[bug#39416] Bulk import of R packages

[bug#39416] Bulk import of R packages

[Lars-Dominik Braun]

Hi,

this patch series adds 34 packages from CRAN imported using `guix import cran
-r`. Most of them are unmodified, but a few needed manual tweaks (missing
dependencies, wrong home-page URL, missing license).

Lars

[bug#39416] [PATCH 01/34] gnu: Add package r-fracdiff

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 58ceed06d0..4fbaa6a00f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19259,3 +19259,27 @@ are followed and which ones are not) from one package and use it to check
 another.  This makes it easier to find and correct the most important problems
 first.")
     (license license:gpl3)))
+
+(define-public r-fracdiff
+  (package
+    (name "r-fracdiff")
+    (version "1.5-1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "fracdiff" version))
+        (sha256
+          (base32
+            "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
+    (properties `((upstream-name . "fracdiff")))
+    (build-system r-build-system)
+    (home-page
+      "https://github.com/mmaechler/fracdiff")
+    (synopsis
+      "Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models")
+    (description
+      "Maximum likelihood estimation of the parameters of a fractionally
+differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
+including inference and basic methods.  Some alternative algorithms to estimate
+\"H\".")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 02/34] gnu: Add package r-forecast

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4fbaa6a00f..8c1e719143 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19283,3 +19283,40 @@ differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
 including inference and basic methods.  Some alternative algorithms to estimate
 \"H\".")
     (license license:gpl2+)))
+
+(define-public r-forecast
+  (package
+    (name "r-forecast")
+    (version "8.10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "forecast" version))
+        (sha256
+          (base32
+            "0jccr2wg7sii38lyqrs58fkxf2az7nw6v0jya27hpbz9bg8ib3kr"))))
+    (properties `((upstream-name . "forecast")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-colorspace" ,r-colorspace)
+        ("r-fracdiff" ,r-fracdiff)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-lmtest" ,r-lmtest)
+        ("r-magrittr" ,r-magrittr)
+        ("r-nnet" ,r-nnet)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-timedate" ,r-timedate)
+        ("r-tseries" ,r-tseries)
+        ("r-urca" ,r-urca)
+        ("r-zoo" ,r-zoo)
+        ;; needed for vignettes
+        ("r-knitr" ,r-knitr)))
+    (home-page "http://pkg.robjhyndman.com/forecast/")
+    (synopsis
+      "Forecasting Functions for Time Series and Linear Models")
+    (description
+      "Methods and tools for displaying and analysing univariate time series
+forecasts including exponential smoothing via state space models and automatic
+ARIMA modelling.")
+    (license license:gpl3)))
-- 
2.20.1

[bug#39416] [PATCH 03/34] gnu: Add package r-xmisc

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8c1e719143..9ab1d4ac84 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19320,3 +19320,25 @@ including inference and basic methods.  Some alternative algorithms to estimate
 forecasts including exponential smoothing via state space models and automatic
 ARIMA modelling.")
     (license license:gpl3)))
+
+(define-public r-xmisc
+  (package
+    (name "r-xmisc")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "Xmisc" version))
+        (sha256
+          (base32
+            "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
+    (properties `((upstream-name . "Xmisc")))
+    (build-system r-build-system)
+    (home-page
+      "http://cran.r-project.org/package=Xmisc")
+    (synopsis
+      "Xiaobei's miscellaneous classes and functions")
+    (description
+      "This is Xiaobei's miscellaneous classes and functions useful when
+developing R packages, particularly for OOP using R Reference Class.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 04/34] gnu: Add package r-proxyc

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9ab1d4ac84..9028ff310f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19342,3 +19342,33 @@ ARIMA modelling.")
       "This is Xiaobei's miscellaneous classes and functions useful when
 developing R packages, particularly for OOP using R Reference Class.")
     (license license:gpl2+)))
+
+(define-public r-proxyc
+  (package
+    (name "r-proxyc")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "proxyC" version))
+        (sha256
+          (base32
+            "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
+    (properties `((upstream-name . "proxyC")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-matrix" ,r-matrix)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-rcppparallel" ,r-rcppparallel)))
+    (home-page
+      "https://cran.r-project.org/package=proxyC")
+    (synopsis
+      "Computes Proximity in Large Sparse Matrices")
+    (description
+      "Computes proximity between rows or columns of large matrices efficiently
+in C++.  Functions are optimised for large sparse matrices using the Armadillo
+and Intel TBB libraries.  Among several built-in similarity/distance measures,
+computation of correlation, cosine similarity and Euclidean distance is
+particularly fast.")
+    (license license:gpl3)))
-- 
2.20.1

[bug#39416] [PATCH 05/34] gnu: Add package r-isocodes

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9028ff310f..4bd3be3d0b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19372,3 +19372,26 @@ and Intel TBB libraries.  Among several built-in similarity/distance measures,
 computation of correlation, cosine similarity and Euclidean distance is
 particularly fast.")
     (license license:gpl3)))
+
+(define-public r-isocodes
+  (package
+    (name "r-isocodes")
+    (version "2019.12.22")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "ISOcodes" version))
+        (sha256
+          (base32
+            "1k2f2258bwzs0b3nxma9kcw395qkljvk514a7047rx4dn0iwd874"))))
+    (properties `((upstream-name . "ISOcodes")))
+    (build-system r-build-system)
+    (home-page
+      "https://cran.r-project.org/package=ISOcodes")
+    (synopsis "Selected ISO Codes")
+    (description
+      "ISO language, territory, currency, script and character codes.  Provides
+ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO
+15924 script codes, and the ISO 8859 character codes as well as the UN M.49
+area codes.")
+    (license license:gpl2)))
-- 
2.20.1

