[PATCH 01/35] gnu: Add r-cowplot.

[PATCH 01/35] gnu: Add r-cowplot.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8f72117..1d68636 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4052,3 +4052,27 @@ published by the statistics blog FiveThirtyEight.")
 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
 Farebrother's algorithm or Liu et al.'s algorithm.")
     (license license:gpl2+)))
+
+(define-public r-cowplot
+  (package
+    (name "r-cowplot")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cowplot" version))
+       (sha256
+        (base32
+         "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-plyr" ,r-plyr)))
+    (home-page "https://github.com/wilkelab/cowplot")
+    (synopsis "Streamlined plot theme and plot annotations for ggplot2")
+    (description
+     "This package provides some helpful extensions and modifications to the
+ggplot2 package to combine multiple ggplot2 plots into one and label them 
+with letters, as is often required for scientific publications.")
+    (license license:gpl2)))
-- 
1.9.1

[PATCH 02/35] gnu: Add r-mixtools.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1d68636..1a9ace9 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4076,3 +4076,25 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
 ggplot2 package to combine multiple ggplot2 plots into one and label them 
 with letters, as is often required for scientific publications.")
     (license license:gpl2)))
+
+(define-public r-mixtools
+  (package
+    (name "r-mixtools")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mixtools" version))
+       (sha256
+        (base32
+         "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-segmented" ,r-segmented)))
+    (home-page "http://cran.r-project.org/web/packages/mixtools")
+    (synopsis "Tools for analyzing finite mixture models")
+    (description
+     "This package provides a collection of R functions for analyzing finite
+mixture models.")
+    (license license:gpl2+)))
+
-- 
1.9.1

[PATCH 03/35] gnu: Add r-lars.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1a9ace9..d9b494f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4098,3 +4098,26 @@ with letters, as is often required for scientific publications.")
 mixture models.")
     (license license:gpl2+)))
 
+(define-public r-lars
+  (package
+    (name "r-lars")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lars" version))
+       (sha256
+        (base32
+         "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
+    (synopsis "Least angle regression, lasso and forward stagewise")
+    (description
+     "This package provides an efficient procedures for fitting an entire
+lasso sequence with the cost of a single least squares fit.  Least angle
+regression and infinitesimal forward stagewise regression are related to
+the lasso, as described in the paper below.")
+    (license license:gpl2)))
+
-- 
1.9.1

[PATCH 04/35] gnu: Add r-fastica.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d9b494f..4686212 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4121,3 +4121,24 @@ regression and infinitesimal forward stagewise regression are related to
 the lasso, as described in the paper below.")
     (license license:gpl2)))
 
+(define-public r-fastica
+  (package
+    (name "r-fastica")
+    (version "1.2-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fastICA" version))
+       (sha256
+        (base32
+         "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r"))))
+    (properties `((upstream-name . "fastICA")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/fastICA")
+    (synopsis "FastICA algorithms to perform ICA and projection pursuit")
+    (description
+     "This package provides an implementation of FastICA algorithm to perform
+Independent Component Analysis ICA and projection pursuit.")
+    (license (list license:gpl2
+                   license:gpl3))))
+
-- 
1.9.1

[PATCH 05/35] gnu: Add r-tsne.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4686212..8051e57 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4142,3 +4142,22 @@ Independent Component Analysis ICA and projection pursuit.")
     (license (list license:gpl2
                    license:gpl3))))
 
+(define-public r-tsne
+  (package
+    (name "r-tsne")
+    (version "0.1-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tsne" version))
+       (sha256
+        (base32
+         "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
+    (build-system r-build-system)
+    (home-page
+     "https://github.com/jdonaldson/rtsne/")
+    (synopsis "t-Distributed Stochastic Neighbor Embedding for R t-SNE")
+    (description
+     "This package provides a pure R implementation of the t-SNE algorithm.")
+    (license (list license:gpl2+
+                   license:gpl3+))))
-- 
1.9.1

