From c691c607d7682d08b079e4e168b9392de234b3fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:08:03 +0100
Subject: gnu: Add r-dorng.

* gnu/packages/cran.scm (r-dorng): 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 5bd5c60d49..67a1950756 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10839,3 +10839,32 @@ using @code{S3}.")
 for model selection.  The calibration methods available are based on the slope
 heuristics.")
     (license license:gpl2+)))
+
+(define-public r-dorng
+  (package
+    (name "r-dorng")
+    (version "1.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "doRNG" version))
+       (sha256
+        (base32
+         "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
+    (properties `((upstream-name . "doRNG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-pkgmaker" ,r-pkgmaker)
+       ("r-rngtools" ,r-rngtools)))
+    (home-page "https://renozao.github.io/doRNG/")
+    (synopsis "Generic reproducible parallel backend for foreach loops")
+    (description
+     "This package provides functions to perform reproducible parallel
+@code{foreach} loops, using independent random streams as generated by
+L'Ecuyer's combined multiple-recursive generator.  It enables to easily
+convert standard @code{%dopar%} loops into fully reproducible loops,
+independently of the number of workers, the task scheduling strategy, or the
+chosen parallel environment and associated foreach backend.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From f3233beec5c403e95e0ab102fd4d109dffd59219 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:08:59 +0100
Subject: gnu: Add r-blockmodeling.

* gnu/packages/cran.scm (r-blockmodeling): 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 67a1950756..ac0d497e90 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10868,3 +10868,30 @@ convert standard @code{%dopar%} loops into fully reproducible loops,
 independently of the number of workers, the task scheduling strategy, or the
 chosen parallel environment and associated foreach backend.")
     (license license:gpl2+)))
+
+(define-public r-blockmodeling
+  (package
+    (name "r-blockmodeling")
+    (version "0.3.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "blockmodeling" version))
+       (sha256
+        (base32
+         "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-dorng" ,r-dorng)
+       ("r-foreach" ,r-foreach)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/blockmodeling")
+    (synopsis "Generalized and classical blockmodeling of valued networks")
+    (description
+     "This package is primarily meant as an implementation of generalized
+blockmodeling for valued networks.  In addition, measures of similarity or
+dissimilarity based on structural equivalence and regular equivalence (REGE
+algorithms) can be computed and partitioned matrices can be plotted.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 4af186a96321d4245560d3d8dc315376eba5797b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:09:21 +0100
Subject: gnu: Add r-upsetr.

* gnu/packages/cran.scm (r-upsetr): 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 ac0d497e90..7e7a3af1ce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10895,3 +10895,30 @@ blockmodeling for valued networks.  In addition, measures of similarity or
 dissimilarity based on structural equivalence and regular equivalence (REGE
 algorithms) can be computed and partitioned matrices can be plotted.")
     (license license:gpl2+)))
+
+(define-public r-upsetr
+  (package
+    (name "r-upsetr")
+    (version "1.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "UpSetR" version))
+       (sha256
+        (base32
+         "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz"))))
+    (properties `((upstream-name . "UpSetR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-plyr" ,r-plyr)
+       ("r-scales" ,r-scales)))
+    (home-page "https://github.com/hms-dbmi/UpSetR")
+    (synopsis "Visualize intersecting sets")
+    (description
+     "This package provides a more scalable alternative to Venn and Euler
+diagrams for visualizing intersecting sets.  Create visualizations of
+intersecting sets using a novel matrix design, along with visualizations of
+several common set, element and attribute related tasks.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 1901a53241708f64a4c97df5f12c6412a49e697a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:09:57 +0100
Subject: gnu: Add r-outliers.

* gnu/packages/cran.scm (r-outliers): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7e7a3af1ce..7a49beee4e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10922,3 +10922,22 @@ diagrams for visualizing intersecting sets.  Create visualizations of
 intersecting sets using a novel matrix design, along with visualizations of
 several common set, element and attribute related tasks.")
     (license license:expat)))
+
+(define-public r-outliers
+  (package
+    (name "r-outliers")
+    (version "0.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "outliers" version))
+       (sha256
+        (base32
+         "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
+    (synopsis "Tests for outliers")
+    (description
+     "This package provides a collection of some tests commonly used for
+identifying outliers.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 8cd3f49d464935d2b266de112aa4b69e7609fae0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:12:44 +0100
Subject: gnu: Add r-bayesm.