[bug#39416] [PATCH 06/34] gnu: Add package r-stopwords

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4bd3be3d0b..4330ebf3d3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19395,3 +19395,25 @@ ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO
 15924 script codes, and the ISO 8859 character codes as well as the UN M.49
 area codes.")
     (license license:gpl2)))
+
+(define-public r-stopwords
+  (package
+    (name "r-stopwords")
+    (version "1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "stopwords" version))
+        (sha256
+          (base32
+            "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
+    (properties `((upstream-name . "stopwords")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-isocodes" ,r-isocodes)))
+    (home-page
+      "https://github.com/quanteda/stopwords")
+    (synopsis "Multilingual Stopword Lists")
+    (description
+      "This package provides multiple sources of stopwords, for use in text
+analysis and natural language processing.")
+    (license license:expat)))
-- 
2.20.1

[bug#39416] [PATCH 07/34] gnu: Add package r-spacyr

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4330ebf3d3..819aed90e4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19417,3 +19417,26 @@ area codes.")
       "This package provides multiple sources of stopwords, for use in text
 analysis and natural language processing.")
     (license license:expat)))
+
+(define-public r-spacyr
+  (package
+    (name "r-spacyr")
+    (version "1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "spacyr" version))
+        (sha256
+          (base32
+            "1xsiz6zx89vs6ykrkkp011d8fz4ksdgnf5nyaq5ynjr6zv865vks"))))
+    (properties `((upstream-name . "spacyr")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-data-table" ,r-data-table)
+        ("r-reticulate" ,r-reticulate)))
+    (home-page "https://spacyr.quanteda.io")
+    (synopsis "Wrapper to the 'spaCy' NLP Library")
+    (description
+      "An R wrapper to the Python @code{spaCy} NLP library, from
+<http://spacy.io>.")
+    (license license:gpl3)))
-- 
2.20.1

[bug#39416] [PATCH 08/34] gnu: Add package r-snowballc

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 819aed90e4..235f7d3ab3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19440,3 +19440,28 @@ analysis and natural language processing.")
       "An R wrapper to the Python @code{spaCy} NLP library, from
 <http://spacy.io>.")
     (license license:gpl3)))
+
+(define-public r-snowballc
+  (package
+    (name "r-snowballc")
+    (version "0.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "SnowballC" version))
+        (sha256
+          (base32
+            "0b7pqdavf5jbf8si4ybnii5fff39p3b1rb5rym05j8s48hs7sqb1"))))
+    (properties `((upstream-name . "SnowballC")))
+    (build-system r-build-system)
+    (home-page
+      "https://r-forge.r-project.org/projects/r-temis/")
+    (synopsis
+      "Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library")
+    (description
+      "An R interface to the C @code{libstemmer} library that implements Porter's
+word stemming algorithm for collapsing words to a common root to aid comparison
+of vocabulary.  Currently supported languages are Danish, Dutch, English,
+Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian,
+Russian, Spanish, Swedish and Turkish.")
+    (license license:bsd-3)))
-- 
2.20.1

[bug#39416] [PATCH 09/34] gnu: Add package r-quanteda

[Lars-Dominik Braun]

* gnu/packages/cran.scm (r-quanteda): New variable.
---
 gnu/packages/cran.scm | 48 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 235f7d3ab3..917b5df643 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19465,3 +19465,51 @@ of vocabulary.  Currently supported languages are Danish, Dutch, English,
 Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian,
 Russian, Spanish, Swedish and Turkish.")
     (license license:bsd-3)))
+
+(define-public r-quanteda
+  (package
+    (name "r-quanteda")
+    (version "1.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "quanteda" version))
+        (sha256
+          (base32
+            "0iv25rpx5cl9ansazjs0qb97pniajrxf4mqsnb5q98y2hil9ipd3"))))
+    (properties `((upstream-name . "quanteda")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-data-table" ,r-data-table)
+        ("r-extrafont" ,r-extrafont)
+        ("r-fastmatch" ,r-fastmatch)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-ggrepel" ,r-ggrepel)
+        ("r-lubridate" ,r-lubridate)
+        ("r-magrittr" ,r-magrittr)
+        ("r-matrix" ,r-matrix)
+        ("r-network" ,r-network)
+        ("r-proxyc" ,r-proxyc)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-rcppparallel" ,r-rcppparallel)
+        ("r-rspectra" ,r-rspectra)
+        ("r-sna" ,r-sna)
+        ("r-snowballc" ,r-snowballc)
+        ("r-spacyr" ,r-spacyr)
+        ("r-stopwords" ,r-stopwords)
+        ("r-stringi" ,r-stringi)
+        ("r-xml2" ,r-xml2)
+        ("r-yaml" ,r-yaml)))
+    (home-page "https://quanteda.io")
+    (synopsis
+      "Quantitative Analysis of Textual Data")
+    (description
+      "This package provides a fast, flexible, and comprehensive framework for
+quantitative text analysis in R.  Provides functionality for corpus management,
+creating and manipulating tokens and ngrams, exploring keywords in context,
+forming and manipulating sparse matrices of documents by features and feature
+co-occurrences, analyzing keywords, computing feature similarities and
+distances, applying content dictionaries, applying supervised and unsupervised
+machine learning, visually representing text and text analyses, and more.")
+    (license license:gpl3)))
-- 
2.20.1