[PATCH 06/35] gnu: Add r-diptest.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8051e57..99c2b12 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4161,3 +4161,23 @@ Independent Component Analysis ICA and projection pursuit.")
      "This package provides a pure R implementation of the t-SNE algorithm.")
     (license (list license:gpl2+
                    license:gpl3+))))
+
+(define-public r-diptest
+  (package
+    (name "r-diptest")
+    (version "0.75-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diptest" version))
+       (sha256
+        (base32
+         "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/diptest")
+    (synopsis "Hartigan's dip test statistic for unimodality - corrected")
+    (description
+     "This package computes Hartigan's dip test statistic for unimodality,
+ multimodality and provides a test with simulation based p-values, where 
+the original public code has been corrected.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 07/35] gnu: Add r-modeltools.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 99c2b12..3f3f4a7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4181,3 +4181,23 @@ Independent Component Analysis ICA and projection pursuit.")
  multimodality and provides a test with simulation based p-values, where 
 the original public code has been corrected.")
     (license license:gpl2+)))
+
+(define-public r-modeltools
+  (package
+    (name "r-modeltools")
+    (version "0.2-21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "modeltools" version))
+       (sha256
+        (base32
+         "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/modeltools")
+    (synopsis "Tools and classes for statistical models")
+    (description
+     "This package provides a collection of tools to deal with statistical
+models.  The functionality is experimental and the user interface is likely
+to change in the future.")
+    (license license:gpl2)))
-- 
1.9.1

[PATCH 08/35] gnu: Add r-flexmix.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 3f3f4a7..22b5b24 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4201,3 +4201,27 @@ the original public code has been corrected.")
 models.  The functionality is experimental and the user interface is likely
 to change in the future.")
     (license license:gpl2)))
+
+(define-public r-flexmix
+  (package
+    (name "r-flexmix")
+    (version "2.3-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "flexmix" version))
+       (sha256
+        (base32
+         "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-modeltools" ,r-modeltools)))
+    (home-page "http://cran.r-project.org/web/packages/flexmix")
+    (synopsis "Flexible mixture modeling")
+    (description
+     "This package implements a general framework for finite mixtures of
+regression models using the EM algorithm.  FlexMix provides the E-step and
+all data handling, while the M-step can be supplied by the user to easily
+define new models.  Existing drivers implement mixtures of standard linear
+models, generalized linear models and model-based clustering.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 09/35] gnu: Add r-mclust.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 22b5b24..6ce05a3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4225,3 +4225,27 @@ all data handling, while the M-step can be supplied by the user to easily
 define new models.  Existing drivers implement mixtures of standard linear
 models, generalized linear models and model-based clustering.")
     (license license:gpl2+)))
+
+(define-public r-mclust
+  (package
+    (name "r-mclust")
+    (version "5.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mclust" version))
+       (sha256
+        (base32
+         "08swza5zg6dxlgwfl30nwh7170mxb5fhsrq5b42fffawsc86v8k5"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://www.stat.washington.edu/mclust/")
+    (synopsis "Gaussian mixture modelling for model-based clustering, classification, and density estimation")
+    (description
+     "This package provides Gaussian finite mixture models fitted via EM
+algorithm for model-based clustering, classification, and density estimation,
+including Bayesian regularization, dimension reduction for visualisation,
+and resampling-based inference.")
+    (license license:gpl2+)))
+
-- 
1.9.1

[PATCH 10/35] gnu: Add r-prabclus.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6ce05a3..2bf38a7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4249,3 +4249,25 @@ including Bayesian regularization, dimension reduction for visualisation,
 and resampling-based inference.")
     (license license:gpl2+)))
 
+(define-public r-prabclus
+  (package
+    (name "r-prabclus")
+    (version "2.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "prabclus" version))
+       (sha256
+        (base32
+         "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mclust" ,r-mclust)))
+    (home-page "http://www.homepages.ucl.ac.uk/~ucakche")
+    (synopsis "Functions for clustering of presence-absence, abundance and multilocus genetic data")
+    (description
+     "This package provides a distance-based parametric bootstrap tests
+for clustering with spatial neighborhood information.  Some distance measures,
+clustering of presence-absence, abundance and multilocus genetical data for
+species delimitation, nearest neighbor based noise detection.")
+    (license (list license:gpl2+
+                   license:gpl3+))))
-- 
1.9.1