* gnu/packages/cran.scm (r-bayesm): New variable.
---
 gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7a49beee4e..877ddea19b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10941,3 +10941,38 @@ several common set, element and attribute related tasks.")
      "This package provides a collection of some tests commonly used for
 identifying outliers.")
     (license license:gpl2+)))
+
+(define-public r-bayesm
+  (package
+    (name "r-bayesm")
+    (version "3.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bayesm" version))
+       (sha256
+        (base32
+         "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "http://www.perossi.org/home/bsm-1")
+    (synopsis "Bayesian inference for marketing/micro-econometrics")
+    (description
+     "This package covers many important models used in marketing and
+micro-econometrics applications, including Bayes Regression (univariate or
+multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
+Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
+Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
+Mixtures of Normals (including clustering), Dirichlet Process Prior Density
+Estimation with normal base, Hierarchical Linear Models with normal prior and
+covariates, Hierarchical Linear Models with a mixture of normals prior and
+covariates, Hierarchical Multinomial Logits with a mixture of normals prior
+and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
+and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
+analysis of choice-based conjoint data, Bayesian treatment of linear
+instrumental variables models, Analysis of Multivariate Ordinal survey data
+with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
+Coefficient Logit Models.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 262ab4b17cd75e51b60ee34e6303722b654d3e09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:17:41 +0100
Subject: gnu: Add r-tensora.

* gnu/packages/cran.scm (r-tensora): 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 877ddea19b..32505a1208 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10976,3 +10976,26 @@ instrumental variables models, Analysis of Multivariate Ordinal survey data
 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
 Coefficient Logit Models.")
     (license license:gpl2+)))
+
+(define-public r-tensora
+  (package
+    (name "r-tensora")
+    (version "0.36.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tensorA" version))
+       (sha256
+        (base32
+         "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
+    (properties `((upstream-name . "tensorA")))
+    (build-system r-build-system)
+    (home-page "http://www.stat.boogaart.de/tensorA")
+    (synopsis "Advanced tensor arithmetic with named indices")
+    (description
+     "This package provides convenience functions for advanced linear algebra
+with tensors and computation with datasets of tensors on a higher level
+abstraction.  It includes Einstein and Riemann summing conventions, dragging,
+co- and contravariate indices, and parallel computations on sequences of
+tensors.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 7d779142ab663f898aae316b12cee3b52840ec38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:18:42 +0100
Subject: gnu: Add r-rarpack.

* gnu/packages/cran.scm (r-rarpack): 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 32505a1208..6d200d0768 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10999,3 +10999,27 @@ abstraction.  It includes Einstein and Riemann summing conventions, dragging,
 co- and contravariate indices, and parallel computations on sequences of
 tensors.")
     (license license:gpl2+)))
+
+(define-public r-rarpack
+  (package
+    (name "r-rarpack")
+    (version "0.11-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rARPACK" version))
+       (sha256
+        (base32
+         "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
+    (properties `((upstream-name . "rARPACK")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rspectra" ,r-rspectra)))
+    (home-page "https://github.com/yixuan/rARPACK")
+    (synopsis "Solvers for large scale eigenvalue and SVD problems")
+    (description
+     "This package was previously an R wrapper of the ARPACK library, and now
+a shell of the R package RSpectra, an R interface to the Spectra library for
+solving large scale eigenvalue/vector problems.  The current version of
+rARPACK simply imports and exports the functions provided by RSpectra.  New
+users of rARPACK are advised to switch to the RSpectra package.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 5fde35b3859b23b2063750bcb569efdb63c2ac52 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:19:37 +0100
Subject: gnu: Add r-compositions.

* gnu/packages/cran.scm (r-compositions): 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 6d200d0768..07a6da3c01 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11023,3 +11023,28 @@ solving large scale eigenvalue/vector problems.  The current version of
 rARPACK simply imports and exports the functions provided by RSpectra.  New
 users of rARPACK are advised to switch to the RSpectra package.")
     (license license:bsd-3)))
+
+(define-public r-compositions
+  (package
+    (name "r-compositions")
+    (version "1.40-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "compositions" version))
+       (sha256
+        (base32
+         "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bayesm" ,r-bayesm)
+       ("r-energy" ,r-energy)
+       ("r-robustbase" ,r-robustbase)
+       ("r-tensora" ,r-tensora)))
+    (home-page "http://www.stat.boogaart.de/compositions")
+    (synopsis "Compositional data analysis")
+    (description
+     "This package provides functions for the consistent analysis of
+compositional data (e.g. portions of substances) and positive
+numbers (e.g. concentrations).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5f673e2c1c6d0af1475f97dca087c6ccb2dd4d4f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:20:38 +0100
Subject: gnu: Add r-cobs.