[bug#39416] [PATCH 10/34] gnu: Add package r-topicmodels

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 917b5df643..9e5006b5f3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19513,3 +19513,33 @@ co-occurrences, analyzing keywords, computing feature similarities and
 distances, applying content dictionaries, applying supervised and unsupervised
 machine learning, visually representing text and text analyses, and more.")
     (license license:gpl3)))
+
+(define-public r-topicmodels
+  (package
+    (name "r-topicmodels")
+    (version "0.2-9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "topicmodels" version))
+        (sha256
+          (base32
+            "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
+    (properties `((upstream-name . "topicmodels")))
+    (build-system r-build-system)
+    (native-inputs
+      `(("gsl" ,gsl)))
+    (propagated-inputs
+      `(("r-modeltools" ,r-modeltools)
+        ("r-slam" ,r-slam)
+        ("r-tm" ,r-tm)))
+    (home-page
+      "https://cran.r-project.org/package=topicmodels")
+    (synopsis "Topic Models")
+    (description
+      "This package provides an interface to the C code for Latent Dirichlet
+Allocation (LDA) models and Correlated Topics Models (CTM) by David M.  Blei
+and co-authors and the C++ code for fitting LDA models using Gibbs sampling by
+Xuan-Hieu Phan and co-authors.")
+    (license license:gpl2)))
+
-- 
2.20.1

[bug#39416] [PATCH 11/34] gnu: Add package r-stm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9e5006b5f3..4b7ce21b1f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19543,3 +19543,40 @@ and co-authors and the C++ code for fitting LDA models using Gibbs sampling by
 Xuan-Hieu Phan and co-authors.")
     (license license:gpl2)))
 
+(define-public r-stm
+  (package
+    (name "r-stm")
+    (version "1.3.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "stm" version))
+        (sha256
+          (base32
+            "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
+    (properties `((upstream-name . "stm")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-data-table" ,r-data-table)
+        ("r-glmnet" ,r-glmnet)
+        ("r-lda" ,r-lda)
+        ("r-matrix" ,r-matrix)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-quadprog" ,r-quadprog)
+        ("r-quanteda" ,r-quanteda)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-slam" ,r-slam)
+        ("r-stringr" ,r-stringr)))
+    (home-page "http://www.structuraltopicmodel.com/")
+    (synopsis
+      "Estimation of the Structural Topic Model")
+    (description
+      "The Structural Topic Model (STM) allows researchers to estimate topic
+models with document-level covariates.  The package also includes tools for
+model selection, visualization, and estimation of topic-covariate regressions.
+Methods developed in Roberts et al (2014) <doi:10.1111/ajps.12103> and Roberts
+et al (2016) <doi:10.1080/01621459.2016.1141684>.  Vignette is Roberts et al
+(2019) <doi:10.18637/jss.v091.i02>.")
+    (license license:expat)))
+
-- 
2.20.1

[bug#39416] [PATCH 12/34] gnu: Add package r-polycor

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4b7ce21b1f..8c436d4c75 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19580,3 +19580,27 @@ et al (2016) <doi:10.1080/01621459.2016.1141684>.  Vignette is Roberts et al
 (2019) <doi:10.18637/jss.v091.i02>.")
     (license license:expat)))
 