[PATCH 11/35] gnu: Add r-deoptimr.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2bf38a7..29c8cf2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4271,3 +4271,23 @@ clustering of presence-absence, abundance and multilocus genetical data for
 species delimitation, nearest neighbor based noise detection.")
     (license (list license:gpl2+
                    license:gpl3+))))
+
+(define-public r-deoptimr
+  (package
+    (name "r-deoptimr")
+    (version "1.0-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "DEoptimR" version))
+       (sha256
+        (base32
+         "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
+    (properties `((upstream-name . "DEoptimR")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/DEoptimR")
+    (synopsis "Differential evolution optimization in pure R")
+    (description
+     "This package provides a differential evolution stochastic algorithms
+for global optimization of problems with and without constraints.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 12/35] gnu: Add r-robustbase.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 29c8cf2..c99963f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4291,3 +4291,27 @@ species delimitation, nearest neighbor based noise detection.")
      "This package provides a differential evolution stochastic algorithms
 for global optimization of problems with and without constraints.")
     (license license:gpl2+)))
+
+(define-public r-robustbase
+  (package
+    (name "r-robustbase")
+    (version "0.92-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "robustbase" version))
+       (sha256
+        (base32
+         "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (propagated-inputs
+     `(("r-deoptimr" ,r-deoptimr)))
+    (home-page "http://robustbase.r-forge.r-project.org/")
+    (synopsis "Basic robust statistics")
+    (description
+     "This packages allows to analyze data with robust methods such as
+regression methodology including model selections and multivariate statistics.")
+    (license license:gpl2+)))
+
-- 
1.9.1

[PATCH 13/35] gnu: Add r-trimcluster.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

* gnu/packages/statistics.scm (r-trimcluster): New variable.
---
 gnu/packages/statistics.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c99963f..d729e6d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4315,3 +4315,21 @@ for global optimization of problems with and without constraints.")
 regression methodology including model selections and multivariate statistics.")
     (license license:gpl2+)))
 
+(define-public r-trimcluster
+  (package
+    (name "r-trimcluster")
+    (version "0.1-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "trimcluster" version))
+       (sha256
+        (base32
+         "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
+    (build-system r-build-system)
+    (home-page "http://www.www.homepages.ucl.ac.uk/~ucakche/")
+    (synopsis "Cluster analysis with trimming")
+    (description
+     "Trimmed k-means clustering.")
+    (license (list license:gpl2+
+                   license:gpl3+))))
-- 
1.9.1

[PATCH 14/35] gnu: Add r-fpc.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d729e6d..336b7c0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4333,3 +4333,32 @@ regression methodology including model selections and multivariate statistics.")
      "Trimmed k-means clustering.")
     (license (list license:gpl2+
                    license:gpl3+))))
+
+(define-public r-fpc
+  (package
+    (name "r-fpc")
+    (version "2.1-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fpc" version))
+       (sha256
+        (base32
+         "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-diptest" ,r-diptest)
+       ("r-flexmix" ,r-flexmix)
+       ("r-kernlab" ,r-kernlab)
+       ("r-mclust" ,r-mclust)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-prabclus" ,r-prabclus)
+       ("r-robustbase" ,r-robustbase)
+       ("r-trimcluster" ,r-trimcluster)))
+    (home-page "http://www.homepages.ucl.ac.uk/~ucakche/")
+    (synopsis "Flexible procedures for clustering")
+    (description
+     "This package provides various methods for clustering and cluster validation.
+Fixed point clustering.")
+  (license (list license:gpl2+
+                 license:gpl3+))))
-- 
1.9.1

[PATCH 15/35] gnu: Add r-ape.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 336b7c0..9defb9f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4362,3 +4362,25 @@ regression methodology including model selections and multivariate statistics.")
 Fixed point clustering.")
   (license (list license:gpl2+
                  license:gpl3+))))
+
+(define-public r-ape
+  (package
+    (name "r-ape")
+  (version "4.0")
+  (source
+   (origin
+     (method url-fetch)
+     (uri (cran-uri "ape" version))
+     (sha256
+      (base32
+       "017jzwnknwxggpv9lkj9yyc66qv3mcl5psvbbszfivpmj26k79f9"))))
+  (build-system r-build-system)
+  (home-page "http://ape-package.ird.fr/")
+  (synopsis "Analyses of phylogenetics and evolution")
+  (description
+   "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+  (license license:gpl2+)))
-- 
1.9.1

