "2.2-0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "archetypes" version))
+       (sha256
+        (base32
+         "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
+    (properties `((upstream-name . "archetypes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-modeltools" ,r-modeltools)
+       ("r-nnls" ,r-nnls)))
+    (home-page "https://cran.r-project.org/web/packages/archetypes")
+    (synopsis "Archetypal analysis")
+    (description
+     "The main function @code{archetypes} implements a framework for
+archetypal analysis supporting arbitrary problem solving mechanisms for the
+different conceptual parts of the algorithm.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From c71724653ab2b75ef533e9b9920e7b3f735154ad Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:32:49 +0100
Subject: gnu: Add r-shapes.

* gnu/packages/cran.scm (r-shapes): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index dbaf4f88af..6ef9f2e680 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18563,3 +18563,32 @@ spherical depths are supported.")
 archetypal analysis supporting arbitrary problem solving mechanisms for the
 different conceptual parts of the algorithm.")
     (license license:gpl2+)))
+
+(define-public r-shapes
+  (package
+    (name "r-shapes")
+    (version "1.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shapes" version))
+       (sha256
+        (base32
+         "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
+    (properties `((upstream-name . "shapes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-minpack-lm" ,r-minpack-lm)
+       ("r-rgl" ,r-rgl)
+       ("r-scatterplot3d" ,r-scatterplot3d)))
+    (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
+    (synopsis "Statistical shape analysis")
+    (description
+     "This package provides routines for the statistical analysis of landmark
+shapes, including Procrustes analysis, graphical displays, principal
+components analysis, permutation and bootstrap tests, thin-plate spline
+transformation grids and comparing covariance matrices.  See Dryden, I.L.  and
+Mardia, K.V. (2016).  Statistical shape analysis, with Applications in R (2nd
+Edition), John Wiley and Sons.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From c67508079d2abf9b286812c3b2889f4bbbcf2735 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:34:09 +0100
Subject: gnu: Add r-anthropometry.

* gnu/packages/cran.scm (r-anthropometry): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6ef9f2e680..9e11802224 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18592,3 +18592,36 @@ transformation grids and comparing covariance matrices.  See Dryden, I.L.  and
 Mardia, K.V. (2016).  Statistical shape analysis, with Applications in R (2nd
 Edition), John Wiley and Sons.")
     (license license:gpl2)))
+
+(define-public r-anthropometry
+  (package
+    (name "r-anthropometry")
+    (version "1.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Anthropometry" version))
+       (sha256
+        (base32
+         "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
+    (properties `((upstream-name . "Anthropometry")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-archetypes" ,r-archetypes)
+       ("r-biclust" ,r-biclust)
+       ("r-cluster" ,r-cluster)
+       ("r-depth" ,r-depth)
+       ("r-fnn" ,r-fnn)
+       ("r-icge" ,r-icge)
+       ("r-nnls" ,r-nnls)
+       ("r-rgl" ,r-rgl)
+       ("r-shapes" ,r-shapes)))
+    (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
+    (synopsis "Statistical methods for anthropometric data")
+    (description
+     "This package provides statistical methods especially developed to
+analyze anthropometric data.  These methods are aimed at providing effective
+solutions to some commons problems related to Ergonomics and Anthropometry.
+They are based on clustering, the statistical concept of data depth,
+statistical shape analysis and archetypal analysis.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5c0b5b8ad7351a0d951ee2227093aacefdae28e4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 13:34:32 +0100
Subject: gnu: Add r-adamethods.