* gnu/packages/cran.scm (r-cobs): 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 07a6da3c01..85b75dead7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11048,3 +11048,25 @@ users of rARPACK are advised to switch to the RSpectra package.")
 compositional data (e.g. portions of substances) and positive
 numbers (e.g. concentrations).")
     (license license:gpl2+)))
+
+(define-public r-cobs
+  (package
+    (name "r-cobs")
+    (version "1.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cobs" version))
+       (sha256
+        (base32
+         "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-quantreg" ,r-quantreg)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "https://cran.r-project.org/web/packages/cobs")
+    (synopsis "Constrained B-Splines (sparse matrix based)")
+    (description
+     "This package provides qualitatively constrained (regression) smoothing
+splines via linear programming and sparse matrices.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From c60e3e10f3b26629b4468b357a6b0e2761872941 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:21:08 +0100
Subject: gnu: Add r-drimpute.

* gnu/packages/cran.scm (r-drimpute): 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 85b75dead7..2cfa277e69 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11070,3 +11070,28 @@ numbers (e.g. concentrations).")
      "This package provides qualitatively constrained (regression) smoothing
 splines via linear programming and sparse matrices.")
     (license license:gpl2+)))
+
+(define-public r-drimpute
+  (package
+    (name "r-drimpute")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "DrImpute" version))
+       (sha256
+        (base32
+         "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
+    (properties `((upstream-name . "DrImpute")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://github.com/ikwak2/DrImpute")
+    (synopsis "Imputing dropout events in single-cell RNA-Seq data")
+    (description
+     "This is an R package for imputing dropout events.  Many statistical
+methods in cell type identification, visualization and lineage reconstruction
+do not account for dropout events.  DrImpute can improve the performance of
+such software by imputing dropout events.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 061a4b68500a7aa002a89b2eea5bea8374ed905d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:22:53 +0100
Subject: gnu: Add r-gamlss-dist.

* gnu/packages/cran.scm (r-gamlss-dist): 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 2cfa277e69..f3f964d70e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11095,3 +11095,30 @@ methods in cell type identification, visualization and lineage reconstruction
 do not account for dropout events.  DrImpute can improve the performance of
 such software by imputing dropout events.")
     (license license:gpl3)))
+
+(define-public r-gamlss-dist
+  (package
+    (name "r-gamlss-dist")
+    (version "5.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gamlss.dist" version))
+       (sha256
+        (base32
+         "1cd0vl9klcb849i8xwyjm8ihb1da92631j1rxdbnflgffkzrkya4"))))
+    (properties `((upstream-name . "gamlss.dist")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "http://www.gamlss.org/")
+    (synopsis "Distributions for Generalized Additive Models for location scale and shape")
+    (description
+     "This package provides a set of distributions which can be used for
+modelling the response variables in Generalized Additive Models for Location
+Scale and Shape.  The distributions can be continuous, discrete or mixed
+distributions.  Extra distributions can be created, by transforming, any
+continuous distribution defined on the real line, to a distribution defined on
+ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
+transformation, respectively.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 4fd994432f032446fbf3654ddd55c738e145e0ba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:23:36 +0100
Subject: gnu: Add r-minpack-lm.

* gnu/packages/cran.scm (r-minpack-lm): 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 f3f964d70e..921a33fb26 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11122,3 +11122,27 @@ ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
 transformation, respectively.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-minpack-lm
+  (package
+    (name "r-minpack-lm")
+    (version "1.2-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "minpack.lm" version))
+       (sha256
+        (base32
+         "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
+    (properties `((upstream-name . "minpack.lm")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/minpack.lm")
+    (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
+    (description
+     "The @code{nls.lm} function provides an R interface to @code{lmder} and
+@code{lmdif} from the MINPACK library, for solving nonlinear least-squares
+problems by a modification of the Levenberg-Marquardt algorithm, with support
+for lower and upper parameter bounds.  The implementation can be used via
+@rode{nls}-like calls using the @code{nlsLM} function.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 01fe44cbdca1f59e993ff6fceeaa410df0fed27d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:24:01 +0100
Subject: gnu: Add r-moments.

* gnu/packages/cran.scm (r-moments): 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 921a33fb26..2b5c2b021e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11146,3 +11146,23 @@ problems by a modification of the Levenberg-Marquardt algorithm, with support
 for lower and upper parameter bounds.  The implementation can be used via
 @rode{nls}-like calls using the @code{nlsLM} function.")
     (license license:gpl3)))
+
+(define-public r-moments
+  (package
+    (name "r-moments")
+    (version "0.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "moments" version))
+       (sha256
+        (base32
+         "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/moments")
+    (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
+    (description
+     "This package provides functions to calculate: moments, Pearson's
+kurtosis, Geary's kurtosis and skewness; it also includes tests related to
+them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 9e2ff342aa0d6e870267441f3ba4c6d6de16d366 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:24:23 +0100
Subject: gnu: Add r-msir.