[PATCH 16/35] gnu: Add r-vgam.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9defb9f..9a64248 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4384,3 +4384,29 @@ phylogenetic framework, ancestral character analyses, analyses of
 diversification and macroevolution, computing distances from DNA sequences,
 and several other tools.")
   (license license:gpl2+)))
+
+(define-public r-vgam
+  (package
+    (name "r-vgam")
+    (version "1.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "VGAM" version))
+       (sha256
+        (base32
+         "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3"))))
+    (properties `((upstream-name . "VGAM")))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
+    (synopsis "Vector generalized linear and additive models")
+    (description
+    "This package is an implementation of about 6 major classes of statistical
+regression models.  Currently only fixed-effects models are implemented, i.e.,
+no random-effects models.  Many (150+) models and distributions are estimated
+by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
+VGLMs can be loosely thought of as multivariate GLMs.")
+    (license (list license:gpl2
+                   license:gpl3))))
-- 
1.9.1

[PATCH 17/35] gnu: Add r-pbapply.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9a64248..862292f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4410,3 +4410,23 @@ by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
 VGLMs can be loosely thought of as multivariate GLMs.")
     (license (list license:gpl2
                    license:gpl3))))
+
+(define-public r-pbapply
+  (package
+    (name "r-pbapply")
+    (version "1.3-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbapply" version))
+       (sha256
+        (base32
+         "053i92j0ch3msywapdia08mmk1w8bhcs6x7cl0han2r9sfliwkzw"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/psolymos/pbapply")
+    (synopsis "Adding progress bar to apply functions")
+    (description
+     "This package provides a lightweight package that adds progress bar
+to vectorized R functions apply.  The implementation can easily be added
+to functions where showing the progress is useful e.g. bootstrap.")
+    (license license:gpl2)))
-- 
1.9.1

[PATCH 18/35] gnu: Add r-fnn.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 862292f..9a26114 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4430,3 +4430,24 @@ VGLMs can be loosely thought of as multivariate GLMs.")
 to vectorized R functions apply.  The implementation can easily be added
 to functions where showing the progress is useful e.g. bootstrap.")
     (license license:gpl2)))
+
+(define-public r-fnn
+  (package
+    (name "r-fnn")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FNN" version))
+       (sha256
+        (base32
+         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+    (properties `((upstream-name . "FNN")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (synopsis "Fast nearest neighbor search algorithms and applications")
+    (description
+     "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms and related applications including KNN classification,
+regression and information measures.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 19/35] gnu: Add r-pbkrtest.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9a26114..3a69f49 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4451,3 +4451,24 @@ to functions where showing the progress is useful e.g. bootstrap.")
 search algorithms and related applications including KNN classification,
 regression and information measures.")
     (license license:gpl2+)))
+
+(define-public r-pbkrtest
+  (package
+    (name "r-pbkrtest")
+    (version "0.4-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbkrtest" version))
+       (sha256
+        (base32
+         "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-lme4" ,r-lme4)))
+    (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
+    (synopsis "Parametric bootstrap and Kenward Roger based methods for mixed model comparison")
+    (description
+     "This package implements a parametric bootstrap test and a Kenward Roger
+modification of F-tests for linear mixed effects models and a parametric
+bootstrap test for generalized linear mixed models.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 20/35] gnu: Add r-modelmetrics.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 3a69f49..5955cea 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4472,3 +4472,25 @@ regression and information measures.")
 modification of F-tests for linear mixed effects models and a parametric
 bootstrap test for generalized linear mixed models.")
     (license license:gpl2+)))
+
+(define-public r-modelmetrics
+  (package
+    (name "r-modelmetrics")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+        (uri (cran-uri "ModelMetrics" version))
+        (sha256
+         (base32
+          "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
+    (properties `((upstream-name . "ModelMetrics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
+    (synopsis "Rapid calculation of model metrics")
+    (description
+      "This package provides a collection of metrics for evaluating
+models written in C++ using Rcpp.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 21/35] gnu: Add r-matrixmodels.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5955cea..9f8f53d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4494,3 +4494,23 @@ bootstrap test for generalized linear mixed models.")
       "This package provides a collection of metrics for evaluating
 models written in C++ using Rcpp.")
     (license license:gpl2+)))
+
+(define-public r-matrixmodels
+  (package
+    (name "r-matrixmodels")
+    (version "0.4-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "MatrixModels" version))
+       (sha256
+        (base32
+         "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
+    (properties `((upstream-name . "MatrixModels")))
+    (build-system r-build-system)
+    (home-page "http://Matrix.R-forge.R-project.org/")
+    (synopsis "Modelling with sparse and dense matrices")
+    (description
+     "This package models with sparse and dense matrix matrices,
+using modular prediction and response module classes.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 22/35] gnu: Add r-quantreg.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