+(define-public r-polycor
+  (package
+    (name "r-polycor")
+    (version "0.7-10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "polycor" version))
+        (sha256
+          (base32
+            "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
+    (properties `((upstream-name . "polycor")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm)))
+    (home-page
+      "https://r-forge.r-project.org/projects/polycor/")
+    (synopsis
+      "Polychoric and Polyserial Correlations")
+    (description
+      "Computes polychoric and polyserial correlations by quick \"two-step\"
+methods or ML, optionally with standard errors; tetrachoric and biserial
+correlations are special cases.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 13/34] gnu: Add package r-msm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8c436d4c75..8606695b7c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19604,3 +19604,32 @@ et al (2016) <doi:10.1080/01621459.2016.1141684>.  Vignette is Roberts et al
 methods or ML, optionally with standard errors; tetrachoric and biserial
 correlations are special cases.")
     (license license:gpl2+)))
+
+(define-public r-msm
+  (package
+    (name "r-msm")
+    (version "1.6.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "msm" version))
+        (sha256
+          (base32
+            "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
+    (properties `((upstream-name . "msm")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-expm" ,r-expm)
+        ("r-mvtnorm" ,r-mvtnorm)
+        ("r-survival" ,r-survival)))
+    (home-page "https://github.com/chjackson/msm")
+    (synopsis
+      "Multi-State Markov and Hidden Markov Models in Continuous Time")
+    (description
+      "This package provides functions for fitting continuous-time Markov and
+hidden Markov multi-state models to longitudinal data.  Designed for processes
+observed at arbitrary times in continuous time (panel data) but some other
+observation schemes are supported.  Both Markov transition rates and the hidden
+Markov output process can be modelled in terms of covariates, which may be
+constant or piecewise-constant in time.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 14/34] gnu: Add package r-ltm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8606695b7c..73dc753945 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19633,3 +19633,30 @@ observation schemes are supported.  Both Markov transition rates and the hidden
 Markov output process can be modelled in terms of covariates, which may be
 constant or piecewise-constant in time.")
     (license license:gpl2+)))
+
+(define-public r-ltm
+  (package
+    (name "r-ltm")
+    (version "1.1-1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "ltm" version))
+        (sha256
+          (base32
+            "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
+    (properties `((upstream-name . "ltm")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-mass" ,r-mass)
+        ("r-msm" ,r-msm)
+        ("r-polycor" ,r-polycor)))
+    (home-page "https://github.com/drizopoulos/ltm")
+    (synopsis "Latent Trait Models under IRT")
+    (description
+      "Analysis of multivariate dichotomous and polytomous data using latent
+trait models under the Item Response Theory approach.  It includes the Rasch,
+the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded
+Response, and the Generalized Partial Credit Models.")
+    (license license:gpl2+)))
+
-- 
2.20.1

[bug#39416] [PATCH 15/34] gnu: Add package r-mi

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 73dc753945..b26b63afcb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19660,3 +19660,25 @@ the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded
 Response, and the Generalized Partial Credit Models.")
     (license license:gpl2+)))
 
+(define-public r-mi
+  (package
+    (name "r-mi")
+    (version "1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "mi" version))
+        (sha256
+          (base32
+            "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
+    (properties `((upstream-name . "mi")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-arm" ,r-arm) ("r-matrix" ,r-matrix)))
+    (home-page
+      "http://www.stat.columbia.edu/~gelman/")
+    (synopsis
+      "Missing Data Imputation and Model Checking")
+    (description
+      "The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 16/34] gnu: Add package r-matrixcalc

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b26b63afcb..81e8731383 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19682,3 +19682,24 @@ Response, and the Generalized Partial Credit Models.")
     (description
       "The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.")
     (license license:gpl2+)))
+
+(define-public r-matrixcalc
+  (package
+    (name "r-matrixcalc")
+    (version "1.0-3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "matrixcalc" version))
+        (sha256
+          (base32
+            "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
+    (properties `((upstream-name . "matrixcalc")))
+    (build-system r-build-system)
+    (home-page
+      "https://cran.r-project.org/web/packages/matrixcalc")
+    (synopsis
+      "Collection of functions for matrix calculations")
+    (description
+      "This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis.  There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.  This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 17/34] gnu: Add package r-sem

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 81e8731383..d318f2a33e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19703,3 +19703,30 @@ Response, and the Generalized Partial Credit Models.")
     (description
       "This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis.  There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.  This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.")
     (license license:gpl2+)))
+
+(define-public r-sem
+  (package
+    (name "r-sem")
+    (version "3.1-9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "sem" version))
+        (sha256
+          (base32
+            "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
+    (properties `((upstream-name . "sem")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-boot" ,r-boot)
+        ("r-mass" ,r-mass)
+        ("r-matrixcalc" ,r-matrixcalc)
+        ("r-mi" ,r-mi)))
+    (home-page "https://cran.r-project.org/package=sem")
+    (synopsis "Structural Equation Models")
+    (description
+      "This package provides functions for fitting general linear structural
+equation models (with observed and latent variables) using the RAM approach,
+and for fitting structural equations in observed-variable models by two-stage
+least squares.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 18/34] gnu: Add package r-semtools

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d318f2a33e..100d9bd4dd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19730,3 +19730,25 @@ equation models (with observed and latent variables) using the RAM approach,
 and for fitting structural equations in observed-variable models by two-stage
 least squares.")
     (license license:gpl2+)))
+
+(define-public r-semtools
+  (package
+    (name "r-semtools")
+    (version "0.5-2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "semTools" version))
+        (sha256
+          (base32
+            "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
+    (properties `((upstream-name . "semTools")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-lavaan" ,r-lavaan)))
+    (home-page
+      "https://github.com/simsem/semTools/wiki")
+    (synopsis
+      "Useful Tools for Structural Equation Modeling")
+    (description
+      "This package provides useful tools for structural equation modeling.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 19/34] gnu: Add package r-regsem

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 100d9bd4dd..cf230ec076 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19752,3 +19752,33 @@ least squares.")
     (description
       "This package provides useful tools for structural equation modeling.")
     (license license:gpl2+)))
+
+(define-public r-regsem
+  (package
+    (name "r-regsem")
+    (version "1.3.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "regsem" version))
+        (sha256
+          (base32
+            "1klml4bp76mplipxaca7fk653cjxgdmmiciksxgiglxkzmf2bdps"))))
+    (properties `((upstream-name . "regsem")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-lavaan" ,r-lavaan)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-rsolnp" ,r-rsolnp)))
+    (home-page
+      "https://cran.r-project.org/package=regsem")
+    (synopsis
+      "Regularized Structural Equation Modeling")
+    (description
+      "Uses both ridge and lasso penalties (and extensions) to penalize
+specific parameters in structural equation models.  The package offers
+additional cost functions, cross validation, and other extensions beyond
+traditional structural equation models.  Also contains a function to perform
+exploratory mediation (XMed).")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 20/34] gnu: Add package r-stanheaders