* gnu/packages/cran.scm (r-adamethods): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9e11802224..bbe44d60b8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18625,3 +18625,33 @@ solutions to some commons problems related to Ergonomics and Anthropometry.
 They are based on clustering, the statistical concept of data depth,
 statistical shape analysis and archetypal analysis.")
     (license license:gpl2+)))
+
+(define-public r-adamethods
+  (package
+    (name "r-adamethods")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "adamethods" version))
+       (sha256
+        (base32
+         "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
+    (properties `((upstream-name . "adamethods")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-anthropometry" ,r-anthropometry)
+       ("r-archetypes" ,r-archetypes)
+       ("r-fnn" ,r-fnn)
+       ("r-foreach" ,r-foreach)
+       ("r-nnls" ,r-nnls)
+       ("r-tolerance" ,r-tolerance)
+       ("r-univoutl" ,r-univoutl)))
+    (home-page "https://cran.r-project.org/web/packages/adamethods/")
+    (synopsis "Archetypoid algorithms and anomaly detection")
+    (description
+     "This package is a collection of several algorithms to obtain
+archetypoids with small and large databases and with both classical
+multivariate data and functional data (univariate and multivariate).  Some of
+these algorithms also allow to detect anomalies (outliers).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From b5b6e74e150469e48111f0e6e5a83ab9f6b40cd8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 15:52:29 +0100
Subject: gnu: Add r-idpmisc.

* gnu/packages/cran.scm (r-idpmisc): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bbe44d60b8..b12d984387 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18655,3 +18655,32 @@ archetypoids with small and large databases and with both classical
 multivariate data and functional data (univariate and multivariate).  Some of
 these algorithms also allow to detect anomalies (outliers).")
     (license license:gpl2+)))
+
+(define-public r-idpmisc
+  (package
+    (name "r-idpmisc")
+    (version "1.1.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IDPmisc" version))
+       (sha256
+        (base32
+         "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
+    (properties `((upstream-name . "IDPmisc")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)))
+    (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
+    (synopsis "Functions for data analyses and visualization")
+    (description
+     "This package provides different high-level graphics functions for
+displaying large datasets, displaying circular data in a very flexible way,
+finding local maxima, brewing color ramps, drawing nice arrows, zooming
+2D-plots, creating figures with differently colored margin and plot region.
+In addition, the package contains auxiliary functions for data manipulation
+like omitting observations with irregular values or selecting data by logical
+vectors, which include NAs.  Other functions are especially useful in
+spectroscopy and analyses of environmental data: robust baseline fitting,
+finding peaks in spectra, converting humidity measures.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From eb15df8deab4f8a1560389dc41dc51c7270779d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 16:36:05 +0100
Subject: gnu: Add r-qqman.

* gnu/packages/cran.scm (r-qqman): 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 b12d984387..c9dfafa9b1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18684,3 +18684,25 @@ vectors, which include NAs.  Other functions are especially useful in
 spectroscopy and analyses of environmental data: robust baseline fitting,
 finding peaks in spectra, converting humidity measures.")
     (license license:gpl3+)))
+
+(define-public r-qqman
+  (package
+    (name "r-qqman")
+    (version "0.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qqman" version))
+       (sha256
+        (base32
+         "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
+    (properties `((upstream-name . "qqman")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-calibrate" ,r-calibrate)))
+    (home-page "https://cran.r-project.org/web/packages/qqman/")
+    (synopsis "Q-Q and Manhattan plots for GWAS data")
+    (description
+     "This package allows you to create Q-Q and Manhattan plots for GWAS data
+from PLINK results.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 5aa7e882fa3f198fa8e108827162d71b0229033c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 16:46:12 +0100
Subject: gnu: Add r-ggplot-multistats.

* gnu/packages/cran.scm (r-ggplot-multistats): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c9dfafa9b1..3190cee592 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18706,3 +18706,31 @@ finding peaks in spectra, converting humidity measures.")
      "This package allows you to create Q-Q and Manhattan plots for GWAS data
 from PLINK results.")
     (license license:gpl3)))
+
+(define-public r-ggplot-multistats
+  (package
+    (name "r-ggplot-multistats")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggplot.multistats" version))
+       (sha256
+        (base32
+         "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
+    (properties
+     `((upstream-name . "ggplot.multistats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-hexbin" ,r-hexbin)
+       ("r-rlang" ,r-rlang)
+       ("r-scales" ,r-scales)))
+    (home-page "https://github.com/flying-sheep/ggplot.multistats")
+    (synopsis "Multiple summary statistics for binned stats/geometries")
+    (description
+     "This package provides the ggplot binning layer @code{stat_summaries_hex()},
+which functions similar to its singular form, but allows the use of multiple
+statistics per bin.  Those statistics can be mapped to multiple bin
+aesthetics.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 257b3b812ce5ef605090c079e6e59cb5383a2100 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Dec 2019 19:34:06 +0100
Subject: gnu: Add r-knn-covertree.