* gnu/packages/cran.scm (r-msir): 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 2b5c2b021e..3f2c80d3f0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11166,3 +11166,25 @@ for lower and upper parameter bounds.  The implementation can be used via
 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
     (license license:gpl2+)))
+
+(define-public r-msir
+  (package
+    (name "r-msir")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "msir" version))
+       (sha256
+        (base32
+         "1ipzgdffsqly3dp91pw7yp3h5cwn08l9qsj7cdmrykd42jc98950"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mclust" ,r-mclust)
+       ("r-rgl" ,r-rgl)))
+    (home-page "https://cran.r-project.org/web/packages/msir")
+    (synopsis "Model-based sliced inverse regression")
+    (description
+     "This is an R package for dimension reduction based on finite Gaussian
+mixture modeling of inverse regression.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From e8be5a00983c05b2dd9199cc3e3c752630a5a65d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:24:44 +0100
Subject: gnu: Add r-pbivnorm.

* gnu/packages/cran.scm (r-pbivnorm): 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 3f2c80d3f0..d619c576fb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11188,3 +11188,23 @@ them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
      "This is an R package for dimension reduction based on finite Gaussian
 mixture modeling of inverse regression.")
     (license license:gpl2+)))
+
+(define-public r-pbivnorm
+  (package
+    (name "r-pbivnorm")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbivnorm" version))
+       (sha256
+        (base32
+         "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://github.com/brentonk/pbivnorm")
+    (synopsis "Vectorized bivariate normal CDF")
+    (description
+     "This package provides a vectorized R function for calculating
+probabilities from a standard bivariate normal CDF.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From ca3f13704ac1f5c6fcc1e0efaec851453ad973d1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:25:36 +0100
Subject: gnu: Add r-lavaan.

* gnu/packages/cran.scm (r-lavaan): 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 d619c576fb..0d9b721f94 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11208,3 +11208,28 @@ mixture modeling of inverse regression.")
      "This package provides a vectorized R function for calculating
 probabilities from a standard bivariate normal CDF.")
     (license license:gpl2+)))
+
+(define-public r-lavaan
+  (package
+    (name "r-lavaan")
+    (version "0.6-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lavaan" version))
+       (sha256
+        (base32
+         "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-mnormt" ,r-mnormt)
+       ("r-numderiv" ,r-numderiv)
+       ("r-pbivnorm" ,r-pbivnorm)))
+    (home-page "http://lavaan.ugent.be")
+    (synopsis "Latent variable analysis")
+    (description
+     "This package provides tools to fit a variety of latent variable models,
+including confirmatory factor analysis, structural equation modeling and
+latent growth curve models.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 4d1f19e02c99ca13de95fa57afa8e1e2a0702384 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:26:46 +0100
Subject: gnu: Add r-nonnest2.

* gnu/packages/cran.scm (r-nonnest2): 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 0d9b721f94..d087ffd26e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11233,3 +11233,30 @@ probabilities from a standard bivariate normal CDF.")
 including confirmatory factor analysis, structural equation modeling and
 latent growth curve models.")
     (license license:gpl2+)))
+
+(define-public r-nonnest2
+  (package
+    (name "r-nonnest2")
+    (version "0.5-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nonnest2" version))
+       (sha256
+        (base32
+         "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-compquadform" ,r-compquadform)
+       ("r-lavaan" ,r-lavaan)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-sandwich" ,r-sandwich)))
+    (home-page "https://cran.r-project.org/web/packages/nonnest2/")
+    (synopsis "Tests of non-nested models")
+    (description
+     "This package allows for testing of non-nested models.  It includes tests
+of model distinguishability and of model fit that can be applied to both
+nested and non-nested models.  The package also includes functionality to
+obtain confidence intervals associated with AIC and BIC.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From be0777ba865550e3bc80d6ef962e230233bae45f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:27:10 +0100
Subject: gnu: Add r-penalized.

* gnu/packages/cran.scm (r-penalized): 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 d087ffd26e..0c789dd69f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11260,3 +11260,31 @@ nested and non-nested models.  The package also includes functionality to
 obtain confidence intervals associated with AIC and BIC.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-penalized
+  (package
+    (name "r-penalized")
+    (version "0.9-51")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "penalized" version))
+       (sha256
+        (base32
+         "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/penalized/")
+    (synopsis "Penalized estimation in GLMs and in the Cox model")
+    (description
+     "This package provides tools for fitting possibly high dimensional
+penalized regression models.  The penalty structure can be any combination of
+an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
+constraint on the regression coefficients.  The supported regression models
+are linear, logistic and Poisson regression and the Cox Proportional Hazards
+model.  Cross-validation routines allow optimization of the tuning
+parameters.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5570804a69f6cf8a69f6da24411c99b129130893 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Mar 2019 22:27:29 +0100
Subject: gnu: Add r-zim.