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cf230ec076..47acdf95ae 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19782,3 +19782,38 @@ additional cost functions, cross validation, and other extensions beyond
 traditional structural equation models.  Also contains a function to perform
 exploratory mediation (XMed).")
     (license license:gpl2+)))
+
+(define-public r-stanheaders
+  (package
+    (name "r-stanheaders")
+    (version "2.19.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "StanHeaders" version))
+        (sha256
+          (base32
+            "0kyka130sin4nbji7p840394ynhmaynv9jyi94ddbplj83i2nhx3"))))
+    (properties `((upstream-name . "StanHeaders")))
+    (build-system r-build-system)
+    (inputs `(("pandoc" ,ghc-pandoc)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://mc-stan.org/")
+    (synopsis "C++ Header Files for Stan")
+    (description
+      "The C++ header files of the Stan project are provided by this package,
+but it contains no R code or function documentation.  There is a shared object
+containing part of the @code{CVODES} library, but it is not accessible from R.
+@code{r-stanheaders} is only useful for developers who want to utilize the
+@code{LinkingTo} directive of their package's DESCRIPTION file to build on the
+Stan library without incurring unnecessary dependencies.  The Stan project
+develops a probabilistic programming language that implements full or
+approximate Bayesian statistical inference via Markov Chain Monte Carlo or
+variational methods and implements (optionally penalized) maximum likelihood
+estimation via optimization.  The Stan library includes an advanced automatic
+differentiation scheme, templated statistical and linear algebra functions that
+can handle the automatically differentiable scalar types (and doubles, ints,
+etc.), and a parser for the Stan language.  The @code{r-rstan} package provides
+user-facing R functions to parse, compile, test, estimate, and analyze Stan
+models.")
+    (license license:bsd-3)))
-- 
2.20.1

[bug#39416] [PATCH 21/34] gnu: Add package r-rpf

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 47acdf95ae..a607abd262 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19817,3 +19817,29 @@ etc.), and a parser for the Stan language.  The @code{r-rstan} package provides
 user-facing R functions to parse, compile, test, estimate, and analyze Stan
 models.")
     (license license:bsd-3)))
+
+(define-public r-rpf
+  (package
+    (name "r-rpf")
+    (version "0.62")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "rpf" version))
+        (sha256
+          (base32
+            "1vgqhwi676bi9jjxljnxblw65b5szjwbp87wnsabc11vfjzc9wki"))))
+    (properties `((upstream-name . "rpf")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-mvtnorm" ,r-mvtnorm)
+        ("r-rcppeigen" ,r-rcppeigen)))
+    (home-page "https://github.com/jpritikin/rpf")
+    (synopsis "Response Probability Functions")
+    (description
+      "The purpose of this package is to factor out logic and math common to
+Item Factor Analysis fitting, diagnostics, and analysis.  It is envisioned as
+core support code suitable for more specialized IRT packages to build upon.
+Complete access to optimized C functions are made available with
+@code{R_RegisterCCallable()}.")
+    (license license:gpl3+)))
-- 
2.20.1

[bug#39416] [PATCH 22/34] gnu: Add package r-openmx

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a607abd262..0223b97a62 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19843,3 +19843,41 @@ core support code suitable for more specialized IRT packages to build upon.
 Complete access to optimized C functions are made available with
 @code{R_RegisterCCallable()}.")
     (license license:gpl3+)))
+
+(define-public r-openmx
+  (package
+    (name "r-openmx")
+    (version "2.15.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "OpenMx" version))
+        (sha256
+          (base32
+            "1wbzhmyb1lnk39dkcyccmblxvniwsghh0jd94x05pk6yrcq8im5v"))))
+    (properties `((upstream-name . "OpenMx")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bh" ,r-bh)
+        ("r-digest" ,r-digest)
+        ("r-mass" ,r-mass)
+        ("r-matrix" ,r-matrix)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcppeigen" ,r-rcppeigen)
+        ("r-rpf" ,r-rpf)
+        ("r-stanheaders" ,r-stanheaders)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://openmx.ssri.psu.edu")
+    (synopsis
+      "Extended Structural Equation Modelling")
+    (description
+      "Create structural equation models that can be manipulated
+programmatically.  Models may be specified with matrices or paths (LISREL or
+RAM) Example models include confirmatory factor, multiple group, mixture
+distribution, categorical threshold, modern test theory, differential Fit
+functions include full information maximum likelihood, maximum likelihood, and
+weighted least squares.  equations, state space, and many others.  Support and
+advanced package binaries available at <http://openmx.ssri.psu.edu>.  The
+software is described in Neale, Hunter, Pritikin, Zahery, Brick, Kirkpatrick,
+Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.")
+    (license license:asl2.0)))
-- 
2.20.1