* gnu/packages/cran.scm (r-knn-covertree): 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 3190cee592..349ea62e6b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18734,3 +18734,29 @@ which functions similar to its singular form, but allows the use of multiple
 statistics per bin.  Those statistics can be mapped to multiple bin
 aesthetics.")
     (license license:gpl3)))
+
+(define-public r-knn-covertree
+  (package
+    (name "r-knn-covertree")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "knn.covertree" version))
+       (sha256
+        (base32
+         "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
+    (properties `((upstream-name . "knn.covertree")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)))
+    (home-page "https://github.com/flying-sheep/knn.covertree")
+    (synopsis "Accurate kNN Implementation with multiple distance measures")
+    (description
+     "Similarly to the FNN package, this package allows calculation of the k
+nearest neighbors (kNN) of a data matrix.  The implementation is based on
+cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
+Langford (2006) @url{doi:10.1145/1143844.1143857}.")
+    (license license:agpl3+)))
-- 
cgit v1.2.3


From 0128a9df8f896e011ceb6b44781ed1521492bf45 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:49:20 +0100
Subject: gnu: r-rgooglemaps: Update to 1.4.5.

* gnu/packages/cran.scm (r-rgooglemaps): Update to 1.4.5.
---
 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 349ea62e6b..b9d75ae0b9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1292,14 +1292,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
     (name "r-rgooglemaps")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
+         "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7"))))
     (properties `((upstream-name . "RgoogleMaps")))
     (build-system r-build-system)
     (propagated-inputs `(("r-png" ,r-png)))
-- 
cgit v1.2.3


From 3dc1d4330056acd9540e6aa9542e1927e8bb2755 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:49:37 +0100
Subject: gnu: r-amap: Update to 0.8-18.

* gnu/packages/cran.scm (r-amap): Update to 0.8-18.
---
 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 b9d75ae0b9..8ab15957e1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1424,13 +1424,13 @@ embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
 (define-public r-amap
   (package
     (name "r-amap")
-    (version "0.8-17")
+    (version "0.8-18")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "amap" version))
               (sha256
                (base32
-                "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
+                "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
-- 
cgit v1.2.3


From c9a0f6106912905ad814549764731e659715f4ec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:49:44 +0100
Subject: gnu: r-rmysql: Update to 0.10.18.

* gnu/packages/cran.scm (r-rmysql): Update to 0.10.18.
---
 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 8ab15957e1..713f4375eb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2777,14 +2777,14 @@ dimensioned arrays.")
 (define-public r-rmysql
   (package
     (name "r-rmysql")
-    (version "0.10.17")
+    (version "0.10.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RMySQL" version))
        (sha256
         (base32
-         "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
+         "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4"))))
     (properties `((upstream-name . "RMySQL")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From a3b51a34f448c1986f2625f90a32ca71663bfb69 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:49:52 +0100
Subject: gnu: r-broom: Update to 0.5.3.

* gnu/packages/cran.scm (r-broom): Update to 0.5.3.
---
 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 713f4375eb..1a2d7f9622 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3045,14 +3045,14 @@ by base R methods related to model fitting.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
+         "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
-- 
cgit v1.2.3


From c79e80f81b5c4e9dde4b86bbba720aa29ff5e91b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:00 +0100
Subject: gnu: r-mice: Update to 3.7.0.

* gnu/packages/cran.scm (r-mice): Update to 3.7.0.
---
 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 1a2d7f9622..458d5130e8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3336,14 +3336,14 @@ analysis of multiply imputed data sets.")
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "3.6.0")
+    (version "3.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
+         "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
-- 
cgit v1.2.3


From a8e8a10a762477b94e3c8ae554d1362d7d755e42 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:07 +0100
Subject: gnu: r-tinytex: Update to 0.18.