* gnu/packages/statistics.scm (r-quantreg): New variable.
---
 gnu/packages/statistics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9f8f53d..fc4f6f2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4514,3 +4514,30 @@ models written in C++ using Rcpp.")
      "This package models with sparse and dense matrix matrices,
 using modular prediction and response module classes.")
     (license license:gpl2+)))
+
+(define-public r-quantreg
+  (package
+    (name "r-quantreg")
+    (version "5.29")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quantreg" version))
+       (sha256
+        (base32
+         "098gy8xv9kcl5y0cm93b8chr5sm6crrdxi20bkx9lmwmybl3himv"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (propagated-inputs
+     `(("r-matrixmodels" ,r-matrixmodels)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "http://www.r-project.org")
+    (synopsis "Quantile regression")
+    (description
+     "This package provides an estimation and inference methods for models
+of conditional quantiles: linear and nonlinear parametric and non-parametric
+models for conditional quantiles of a univariate response and several methods
+for handling censored survival data.  Portfolio selection methods based on
+expected shortfall risk are also included.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 23/35] gnu: Add r-car.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index fc4f6f2..9193bfb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4541,3 +4541,25 @@ models for conditional quantiles of a univariate response and several methods
 for handling censored survival data.  Portfolio selection methods based on
 expected shortfall risk are also included.")
     (license license:gpl2+)))
+
+(define-public r-car
+  (package
+    (name "r-car")
+    (version "2.1-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "car" version))
+       (sha256
+        (base32
+         "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-pbkrtest" ,r-pbkrtest)
+       ("r-quantreg" ,r-quantreg)))
+    (home-page "https://r-forge.r-project.org/projects/car/")
+    (synopsis "Companion to applied regression")
+    (description
+      "This package provides functions and datasets from book Companion
+to Applied regression, Second Edition, Sage, 2011.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 24/35] gnu: Add r-rcppeigen.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9193bfb..398e79f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4563,3 +4563,27 @@ expected shortfall risk are also included.")
       "This package provides functions and datasets from book Companion
 to Applied regression, Second Edition, Sage, 2011.")
     (license license:gpl2+)))
+
+(define-public r-rcppeigen
+  (package
+    (name "r-rcppeigen")
+    (version "0.3.2.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppEigen" version))
+       (sha256
+        (base32
+         "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5"))))
+    (properties `((upstream-name . "RcppEigen")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "http://eigen.tuxfamily.org")
+    (synopsis "Rcpp integration for the Eigen templated linear algebra library")
+    (description
+      "This package provides an integration of Eigen in R using a C++ template
+library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
+It supports dense and sparse matrices on integer, floating point and complex numbers,
+decompositions of such matrices, and solutions of linear systems.")
+    (license (list license:gpl2
+                   license:gpl3))))
-- 
1.9.1

[PATCH 25/35] gnu: Add r-minqa.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 398e79f..e602e55 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4587,3 +4587,26 @@ It supports dense and sparse matrices on integer, floating point and complex num
 decompositions of such matrices, and solutions of linear systems.")
     (license (list license:gpl2
                    license:gpl3))))
+
+(define-public r-minqa
+  (package
+    (name "r-minqa")
+    (version "1.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "minqa" version))
+       (sha256
+        (base32
+         "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://optimizer.r-forge.r-project.org")
+    (synopsis "Derivative-free optimization algorithms by quadratic approximation")
+    (description
+      "This package provides a derivative-free optimization by quadratic approximation
+based on an interface to Fortran implementations by M. J. D. Powell.")
+    (license license:gpl2)))
-- 
1.9.1

[PATCH 26/35] gnu: Add r-nloptr.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e602e55..300a57a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4610,3 +4610,26 @@ decompositions of such matrices, and solutions of linear systems.")
       "This package provides a derivative-free optimization by quadratic approximation
 based on an interface to Fortran implementations by M. J. D. Powell.")
     (license license:gpl2)))
+
+(define-public r-nloptr
+  (package
+    (name "r-nloptr")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nloptr" version))
+       (sha256
+        (base32
+         "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("nlopt", nlopt)
+       ("pkg-config" ,pkg-config)))
+    (propagated-inputs
+     `(("nlopt" ,nlopt)))
+    (home-page "http://cran.r-project.org/web/packages/nloptr")
+    (synopsis "R interface to NLopt")
+    (description
+     "This package is interface to NLopt, a library for nonlinear optimization")
+    (license license:lgpl3)))
-- 
1.9.1