[bug#39416] [PATCH 23/34] gnu: Add package r-kutils

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0223b97a62..ebfa5d9529 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19881,3 +19881,38 @@ advanced package binaries available at <http://openmx.ssri.psu.edu>.  The
 software is described in Neale, Hunter, Pritikin, Zahery, Brick, Kirkpatrick,
 Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.")
     (license license:asl2.0)))
+
+(define-public r-kutils
+  (package
+    (name "r-kutils")
+    (version "1.69")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "kutils" version))
+        (sha256
+          (base32
+            "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
+    (properties `((upstream-name . "kutils")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-foreign" ,r-foreign)
+        ("r-lavaan" ,r-lavaan)
+        ("r-openxlsx" ,r-openxlsx)
+        ("r-plyr" ,r-plyr)
+        ("r-runit" ,r-runit)
+        ("r-xtable" ,r-xtable)))
+    (home-page
+      "https://cran.r-project.org/package=kutils")
+    (synopsis "Project Management Tools")
+    (description
+      "Tools for data importation, recoding, and inspection that are used at
+the University of Kansas Center for Research Methods and Data Analysis.  There
+are functions to create new project folders, R code templates, create uniquely
+named output directories, and to quickly obtain a visual summary for each
+variable in a data frame.  The main feature here is the systematic
+implementation of the \"variable key\" framework for data importation and
+recoding.  We are eager to have community feedback about the variable key and
+the vignette about it.  In version 1.67, the function semTable() is deprecated.
+We have proposed a new package of that name.")
+    (license license:gpl2)))
-- 
2.20.1

[bug#39416] [PATCH 24/34] gnu: Add package r-rockchalk

[Lars-Dominik Braun]

* gnu/packages/cran.scm (r-rockchalk): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ebfa5d9529..2df2f90d37 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19916,3 +19916,37 @@ recoding.  We are eager to have community feedback about the variable key and
 the vignette about it.  In version 1.67, the function semTable() is deprecated.
 We have proposed a new package of that name.")
     (license license:gpl2)))
+
+(define-public r-rockchalk
+  (package
+    (name "r-rockchalk")
+    (version "1.8.144")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "rockchalk" version))
+        (sha256
+          (base32
+            "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
+    (properties `((upstream-name . "rockchalk")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-cardata" ,r-cardata)
+        ("r-kutils" ,r-kutils)
+        ("r-lme4" ,r-lme4)
+        ("r-mass" ,r-mass)))
+    (home-page
+      "https://cran.r-project.org/package=rockchalk")
+    (synopsis
+      "Regression Estimation and Presentation")
+    (description
+      "This package provides a collection of functions for interpretation and
+presentation of regression analysis.  These functions are used to produce the
+statistics lectures in <http://pj.freefaculty.org/guides>.  Includes regression
+diagnostics, regression tables, and plots of interactions and \"moderator\"
+variables.  The emphasis is on \"mean-centered\" and \"residual-centered\"
+predictors.  The vignette @code{rockchalk} offers a fairly comprehensive
+overview.  The vignette @code{Rstyle} has advice about coding in R.  The
+package title @code{rockchalk} refers to our school motto, \"Rock Chalk
+Jayhawk, Go K.U.\".")
+    (license license:gpl3+)))
-- 
2.20.1

[bug#39416] [PATCH 25/34] gnu: Add package r-lisreltor

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2df2f90d37..1d6a26c6fa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19950,3 +19950,25 @@ overview.  The vignette @code{Rstyle} has advice about coding in R.  The
 package title @code{rockchalk} refers to our school motto, \"Rock Chalk
 Jayhawk, Go K.U.\".")
     (license license:gpl3+)))
+
+(define-public r-lisreltor
+  (package
+    (name "r-lisreltor")
+    (version "0.1.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "lisrelToR" version))
+        (sha256
+          (base32
+            "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
+    (properties `((upstream-name . "lisrelToR")))
+    (build-system r-build-system)
+    (home-page
+      "https://cran.r-project.org/package=lisrelToR")
+    (synopsis "Import output from LISREL into R")
+    (description
+      "This is an unofficial package aimed at automating the import of LISREL
+output in R.  This package or its maintainer is not in any way affiliated with
+the creators of LISREL and SSI, Inc.")
+    (license license:gpl2)))
-- 
2.20.1