* gnu/packages/cran.scm (r-tinytex): Update to 0.18.
---
 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 458d5130e8..c6861abbf8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4132,14 +4132,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.17")
+    (version "0.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
+         "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
-- 
cgit v1.2.3


From 2beb585c8d4318f09f32364c988d875432347f5d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:15 +0100
Subject: gnu: r-sna: Update to 2.5.

* gnu/packages/cran.scm (r-sna): Update to 2.5.
---
 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 c6861abbf8..7cccb09bb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4225,14 +4225,14 @@ detect possible inconsistencies.")
 (define-public r-sna
   (package
     (name "r-sna")
-    (version "2.4")
+    (version "2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sna" version))
        (sha256
         (base32
-         "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
+         "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-network" ,r-network)
-- 
cgit v1.2.3


From 98ce8a31f0d78ff84361decc1d8ae5f6db91723a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:22 +0100
Subject: gnu: r-renv: Update to 0.9.2.

* gnu/packages/cran.scm (r-renv): Update to 0.9.2.
---
 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 7cccb09bb6..229402f58c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5628,14 +5628,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
 (define-public r-renv
   (package
     (name "r-renv")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "renv" version))
        (sha256
         (base32
-         "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm"))))
+         "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr"))))
     (properties `((upstream-name . "renv")))
     (build-system r-build-system)
     (home-page "https://rstudio.github.io/renv")
-- 
cgit v1.2.3


From cceb86f98263c5420784a9f9b4ad54955f1ca637 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:28 +0100
Subject: gnu: r-rdpack: Update to 0.11-1.

* gnu/packages/cran.scm (r-rdpack): Update to 0.11-1.
---
 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 229402f58c..6239909792 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6148,14 +6148,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
 (define-public r-rdpack
   (package
     (name "r-rdpack")
-    (version "0.11-0")
+    (version "0.11-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rdpack" version))
        (sha256
         (base32
-         "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
+         "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
     (properties `((upstream-name . "Rdpack")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 31fa45b679bca1731eebde64b993f3cc758151c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:35 +0100
Subject: gnu: r-deriv: Update to 4.0.

* gnu/packages/cran.scm (r-deriv): Update to 4.0.
---
 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 6239909792..865d0ece74 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6716,14 +6716,14 @@ Group (Non-)Overlap considerations.")
 (define-public r-deriv
   (package
     (name "r-deriv")
-    (version "3.9.0")
+    (version "4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Deriv" version))
        (sha256
         (base32
-         "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
+         "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
     (properties `((upstream-name . "Deriv")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/Deriv")
-- 
cgit v1.2.3


From f92c0c1efcb978c32445d9f3bc184d20950a6a2e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:45 +0100
Subject: gnu: r-multcomp: Update to 1.4-11.

* gnu/packages/cran.scm (r-multcomp): Update to 1.4-11.
---
 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 865d0ece74..5c7eb2547a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8148,14 +8148,14 @@ packages maintained by Torsten Hothorn.")
 (define-public r-multcomp
   (package
     (name "r-multcomp")
-    (version "1.4-10")
+    (version "1.4-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "multcomp" version))
        (sha256
         (base32
-         "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
+         "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
-- 
cgit v1.2.3


From afc1ff2f0811fc7f81e2c60ab63cc4dba4a19e94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:50:54 +0100
Subject: gnu: r-performance: Update to 0.4.2.

* gnu/packages/cran.scm (r-performance): Update to 0.4.2.
---
 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 5c7eb2547a..d677ecb4ee 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8433,14 +8433,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.4.0")
+    (version "0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
+         "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
-- 
cgit v1.2.3


From d4e8f2070504466ef4ec8d458f7c91dec052d615 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:51:01 +0100
Subject: gnu: r-lmertest: Update to 3.1-1.