[PATCH 27/35] gnu: Add r-caret.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 300a57a..969b557 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4633,3 +4633,29 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
     (description
      "This package is interface to NLopt, a library for nonlinear optimization")
     (license license:lgpl3)))
+
+(define-public r-caret
+  (package
+    (name "r-caret")
+    (version "6.0-73")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "caret" version))
+       (sha256
+        (base32
+         "1jzaqwv4glyqqnfbpalgajd0ag866247vvdh5i83ffqs1yhs984h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-modelmetrics" ,r-modelmetrics)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "https://github.com/topepo/caret/")
+    (synopsis "Classification and regression training")
+    (description
+     "This package provides misc functions for training and plotting
+classification and regression models.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 28/35] gnu: Add r-lme4.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

* gnu/packages/statistics.scm (r-lme4): New variable.
---
 gnu/packages/statistics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 969b557..7afce82 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4659,3 +4659,29 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
      "This package provides misc functions for training and plotting
 classification and regression models.")
     (license license:gpl2+)))
+
+(define-public r-lme4
+  (package
+    (name "r-lme4")
+    (version "1.1-12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lme4" version))
+       (sha256
+        (base32
+         "0j60l5kgx1wvw2wm3jwfqwi63hammaq8gfcxzwa4h552likvaxi9"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-minqa" ,r-minqa)
+       ("r-nloptr" ,r-nloptr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)))
+    (home-page "http://cran.r-project.org/web/packages/lme4")
+    (synopsis "Linear mixed-effects models using eigen and S4")
+    (description
+      "This package provides fit linear and generalized linear mixed-effects models.  
+The models and their components are represented using S4 classes and methods.  
+The core computational algorithms are implemented using the Eigen C++ library for
+numerical linear algebra and RcppEigen glue.")
+    (license license:gpl2+)))
-- 
1.9.1

[PATCH 29/35] gnu: Add r-rcppprogress.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7afce82..c4ee40e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4685,3 +4685,26 @@ The models and their components are represented using S4 classes and methods.
 The core computational algorithms are implemented using the Eigen C++ library for
 numerical linear algebra and RcppEigen glue.")
     (license license:gpl2+)))
+
+(define-public r-rcppprogress
+  (package
+    (name "r-rcppprogress")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppProgress" version))
+       (sha256
+        (base32
+         "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x"))))
+    (properties `((upstream-name . "RcppProgress")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/kforner/rcpp_progress")
+    (synopsis "An interruptible progress bar with OpenMP support for C++ in R packages")
+    (description
+     "This package allows to display a progress bar in the R console for long running
+computations taking place in C++ code, and support for interrupting those computations
+even in multithreaded code, typically using OpenMP.")
+    (license license:gpl3+)))
-- 
1.9.1

[PATCH 30/35] gnu: Add r-mnormt.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c4ee40e..4459bf3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4708,3 +4708,27 @@ numerical linear algebra and RcppEigen glue.")
 computations taking place in C++ code, and support for interrupting those computations
 even in multithreaded code, typically using OpenMP.")
     (license license:gpl3+)))
+
+(define-public r-mnormt
+  (package
+    (name "r-mnormt")
+    (version "1.5-5")
+    (source
+     (origin
+       (method url-fetch)
+        (uri (cran-uri "mnormt" version))
+        (sha256
+          (base32
+           "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
+    (synopsis "The multivariate normal and t distributions")
+    (description
+     "This package provides functions for computing the density and the
+distribution function of multivariate normal and t random variables, and
+for generating random vectors sampled from these distributions.  Probabilities
+are computed via non-Monte Carlo methods.")
+    (license (list license:gpl2
+                   license:gpl3))))
-- 
1.9.1