* gnu/packages/cran.scm (r-zim): 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 0c789dd69f..b41e456735 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11288,3 +11288,31 @@ are linear, logistic and Poisson regression and the Cox Proportional Hazards
 model.  Cross-validation routines allow optimization of the tuning
 parameters.")
     (license license:gpl2+)))
+
+(define-public r-zim
+  (package
+    (name "r-zim")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ZIM" version))
+       (sha256
+        (base32
+         "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
+    (properties `((upstream-name . "ZIM")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "https://github.com/biostatstudio/ZIM")
+    (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
+    (description
+     "Analyze count time series with excess zeros.  Two types of statistical
+models are supported: Markov regression and state-space models.  They are also
+known as observation-driven and parameter-driven models respectively in the
+time series literature.  The functions used for Markov regression or
+observation-driven models can also be used to fit ordinary regression models
+with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
+negative binomial (ZINB) assumption.  The package also contains miscellaneous
+functions to compute density, distribution, quantile, and generate random
+numbers from ZIP and ZINB distributions.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 2f041a4cef82fa339ec0b86b3538e05e2c9705c4 Mon Sep 17 00:00:00 2001
From: Jack Hill <jackhill@jackhill.us>
Date: Tue, 12 Mar 2019 23:27:39 -0400
Subject: gnu: r-minpack-lm: Fix typo in description.

* gnu/packages/cran.scm (r-minpack-lm)[description]: Fix typo.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/cran.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b41e456735..d6301f1a89 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11144,7 +11144,7 @@ transformation, respectively.")
 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
 problems by a modification of the Levenberg-Marquardt algorithm, with support
 for lower and upper parameter bounds.  The implementation can be used via
-@rode{nls}-like calls using the @code{nlsLM} function.")
+@code{nls}-like calls using the @code{nlsLM} function.")
     (license license:gpl3)))
 
 (define-public r-moments
-- 
cgit v1.2.3


From 849350fbce49950348516f702a351cf7e0216af7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:06:36 +0100
Subject: gnu: Add r-shinybs.

* gnu/packages/cran.scm (r-shinybs): 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 d6301f1a89..5b6546e51c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10923,6 +10923,33 @@ intersecting sets using a novel matrix design, along with visualizations of
 several common set, element and attribute related tasks.")
     (license license:expat)))
 
+;; This package includes a JavaScript file, which is not minified.  When
+;; upgrading please check that there are no new minified JavaScript files.
+(define-public r-shinybs
+  (package
+    (name "r-shinybs")
+    (version "0.61")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyBS" version))
+       (sha256
+        (base32
+         "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
+    (properties `((upstream-name . "shinyBS")))
+    (build-system r-build-system)
+    ;; The tests spawn Shiny browser apps.  They cannot be run
+    ;; non-interactively.
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://ebailey78.github.io/shinyBS/")
+    (synopsis "Twitter Bootstrap components for Shiny")
+    (description
+     "This package adds additional Twitter Bootstrap components to Shiny.")
+    (license license:gpl3)))
+
 (define-public r-outliers
   (package
     (name "r-outliers")
-- 
cgit v1.2.3


From 5146a24ece569f8b0fc772deb096857188568cdf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:11:14 +0100
Subject: gnu: Add r-shinyjs.

* gnu/packages/cran.scm (r-shinyjs): 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 5b6546e51c..a204389f9c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11150,6 +11150,36 @@ transformation, respectively.")
     ;; Either version of the GPL.
     (license (list license:gpl2 license:gpl3))))
 
+;; This package includes JavaScript files, which are not minified.  When
+;; upgrading please check that there are no new minified JavaScript files.
+(define-public r-shinyjs
+  (package
+    (name "r-shinyjs")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyjs" version))
+       (sha256
+        (base32
+         "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-htmltools" ,r-htmltools)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://deanattali.com/shinyjs")
+    (synopsis "Improve the user experience of your Shiny apps")
+    (description
+     "Perform common useful JavaScript operations in Shiny apps that will
+greatly improve your apps without having to know any JavaScript.  Examples
+include: hiding an element, disabling an input, resetting an input back to its
+original value, delaying code execution by a few seconds, and many more useful
+functions for both the end user and the developer.  Shinyjs can also be used
+to easily call your own custom JavaScript functions from R.")
+    (license license:agpl3+)))
+
 (define-public r-minpack-lm
   (package
     (name "r-minpack-lm")
-- 
cgit v1.2.3


From c27927dbf5f55c088a017df6fb3976e4b4419e0e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:39:39 +0100
Subject: gnu: Add r-colourpicker.