* gnu/packages/cran.scm (r-lmertest): Update to 3.1-1.
---
 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 d677ecb4ee..0265d508da 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9041,14 +9041,14 @@ experiments using ANOVA or mixed models.")
 (define-public r-lmertest
   (package
     (name "r-lmertest")
-    (version "3.1-0")
+    (version "3.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lmerTest" version))
        (sha256
         (base32
-         "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
+         "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
     (properties `((upstream-name . "lmerTest")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From b744174e7dc02f41075a53acbadf7a66d37e2925 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:51:07 +0100
Subject: gnu: r-fmsb: Update to 0.7.0.

* gnu/packages/cran.scm (r-fmsb): Update to 0.7.0.
---
 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 0265d508da..c3ac14ddc0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9486,14 +9486,14 @@ for evolution along a phylogenetic tree.")
 (define-public r-fmsb
   (package
     (name "r-fmsb")
-    (version "0.6.3")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fmsb" version))
        (sha256
         (base32
-         "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
+         "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
     (build-system r-build-system)
     (home-page "http://minato.sip21c.org/msb/")
     (synopsis "Functions for medical statistics book with demographic data")
-- 
cgit v1.2.3


From 5f99ffb013ca3766c691f666539ba6759790f361 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:51:19 +0100
Subject: gnu: r-tm: Update to 0.7-7.

* gnu/packages/cran.scm (r-tm): Update to 0.7-7.
---
 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 c3ac14ddc0..8d579b364d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9667,14 +9667,14 @@ Processing.")
 (define-public r-tm
   (package
     (name "r-tm")
-    (version "0.7-6")
+    (version "0.7-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tm" version))
        (sha256
         (base32
-         "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
+         "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
     (properties `((upstream-name . "tm")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 126f027b99d0f3620fbca0f9ca402e7efe4f9d5f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:51:25 +0100
Subject: gnu: r-tidytree: Update to 0.3.1.

* gnu/packages/cran.scm (r-tidytree): Update to 0.3.1.
---
 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 8d579b364d..11f98ed893 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9763,13 +9763,13 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
-        (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
+        (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
-- 
cgit v1.2.3


From 074c698e724265c256162dfd7a1c4c8249b9a08a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Dec 2019 15:51:33 +0100
Subject: gnu: r-spam: Update to 2.5-1.

* gnu/packages/cran.scm (r-spam): Update to 2.5-1.
---
 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 11f98ed893..06c793d3cb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11083,13 +11083,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
 (define-public r-spam
   (package
     (name "r-spam")
-    (version "2.5-0")
+    (version "2.5-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spam" version))
        (sha256
-        (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2"))))
+        (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dotcall64" ,r-dotcall64)))
-- 
cgit v1.2.3


From 5ba865a73fbb1a23b2b82b3015a4171b3d9fe3c4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:55:18 +0100
Subject: gnu: Add r-gee.

* gnu/packages/cran.scm (r-gee): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 06c793d3cb..2101cd51c6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7851,6 +7851,27 @@ analysis.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-gee
+  (package
+    (name "r-gee")
+    (version "4.13-20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gee" version))
+       (sha256
+        (base32
+         "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
+    (properties `((upstream-name . "gee")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/gee/")
+    (synopsis "Generalized estimation equation solver")
+    (description
+     "This package provides a solver for generalized estimation equations.")
+    (license license:gpl2)))
+
 (define-public r-dvmisc
   (package
     (name "r-dvmisc")
-- 
cgit v1.2.3


From 3b21f5814c14604d8e940415e27b8d4aa25baf93 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:55:29 +0100
Subject: gnu: Add r-tab.

* gnu/packages/cran.scm (r-tab): 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 2101cd51c6..68b9c50d2f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7872,6 +7872,37 @@ analysis.")
      "This package provides a solver for generalized estimation equations.")
     (license license:gpl2)))
 