[bug#39416] [PATCH 26/34] gnu: Add package r-bdgraph

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1d6a26c6fa..7b9545ca30 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19972,3 +19972,29 @@ Jayhawk, Go K.U.\".")
 output in R.  This package or its maintainer is not in any way affiliated with
 the creators of LISREL and SSI, Inc.")
     (license license:gpl2)))
+
+(define-public r-bdgraph
+  (package
+    (name "r-bdgraph")
+    (version "2.62")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "BDgraph" version))
+        (sha256
+          (base32
+            "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
+    (properties `((upstream-name . "BDgraph")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-igraph" ,r-igraph)))
+    (home-page
+      "https://www.uva.nl/profile/a.mohammadi")
+    (synopsis
+      "Bayesian Structure Learning in Graphical Models using Birth-Death MCMC")
+    (description
+      "Statistical tools for Bayesian structure learning in undirected
+graphical models for continuous, discrete, and mixed data.  The package is
+implemented the recent improvements in the Bayesian graphical models
+literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>,
+Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 27/34] gnu: Add package r-ggm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7b9545ca30..d006c3d663 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19998,3 +19998,26 @@ implemented the recent improvements in the Bayesian graphical models
 literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>,
 Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.")
     (license license:gpl2+)))
+
+(define-public r-ggm
+  (package
+    (name "r-ggm")
+    (version "2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "ggm" version))
+        (sha256
+          (base32
+            "1n4y459x2i0jil8chjjqqjs28a8pzfxrws2fcjkg3il7zy0zwbw3"))))
+    (properties `((upstream-name . "ggm")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-igraph" ,r-igraph)))
+    (home-page
+      "https://cran.r-project.org/package=ggm")
+    (synopsis
+      "Functions for graphical Markov models")
+    (description
+      "This package provides functions and datasets for maximum likelihood
+fitting of some classes of graphical Markov models.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 28/34] gnu: Add package r-d3network

[Lars-Dominik Braun]

* gnu/packages/cran.scm (r-d3network): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d006c3d663..c56d7315b8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20021,3 +20021,29 @@ Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.")
       "This package provides functions and datasets for maximum likelihood
 fitting of some classes of graphical Markov models.")
     (license license:gpl2+)))
+
+(define-public r-d3network
+  (package
+    (name "r-d3network")
+    (version "0.5.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "d3Network" version))
+        (sha256
+          (base32
+            "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
+    (properties `((upstream-name . "d3Network")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-plyr" ,r-plyr)
+        ("r-rjson" ,r-rjson)
+        ("r-whisker" ,r-whisker)))
+    (home-page
+      "http://christophergandrud.github.io/d3Network/")
+    (synopsis
+      "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
+    (description
+      "This packages is intended to make it easy to create D3 JavaScript
+network, tree, dendrogram, and Sankey graphs from R using data frames.")
+    (license license:gpl3+)))
-- 
2.20.1

[bug#39416] [PATCH 29/34] gnu: Add package r-qgraph

[Lars-Dominik Braun]

* gnu/packages/cran.scm (r-qgraph): New variable.
---
 gnu/packages/cran.scm | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c56d7315b8..3f24c9964a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20047,3 +20047,52 @@ fitting of some classes of graphical Markov models.")
       "This packages is intended to make it easy to create D3 JavaScript
 network, tree, dendrogram, and Sankey graphs from R using data frames.")
     (license license:gpl3+)))
+
+(define-public r-qgraph
+  (package
+    (name "r-qgraph")
+    (version "1.6.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "qgraph" version))
+        (sha256
+          (base32
+            "1glg814h7fwl1jfm6dw1d9i80bilmj5jcjjrfln15byrdh4mm1j3"))))
+    (properties `((upstream-name . "qgraph")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-abind" ,r-abind)
+        ("r-bdgraph" ,r-bdgraph)
+        ("r-colorspace" ,r-colorspace)
+        ("r-corpcor" ,r-corpcor)
+        ("r-d3network" ,r-d3network)
+        ("r-dplyr" ,r-dplyr)
+        ("r-fdrtool" ,r-fdrtool)
+        ("r-ggm" ,r-ggm)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-ggraph" ,r-ggraph)
+        ("r-glasso" ,r-glasso)
+        ("r-gtools" ,r-gtools)
+        ("r-hmisc" ,r-hmisc)
+        ("r-huge" ,r-huge)
+        ("r-igraph" ,r-igraph)
+        ("r-jpeg" ,r-jpeg)
+        ("r-lavaan" ,r-lavaan)
+        ("r-matrix" ,r-matrix)
+        ("r-pbapply" ,r-pbapply)
+        ("r-plyr" ,r-plyr)
+        ("r-png" ,r-png)
+        ("r-psych" ,r-psych)
+        ("r-rcpp" ,r-rcpp)
+        ("r-reshape2" ,r-reshape2)
+        ("r-tidygraph" ,r-tidygraph)))
+    (home-page "http://sachaepskamp.com/qgraph/")
+    (synopsis
+      "Graph Plotting Methods, Psychometric Data Visualization and Graphical
+Model Estimation")
+    (description
+      "Weighted network visualization and analysis, as well as Gaussian
+graphical model computation.  See Epskamp et al. (2012)
+<doi:10.18637/jss.v048.i04>.")
+    (license license:gpl2)))
-- 
2.20.1

[bug#39416] [PATCH 30/34] gnu: Add package r-semplot

[Lars-Dominik Braun]

* gnu/packages/cran.scm (r-semplot): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3f24c9964a..fe2ef959dd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20096,3 +20096,37 @@ Model Estimation")
 graphical model computation.  See Epskamp et al. (2012)
 <doi:10.18637/jss.v048.i04>.")
     (license license:gpl2)))
+
+(define-public r-semplot
+  (package
+    (name "r-semplot")
+    (version "1.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "semPlot" version))
+        (sha256
+          (base32
+            "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
+    (properties `((upstream-name . "semPlot")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-colorspace" ,r-colorspace)
+        ("r-corpcor" ,r-corpcor)
+        ("r-igraph" ,r-igraph)
+        ("r-lavaan" ,r-lavaan)
+        ("r-lisreltor" ,r-lisreltor)
+        ("r-openmx" ,r-openmx)
+        ("r-plyr" ,r-plyr)
+        ("r-qgraph" ,r-qgraph)
+        ("r-regsem" ,r-regsem)
+        ("r-rockchalk" ,r-rockchalk)
+        ("r-sem" ,r-sem)
+        ("r-xml" ,r-xml)))
+    (home-page
+      "https://github.com/SachaEpskamp/semPlot")
+    (synopsis
+      "Path Diagrams and Visual Analysis of Various SEM Packages' Output")
+    (description
+      "Path diagrams and visual analysis of various SEM packages' output.")
+    (license license:gpl2)))
-- 
2.20.1