* gnu/packages/cran.scm (r-colourpicker): New variable.
---
 gnu/packages/cran.scm | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a204389f9c..c44749f252 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11180,6 +11180,85 @@ functions for both the end user and the developer.  Shinyjs can also be used
 to easily call your own custom JavaScript functions from R.")
     (license license:agpl3+)))
 
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-colourpicker
+  (package
+    (name "r-colourpicker")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "colourpicker" version))
+       (sha256
+        (base32
+         "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
+    (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"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "js-salvattore")
+                         "examples/colourInput/www/salvattore.min.js")
+                        (,(assoc-ref inputs "js-jquery")
+                         "htmlwidgets/lib/jquery/jquery.min.js")
+                        ("www/shared/colourpicker/js/colourpicker.js"
+                         "www/shared/colourpicker/js/colourpicker.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (delete-file target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-htmltools" ,r-htmltools)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-miniui" ,r-miniui)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyjs" ,r-shinyjs)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ("js-jquery"
+        ,(origin
+           (method url-fetch)
+           (uri "https://code.jquery.com/jquery-3.3.1.js")
+           (sha256
+            (base32
+             "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
+       ("js-salvattore"
+        ,(origin
+           (method url-fetch)
+           (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
+           (sha256
+            (base32
+             "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
+    (home-page "https://github.com/daattali/colourpicker")
+    (synopsis "Color picker tool for Shiny and for selecting colors in plots")
+    (description
+     "This package provides a color picker that can be used as an input in
+Shiny apps or Rmarkdown documents.  The color picker supports alpha opacity,
+custom color palettes, and many more options.  A plot color helper tool is
+available as an RStudio Addin, which helps you pick colors to use in your
+plots.  A more generic color picker RStudio Addin is also provided to let you
+select colors to use in your R code.")
+    (license license:expat)))
+
 (define-public r-minpack-lm
   (package
     (name "r-minpack-lm")
-- 
cgit v1.2.3


From 30f53ec86d536e96ba5d61c526004d9dd1d7b370 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:40:14 +0100
Subject: gnu: Add r-ggextra.

* gnu/packages/cran.scm (r-ggextra): 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 c44749f252..79753eb8d3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11259,6 +11259,35 @@ plots.  A more generic color picker RStudio Addin is also provided to let you
 select colors to use in your R code.")
     (license license:expat)))
 
+(define-public r-ggextra
+  (package
+    (name "r-ggextra")
+    (version "0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggExtra" version))
+       (sha256
+        (base32
+         "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
+    (properties `((upstream-name . "ggExtra")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colourpicker" ,r-colourpicker)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-miniui" ,r-miniui)
+       ("r-scales" ,r-scales)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyjs" ,r-shinyjs)))
+    (home-page "https://github.com/daattali/ggExtra")
+    (synopsis "Marginal histograms for ggplot2 and other enhancements")
+    (description
+     "This package is a collection of functions and layers to enhance ggplot2.
+The flagship function is @code{ggMarginal()}, which can be used to add
+marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
+    (license license:expat)))
+
 (define-public r-minpack-lm
   (package
     (name "r-minpack-lm")
-- 
cgit v1.2.3


From 026dd77c636c33a7ef3e5d7116bd824c6d2c5415 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:43:20 +0100
Subject: gnu: Add r-nor1mix.

* gnu/packages/cran.scm (r-nor1mix): 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 79753eb8d3..a00c71ae7f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11481,3 +11481,24 @@ negative binomial (ZINB) assumption.  The package also contains miscellaneous
 functions to compute density, distribution, quantile, and generate random
 numbers from ZIP and ZINB distributions.")
     (license license:gpl3)))
+
+(define-public r-nor1mix
+  (package
+    (name "r-nor1mix")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nor1mix" version))
+       (sha256
+        (base32
+         "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/nor1mix/")
+    (synopsis "Normal (1-d) mixture models")
+    (description
+     "This package provides S3 classes and methods for one-dimensional normal
+mixture models, for, e.g., density estimation or clustering algorithms
+research and teaching; it provides the widely used Marron-Wand densities.  It
+also provides tools for efficient random number generation and graphics.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 648dbd2702da24a777757413c53c45a9364a8463 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 12:43:35 +0100
Subject: gnu: Add r-beanplot.