+(define-public r-tab
+  (package
+    (name "r-tab")
+    (version "4.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tab" version))
+       (sha256
+        (base32
+         "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
+    (properties `((upstream-name . "tab")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-gee" ,r-gee)
+       ("r-knitr" ,r-knitr)
+       ("r-mass" ,r-mass)
+       ("r-survey" ,r-survey)
+       ("r-survival" ,r-survival)
+       ("r-xtable" ,r-xtable)))
+    (home-page "https://cran.r-project.org/web/packages/tab/")
+    (synopsis "Create summary tables for statistical reports")
+    (description
+     "This package contains functions for creating various types of summary
+tables, e.g. comparing characteristics across levels of a categorical variable
+and summarizing fitted generalized linear models, generalized estimating
+equations, and Cox proportional hazards models.  Functions are available to
+handle data from simple random samples as well as complex surveys.")
+    (license license:gpl3+)))
+
 (define-public r-dvmisc
   (package
     (name "r-dvmisc")
-- 
cgit v1.2.3


From f87c6727899a181a904a624e8e9fff13c5ccd229 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:55:54 +0100
Subject: gnu: r-ordinal: Update to 2019.12-10.

* gnu/packages/cran.scm (r-ordinal): Update to 2019.12-10.
---
 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 68b9c50d2f..7c7710efb0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3236,14 +3236,14 @@ with the package @code{optim}.")
 (define-public r-ordinal
   (package
     (name "r-ordinal")
-    (version "2019.4-25")
+    (version "2019.12-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ordinal" version))
        (sha256
         (base32
-         "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
+         "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
-- 
cgit v1.2.3


From 4d6ccb000008435fbc815bd9ea49b8d66c8b305e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:56:00 +0100
Subject: gnu: r-argparser: Update to 0.6.

* gnu/packages/cran.scm (r-argparser): Update to 0.6.
---
 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 7c7710efb0..b726944dad 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3799,14 +3799,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
 (define-public r-argparser
   (package
     (name "r-argparser")
-    (version "0.4")
+    (version "0.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "argparser" version))
        (sha256
         (base32
-         "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
+         "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
     (build-system r-build-system)
     (home-page "https://bitbucket.org/djhshih/argparser")
     (synopsis "Command-line argument parser")
-- 
cgit v1.2.3


From 6e963260ae1665d06bc7c9011ec6d69931ab1443 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:56:05 +0100
Subject: gnu: r-ttr: Update to 0.23-6.

* gnu/packages/cran.scm (r-ttr): Update to 0.23-6.
---
 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 b726944dad..85b689fc9b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4278,14 +4278,14 @@ of these tests are also included.")
 (define-public r-ttr
   (package
     (name "r-ttr")
-    (version "0.23-5")
+    (version "0.23-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TTR" version))
        (sha256
         (base32
-         "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
+         "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
     (properties `((upstream-name . "TTR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f6e75823bd3f4438a1fbe14f4f1d35f8d58c4ce8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:56:17 +0100
Subject: gnu: r-dvmisc: Update to 1.1.4.

* gnu/packages/cran.scm (r-dvmisc): Update to 1.1.4.
[propagated-inputs]: Add r-tab; remove r-purrr.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 85b689fc9b..2980641102 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7906,13 +7906,13 @@ handle data from simple random samples as well as complex surveys.")
 (define-public r-dvmisc
   (package
     (name "r-dvmisc")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dvmisc" version))
        (sha256
-        (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
+        (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cubature" ,r-cubature)
@@ -7922,10 +7922,10 @@ handle data from simple random samples as well as complex surveys.")
        ("r-mass" ,r-mass)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-pracma" ,r-pracma)
-       ("r-purrr" ,r-purrr)
        ("r-rbenchmark" ,r-rbenchmark)
        ("r-rcpp" ,r-rcpp)
-       ("r-survey" ,r-survey)))
+       ("r-survey" ,r-survey)
+       ("r-tab" ,r-tab)))
     (home-page "https://cran.r-project.org/web/packages/dvmisc/")
     (synopsis "Faster computation of common statistics and miscellaneous functions")
     (description
-- 
cgit v1.2.3