[PATCH 31/35] gnu: Add r-numderiv.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4459bf3..ca199bf 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4732,3 +4732,23 @@ for generating random vectors sampled from these distributions.  Probabilities
 are computed via non-Monte Carlo methods.")
     (license (list license:gpl2
                    license:gpl3))))
+
+(define-public r-numderiv
+  (package
+    (name "r-numderiv")
+    (version "2016.8-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "numDeriv" version))
+       (sha256
+        (base32
+         "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
+    (properties `((upstream-name . "numDeriv")))
+    (build-system r-build-system)
+    (home-page "http://optimizer.r-forge.r-project.org/")
+    (synopsis "Accurate numerical derivatives")
+    (description
+     "This package provides methods for calculating accurate numerical
+first and second order derivatives.")
+    (license license:gpl2)))
-- 
1.9.1

[PATCH 32/35] gnu: Add r-sn.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ca199bf..52a9ad2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4752,3 +4752,29 @@ are computed via non-Monte Carlo methods.")
      "This package provides methods for calculating accurate numerical
 first and second order derivatives.")
     (license license:gpl2)))
+
+(define-public r-sn
+  (package
+    (name "r-sn")
+    (version "1.4-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sn" version))
+       (sha256
+        (base32
+         "1h7gb8rbwpdk9m28f2bnrkbd7lm93y82bjcq3d4mwxmwc8bawqyk"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mnormt" ,r-mnormt)
+       ("r-numderiv" ,r-numderiv)))
+    (home-page "http://azzalini.stat.unipd.it/SN")
+    (synopsis "The skew-normal and skew-t distributions")
+    (description
+     "This packages provides functionalities to build and manipulate
+probability distributions of the skew-normal family and some related
+ones, notably the skew-t family, and provides related statistical
+methods for data fitting and diagnostics, in the univariate and the
+multivariate case.")
+    (license (list license:gpl2
+                   license:gpl3))))
-- 
1.9.1

[PATCH 33/35] gnu: Add r-tclust.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 52a9ad2..4306226 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4778,3 +4778,25 @@ methods for data fitting and diagnostics, in the univariate and the
 multivariate case.")
     (license (list license:gpl2
                    license:gpl3))))
+
+(define-public r-tclust
+  (package
+    (name "r-tclust")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tclust" version))
+       (sha256
+        (base32
+         "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mclust" ,r-mclust)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-sn" ,r-sn)))
+    (home-page "http://cran.r-project.org/web/packages/tclust")
+    (synopsis "Robust trimmed clustering")
+    (description
+     "This package provides a robust trimmed clustering.")
+    (license license:gpl3)))
-- 
1.9.1

[PATCH 34/35] gnu: Add r-ranger.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4306226..57c07fb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4800,3 +4800,25 @@ multivariate case.")
     (description
      "This package provides a robust trimmed clustering.")
     (license license:gpl3)))
+
+(define-public r-ranger
+  (package
+    (name "r-ranger")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ranger" version))
+       (sha256
+        (base32
+         "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/imbs-hl/ranger")
+    (synopsis "A fast implementation of random forests")
+    (description
+     "This package provides a fast implementation of Random Forests,
+particularly suited for high dimensional data.  Ensembles of classification,
+regression, survival and probability prediction trees are supported.  Data from
+genome-wide association studies can be analyzed efficiently.")
+    (license license:gpl3)))
-- 
1.9.1

[PATCH 35/35] gnu: Add r-seurat.

[Raoul Bonnal]