* gnu/packages/cran.scm (r-beanplot): 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 a00c71ae7f..cebc92a627 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11502,3 +11502,23 @@ mixture models, for, e.g., density estimation or clustering algorithms
 research and teaching; it provides the widely used Marron-Wand densities.  It
 also provides tools for efficient random number generation and graphics.")
     (license license:gpl2+)))
+
+(define-public r-beanplot
+  (package
+    (name "r-beanplot")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "beanplot" version))
+       (sha256
+        (base32
+         "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/beanplot/")
+    (synopsis "Visualization via beanplots")
+    (description
+     "This package provides beanplots, an alternative to
+boxplot/stripchart/violin plots.  It can be used to plot univariate comparison
+graphs.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From f313baf0c890f69bf2db6ee9a9934024edb81f09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 14:26:08 +0100
Subject: gnu: Add r-pbdzmq.

* gnu/packages/cran.scm (r-pbdzmq): 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 cebc92a627..2702e62a9a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -58,6 +58,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages networking)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -11522,3 +11523,31 @@ also provides tools for efficient random number generation and graphics.")
 boxplot/stripchart/violin plots.  It can be used to plot univariate comparison
 graphs.")
     (license license:gpl2)))
+
+(define-public r-pbdzmq
+  (package
+    (name "r-pbdzmq")
+    (version "0.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbdZMQ" version))
+       (sha256
+        (base32
+         "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
+    (properties `((upstream-name . "pbdZMQ")))
+    (build-system r-build-system)
+    (inputs
+     `(("zeromq" ,zeromq)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://pbdr.org/")
+    (synopsis "R interface to ZeroMQ")
+    (description
+     "ZeroMQ is a well-known library for high-performance asynchronous
+messaging in scalable, distributed applications.  This package provides high
+level R wrapper functions to easily utilize ZeroMQ.  The main focus is on
+interactive client/server programming frameworks.  A few wrapper functions
+compatible with @code{rzmq} are also provided.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From d17186d626c06d1bf2da1d0e03773dbb799cbb99 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 14:26:25 +0100
Subject: gnu: Add r-repr.

* gnu/packages/cran.scm (r-repr): 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 2702e62a9a..afa56f0e89 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11551,3 +11551,26 @@ level R wrapper functions to easily utilize ZeroMQ.  The main focus is on
 interactive client/server programming frameworks.  A few wrapper functions
 compatible with @code{rzmq} are also provided.")
     (license license:gpl3)))
+
+(define-public r-repr
+  (package
+    (name "r-repr")
+    (version "0.19.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "repr" version))
+       (sha256
+        (base32
+         "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-htmltools" ,r-htmltools)
+       ("r-jsonlite" ,r-jsonlite)))
+    (home-page "https://cran.r-project.org/web/packages/repr/")
+    (synopsis "Serializable representations")
+    (description
+     "This package provides string and binary representations of objects for
+several formats and MIME types.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 664dedd52485e543623e30ef7c06a8cc1dd4dc96 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 14:26:34 +0100
Subject: gnu: Add r-irdisplay.

* gnu/packages/cran.scm (r-irdisplay): 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 afa56f0e89..a61a7c71f4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11574,3 +11574,26 @@ compatible with @code{rzmq} are also provided.")
      "This package provides string and binary representations of objects for
 several formats and MIME types.")
     (license license:gpl3)))
+
+(define-public r-irdisplay
+  (package
+    (name "r-irdisplay")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IRdisplay" version))
+       (sha256
+        (base32
+         "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
+    (properties `((upstream-name . "IRdisplay")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-repr" ,r-repr)))
+    (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
+    (synopsis "Jupyter display machinery")
+    (description
+     "This package provides an interface to the rich display capabilities of
+Jupyter front-ends (e.g. Jupyter Notebook).  It is designed to be used from a
+running IRkernel session.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 984a8aa64462b6ecf197f756260e0f83016ac575 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 14:26:45 +0100
Subject: gnu: Add r-irkernel.