From cd0e2815d5730969cafdcea031e5ccd32547ede4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:57:51 +0100
Subject: gnu: r-ggeffects: Update to 0.14.0.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.14.0.
[propagated-inputs]: Remove r-dplyr and r-rlang.
---
 gnu/packages/cran.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2980641102..88c1a4bf74 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8512,22 +8512,20 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.13.0")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
+         "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
-       ("r-insight" ,r-insight)
+     `(("r-insight" ,r-insight)
        ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
        ("r-purrr" ,r-purrr)
-       ("r-rlang" ,r-rlang)
        ("r-sjlabelled" ,r-sjlabelled)
        ("r-sjmisc" ,r-sjmisc)))
     (home-page "https://github.com/strengejacke/ggeffects")
-- 
cgit v1.2.3


From 5722022f888cfd1947d8835029f094e9b32a8d75 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:58:07 +0100
Subject: gnu: r-repr: Update to 1.0.2.

* gnu/packages/cran.scm (r-repr): Update to 1.0.2.
---
 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 88c1a4bf74..2bf238f2a1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -12482,14 +12482,14 @@ compatible with @code{rzmq} are also provided.")
 (define-public r-repr
   (package
     (name "r-repr")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "repr" version))
        (sha256
         (base32
-         "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
+         "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
-- 
cgit v1.2.3


From aaa74ee57d51537e1c7a768978fec91fdc5b9d35 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 14:58:12 +0100
Subject: gnu: r-pracma: Update to 2.2.9.

* gnu/packages/cran.scm (r-pracma): Update to 2.2.9.
---
 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 2bf238f2a1..795e5db4f1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16036,12 +16036,12 @@ to ODEs by numerical differencing.")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "2.2.5")
+    (version "2.2.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "pracma" version))
               (sha256
-               (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
+               (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/pracma/")
     (synopsis "Practical numerical math functions")
-- 
cgit v1.2.3


From 5828dd030b4cf3920573f7982420999aa5743100 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 19:18:11 +0100
Subject: gnu: Add r-poibin.

* gnu/packages/cran.scm (r-poibin): 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 795e5db4f1..24eade12ec 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18810,3 +18810,26 @@ nearest neighbors (kNN) of a data matrix.  The implementation is based on
 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
     (license license:agpl3+)))
+
+(define-public r-poibin
+  (package
+    (name "r-poibin")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "poibin" version))
+       (sha256
+        (base32
+         "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2"))))
+    (properties `((upstream-name . "poibin")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/poibin/")
+    (synopsis "Poisson binomial distribution")
+    (description
+     "This package provides an implementation of both the exact and
+approximation methods for computing the @dfn{cumulative distribution
+function} (CDF) of the Poisson binomial distribution.  It also provides the
+@dfn{probability mass function} (PMF), quantile function, and random number
+generation for the Poisson binomial distribution.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From c686e53afe184f086576901ee1d2f8a45a474606 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 19:18:26 +0100
Subject: gnu: Add r-diagram.

* gnu/packages/cran.scm (r-diagram): New variable.
---
 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 24eade12ec..117362cd9f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18833,3 +18833,30 @@ function} (CDF) of the Poisson binomial distribution.  It also provides the
 @dfn{probability mass function} (PMF), quantile function, and random number
 generation for the Poisson binomial distribution.")
     (license license:gpl2)))
+
+(define-public r-diagram
+  (package
+    (name "r-diagram")
+    (version "1.6.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diagram" version))
+       (sha256
+        (base32
+         "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
+    (properties `((upstream-name . "diagram")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-shape" ,r-shape)))
+    (home-page "https://cran.r-project.org/web/packages/diagram/")
+    (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
+    (description
+     "This package provides tools to visualize simple graphs (networks) based
+on a transition matrix, utilities to plot flow diagrams, visualizing webs,
+electrical networks, etc.  It also includes supporting material for the book
+\"A practical guide to ecological modelling - using R as a simulation
+platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
+\"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
+Francesca Mazzia (2012).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 96afb6c683175b0f0474cd7589ad6ca44dac4a5b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 19:18:36 +0100
Subject: gnu: Add r-lim.