From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>

* gnu/packages/bioinformatics.scm (r-seurat): New variable.
---
 gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0a77ccf..ea64002 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8504,3 +8504,59 @@ a specified false discovery rate.  It also contains a number of utilities to
 explore the MS/MS results and assess missed and irregular enzymatic cleavages,
 mass measurement accuracy, etc.")
     (license license:artistic2.0)))
+
+(define-public r-seurat
+  (let ((commit "e1eae2da82ada2211e84fbc471615e8d3921b539"))
+    (package
+      (name "r-seurat")
+      (version (string-append "1.4." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/satijalab/seurat")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "03g1bhmlyd8ajsp54n2k3ly6hfrz936cy0ql49l7invaqsv8b130"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-ggplot2" ,r-ggplot2)
+         ("r-rocr" ,r-rocr)
+         ("r-stringr" ,r-stringr)
+         ("r-rtsne" ,r-rtsne)
+         ("r-reshape2" ,r-reshape2)
+         ("r-igraph" ,r-igraph)
+         ("r-plyr" ,r-plyr)
+         ("r-dplyr" ,r-dplyr)
+         ("r-rcolorbrewer" ,r-rcolorbrewer)
+         ("r-irlba" ,r-irlba)
+         ("r-gridextra" ,r-gridextra)
+         ("r-gplots" ,r-gplots)
+         ("r-gdata" ,r-gdata)
+         ("r-rcpp" ,r-rcpp)
+         ("r-cowplot" ,r-cowplot)
+         ("r-mixtools" ,r-mixtools)
+         ("r-lars" ,r-lars)
+         ("r-fastica" ,r-fastica)
+         ("r-tsne" ,r-tsne)
+         ("r-fpc" ,r-fpc)
+         ("r-ape" ,r-ape)
+         ("r-vgam" ,r-vgam)
+         ("r-pbapply" ,r-pbapply)
+         ("r-fnn" ,r-fnn)
+         ("r-caret" ,r-caret)
+         ("r-rcppeigen" ,r-rcppeigen)
+         ("r-rcppprogress" ,r-rcppprogress)
+         ("r-tclust" ,r-tclust)
+         ("r-ranger" ,r-ranger)))
+      (home-page "http://www.satijalab.org/seurat")
+      (synopsis "Seurat is an R toolkit for single cell genomics")
+      (description
+       "This package is an R package designed for QC, analysis, and exploration
+of single cell RNA-seq data.  It easily enables widely-used analytical techniques,
+including the identification of highly variable genes, dimensionality reduction;
+PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering,
+hierarchical clustering, k-means, and the discovery of differentially expressed
+genes and markers.")
+      (license license:gpl3))))
-- 
1.9.1

Re: [PATCH 35/35] gnu: Add r-seurat.

[Ben Woodcroft]

Hi Raoul,

On 20/01/17 04:55, Raoul Bonnal wrote:
> +
> +(define-public r-seurat
> +  (let ((commit "e1eae2da82ada2211e84fbc471615e8d3921b539"))
> +    (package
> +      (name "r-seurat")
> +      (version (string-append "1.4." (string-take commit 7)))
Apologies for the long delay on getting these recipes reviewed. I've 
pushed the rest of them to master now after some minor changes, patch 
reordering and updating, except for this final one.

Seurat seems to have it's last release as v1.4.0, and the usual approach 
would be to package that release. Is there some reason why a specific 
commit was used?

Thanks, ben.

Re: bug#26072: [PATCH 35/35] gnu: Add r-seurat.

[Ricardo Wurmus]

> Seurat seems to have it's last release as v1.4.0, and the usual
> approach would be to package that release. Is there some reason why a
> specific commit was used?

The latest version is 1.4.0.12, which appears to be 8 commits after the
commit selected for this patch.  The downloadable archive, however, does
not contain the sources.

The source archive for version 1.4.0 is from Oct 4, 2016.  The selected
commit probably was the latest version at the time.

I’ll add a comment to the top of this package expression and update the
commit to fccb77d, which is equivalent to the binary release 1.4.0.12.

Thanks for the patches, and thank you Ben for the review! 

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: bug#26072: [PATCH 35/35] gnu: Add r-seurat.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> I’ll add a comment to the top of this package expression and update the
> commit to fccb77d, which is equivalent to the binary release 1.4.0.12.

I also deleted the bundled jar and added a build phase to build it from
source.  It’s now in master: 2441c284140ddbd354b61c9d1606af1357f95c1f.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: [PATCH 01/35] gnu: Add r-cowplot.

[Ludovic Courtès]

Hi Raoul!

I think it’s the first time a newcomer says “hello” with a 35-patch
series, congrats on that.  :-)

To facilitate the process, can you confirm that you ran ‘guix lint’ on
the packages and generally followed
<https://www.gnu.org/software/guix/manual/html_node/Submitting-Patches.html>?

At first sight this looks good.  I suppose Ricardo (hi! :-)) or another
R person will take a look and apply the whole batch.

Thank you, and welcome!

Ludo’.

Re: [PATCH 01/35] gnu: Add r-cowplot.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> At first sight this looks good.  I suppose Ricardo (hi! :-)) or another
> R person will take a look and apply the whole batch.

I’m already on it! :)
I’ve pushed four of the patches with some minor changes already.  More
to come!

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net