* gnu/packages/cran.scm (r-irkernel): New variable.
---
 gnu/packages/cran.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a61a7c71f4..f2fd741fb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -62,6 +62,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
@@ -11597,3 +11598,47 @@ several formats and MIME types.")
 Jupyter front-ends (e.g. Jupyter Notebook).  It is designed to be used from a
 running IRkernel session.")
     (license license:expat)))
+
+(define-public r-irkernel
+  (package
+    (name "r-irkernel")
+    (version "0.8.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IRkernel" version))
+       (sha256
+        (base32
+         "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6"))))
+    (properties `((upstream-name . "IRkernel")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-kernelspec
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "HOME" "/tmp")
+               (invoke "jupyter" "kernelspec" "install"
+                       "--name" "ir"
+                       "--prefix" out
+                       (string-append out "/site-library/IRkernel/kernelspec"))
+               #t))))))
+    (inputs
+     `(("jupyter" ,jupyter)))
+    (propagated-inputs
+     `(("r-crayon" ,r-crayon)
+       ("r-digest" ,r-digest)
+       ("r-evaluate" ,r-evaluate)
+       ("r-irdisplay" ,r-irdisplay)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-pbdzmq" ,r-pbdzmq)
+       ("r-repr" ,r-repr)
+       ("r-uuid" ,r-uuid)))
+    (home-page "https://cran.r-project.org/web/packages/IRkernel/")
+    (synopsis "Native R kernel for Jupyter")
+    (description
+     "The R kernel for the Jupyter environment executes R code which the
+front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
+network.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 51df43408b040effb83526e1342ce336e6ee90e4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 17:10:41 +0100
Subject: gnu: Add r-gmodels.

* gnu/packages/cran.scm (r-gmodels): 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 f2fd741fb6..82a39da6a9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11642,3 +11642,24 @@ running IRkernel session.")
 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
 network.")
     (license license:expat)))
+
+(define-public r-gmodels
+  (package
+    (name "r-gmodels")
+    (version "2.18.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gmodels" version))
+       (sha256
+        (base32
+         "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdata" ,r-gdata)
+       ("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/gmodels/")
+    (synopsis "Various R programming tools for model fitting")
+    (description
+     "This package provides various R programming tools for model fitting.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 3942bf5e4ca175313102a24570212aadc3d1337e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 17:10:53 +0100
Subject: gnu: Add r-apcluster.

* gnu/packages/cran.scm (r-apcluster): 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 82a39da6a9..4baf0307ba 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11663,3 +11663,28 @@ network.")
     (description
      "This package provides various R programming tools for model fitting.")
     (license license:gpl2)))
+
+(define-public r-apcluster
+  (package
+    (name "r-apcluster")
+    (version "1.4.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "apcluster" version))
+       (sha256
+        (base32
+         "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/apcluster/")
+    (synopsis "Affinity propagation clustering")
+    (description
+     "This package implements affinity propagation clustering introduced by
+Frey and Dueck (2007).  The package further provides leveraged affinity
+propagation and an algorithm for exemplar-based agglomerative clustering that
+can also be used to join clusters obtained from affinity propagation.  Various
+plotting functions are available for analyzing clustering results.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From a97796cd5333e7ec0cb07bc480b435c22f8d58fc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 17:19:58 +0100
Subject: gnu: Add r-valr.

* gnu/packages/cran.scm (r-valr): 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 4baf0307ba..b04a69d5c1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11688,3 +11688,32 @@ propagation and an algorithm for exemplar-based agglomerative clustering that
 can also be used to join clusters obtained from affinity propagation.  Various
 plotting functions are available for analyzing clustering results.")
     (license license:gpl2+)))
+
+(define-public r-valr
+  (package
+    (name "r-valr")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "valr" version))
+       (sha256
+        (base32
+         "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readr" ,r-readr)
+       ("r-rlang" ,r-rlang)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)))
+    (home-page "http://github.com/rnabioco/valr")
+    (synopsis "Genome interval arithmetic in R")
+    (description
+     "This package enables you to read and manipulate genome intervals and
+signals.  It provides functionality similar to command-line tool suites within
+R, enabling interactive analysis and visualization of genome-scale data.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 100f56024e72ad5effff340d34cd7a91a34a830a Mon Sep 17 00:00:00 2001
From: Nicolò Balzarotti <anothersms@gmail.com>
Date: Thu, 14 Mar 2019 10:53:25 +0100
Subject: gnu: Add r-rematch2.

* gnu/packages/cran.scm (r-rematch2): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 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 b04a69d5c1..eac6293fc9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
+;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -11717,3 +11718,24 @@ plotting functions are available for analyzing clustering results.")
 signals.  It provides functionality similar to command-line tool suites within
 R, enabling interactive analysis and visualization of genome-scale data.")
     (license license:expat)))
+
+(define-public r-rematch2
+  (package
+    (name "r-rematch2")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rematch2" version))
+       (sha256
+        (base32
+         "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/r-lib/rematch2")
+    (synopsis "Tidy output from regular expression matching")
+    (description
+     "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
+return the match results in tidy data frames.")
+    (license license:expat)))
-- 
cgit v1.2.3