* gnu/packages/cran.scm (r-lim): 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 117362cd9f..3a342bc903 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18860,3 +18860,26 @@ platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
 Francesca Mazzia (2012).")
     (license license:gpl2+)))
+
+(define-public r-lim
+  (package
+    (name "r-lim")
+    (version "1.4.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "LIM" version))
+       (sha256
+        (base32
+         "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
+    (properties `((upstream-name . "LIM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-diagram" ,r-diagram)
+       ("r-limsolve" ,r-limsolve)))
+    (home-page "https://cran.r-project.org/web/packages/LIM/")
+    (synopsis "Linear inverse model examples and solution methods")
+    (description
+     "This package provides functions that read and solve linear inverse
+problems (food web problems, linear programming problems).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 59d485e118fab91c36937704396d1045f2e0815a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 19:18:46 +0100
Subject: gnu: Add r-shinycssloaders.

* gnu/packages/cran.scm (r-shinycssloaders): New variable.
---
 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 3a342bc903..c5e6b96f67 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18883,3 +18883,30 @@ Francesca Mazzia (2012).")
      "This package provides functions that read and solve linear inverse
 problems (food web problems, linear programming problems).")
     (license license:gpl2+)))
+
+(define-public r-shinycssloaders
+  (package
+    (name "r-shinycssloaders")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinycssloaders" version))
+       (sha256
+        (base32
+         "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
+    (properties
+     `((upstream-name . "shinycssloaders")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-glue" ,r-glue)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://github.com/andrewsali/shinycssloaders")
+    (synopsis "Add CSS loading animations to Shiny outputs")
+    (description
+     "This package provides tools to create a lightweight Shiny wrapper for
+the css-loaders created by Luke Hass
+@url{https://github.com/lukehaas/css-loaders}.  Wrapping a Shiny output will
+automatically show a loader when the output is (re)calculating.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 1028bf0a05ee2f44d41f56eecd5ae6f72f150e05 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 17 Dec 2019 19:18:54 +0100
Subject: gnu: Add r-rsvg.

* gnu/packages/cran.scm (r-rsvg): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c5e6b96f67..1f15e29b06 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18910,3 +18910,31 @@ the css-loaders created by Luke Hass
 @url{https://github.com/lukehaas/css-loaders}.  Wrapping a Shiny output will
 automatically show a loader when the output is (re)calculating.")
     (license license:gpl3)))
+
+(define-public r-rsvg
+  (package
+    (name "r-rsvg")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rsvg" version))
+       (sha256
+        (base32
+         "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
+    (properties `((upstream-name . "rsvg")))
+    (build-system r-build-system)
+    (inputs
+     `(("librsvg" ,librsvg)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/jeroen/rsvg#readme")
+    (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
+    (description
+     "This package allows you to render vector-based SVG images into
+high-quality custom-size bitmap arrays using the librsvg2 library.  The
+resulting bitmap can be written to e.g. PNG, JPEG or WEBP format.  In
+addition, the package can convert images directly to various formats such as
+PDF or PostScript.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 3eacc8fa8f9625427cbc07f27e5249c7b24fcb62 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 18 Dec 2019 15:24:05 +0100
Subject: gnu: Add r-influencer.

* gnu/packages/cran.scm (r-influencer): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1f15e29b06..040c2ead4a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18938,3 +18938,31 @@ resulting bitmap can be written to e.g. PNG, JPEG or WEBP format.  In
 addition, the package can convert images directly to various formats such as
 PDF or PostScript.")
     (license license:expat)))
+
+(define-public r-influencer
+  (package
+    (name "r-influencer")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "influenceR" version))
+       (sha256
+        (base32
+         "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
+    (properties `((upstream-name . "influenceR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)))
+    (home-page "https://github.com/rcc-uchicago/influenceR")
+    (synopsis "Tools to quantify structural importance of nodes in a network")
+    (description
+     "This package provides functionality to compute various node centrality
+measures on networks.  Included are functions to compute betweenness
+centrality (by utilizing Madduri and Bader's SNAP library), implementations of
+Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
+algorithm to identify key players, and Valente's bridging metric.  The
+betweenness, Key Players, and bridging implementations are parallelized with
+OpenMP.")
+    (license license:gpl2)))
-- 
cgit v1.2.3