[bug#39416] [PATCH 31/34] gnu: Add package r-cdm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fe2ef959dd..396e9521a6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20130,3 +20130,41 @@ graphical model computation.  See Epskamp et al. (2012)
     (description
       "Path diagrams and visual analysis of various SEM packages' output.")
     (license license:gpl2)))
+
+(define-public r-cdm
+  (package
+    (name "r-cdm")
+    (version "7.4-19")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "CDM" version))
+        (sha256
+          (base32
+            "1ln1r3rk004fmk55iy08bjh3vv4wnkb8zg2wj3r9rq7pi8jn8fv4"))))
+    (properties `((upstream-name . "CDM")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-mvtnorm" ,r-mvtnorm)
+        ("r-polycor" ,r-polycor)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page
+      "https://github.com/alexanderrobitzsch/CDM")
+    (synopsis "Cognitive Diagnosis Modeling")
+    (description
+      "Functions for cognitive diagnosis modeling and multidimensional item
+response modeling for dichotomous and polytomous item responses.  This package
+enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001,
+<doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model
+(de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA
+model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general
+diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the
+structured latent class model (SLCA; Formann, 1992,
+<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
+(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).  See George,
+Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> for
+further details on estimation and the package structure.  For tutorials on how
+to use the CDM package see George and Robitzsch (2015,
+<doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 32/34] gnu: Add package r-tam

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 396e9521a6..d7da059bee 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20168,3 +20168,36 @@ further details on estimation and the package structure.  For tutorials on how
 to use the CDM package see George and Robitzsch (2015,
 <doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).")
     (license license:gpl2+)))
+
+(define-public r-tam
+  (package
+    (name "r-tam")
+    (version "3.3-10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "TAM" version))
+        (sha256
+          (base32
+            "1rkjp5x6wrk1dfspp1imvfals0wvy4w1wb8a5mhfbnilc7vgnlbq"))))
+    (properties `((upstream-name . "TAM")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-cdm" ,r-cdm)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page
+      "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
+    (synopsis "Test Analysis Modules")
+    (description
+      "Includes marginal maximum likelihood estimation and joint maximum
+likelihood estimation for unidimensional and multidimensional item response
+models.  The package functionality covers the Rasch model, 2PL model, 3PL
+model, generalized partial credit model, multi-faceted Rasch model, nominal
+item response model, structured latent class model, mixture distribution IRT
+models, and located latent class models.  Latent regression models and
+plausible value imputation are also supported.  For details see Adams, Wilson
+and Wang, 1997 <doi:10.1177/0146621697211001>, Adams, Wilson and Wu, 1997
+<doi:10.3102/10769986022001047>, Formann, 1982 <doi:10.1002/bimj.4710240209>,
+Formann, 1992 <doi:10.1080/01621459.1992.10475229>.")
+    (license license:gpl2+)))
-- 
2.20.1

[bug#39416] [PATCH 33/34] gnu: Add package r-erm

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d7da059bee..7e466e3fdf 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20201,3 +20201,35 @@ and Wang, 1997 <doi:10.1177/0146621697211001>, Adams, Wilson and Wu, 1997
 <doi:10.3102/10769986022001047>, Formann, 1982 <doi:10.1002/bimj.4710240209>,
 Formann, 1992 <doi:10.1080/01621459.1992.10475229>.")
     (license license:gpl2+)))
+
+(define-public r-erm
+  (package
+    (name "r-erm")
+    (version "1.0-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "eRm" version))
+        (sha256
+          (base32
+            "11p8j61arq1ih2qi33wf0442vcdbp3zvknzm5aknsifwl4mbzzly"))))
+    (properties `((upstream-name . "eRm")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-lattice" ,r-lattice)
+        ("r-mass" ,r-mass)
+        ("r-matrix" ,r-matrix)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page
+      "https://cran.r-project.org/package=eRm")
+    (synopsis "Extended Rasch Modeling")
+    (description
+      "Fits Rasch models (RM), linear logistic test models (LLTM), rating scale
+model (RSM), linear rating scale models (LRSM), partial credit models (PCM),
+and linear partial credit models (LPCM).  Missing values are allowed in the
+data matrix.  Additional features are the ML estimation of the person
+parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
+nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
+infit and outfit measures, ICC and other plots, automated stepwise item
+elimination, simulation module for various binary data matrices.")
+    (license license:gpl3)))
-- 
2.20.1

[bug#39416] [PATCH 34/34] gnu: Add package r-irtoys

[Lars-Dominik Braun]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7e466e3fdf..f83ac22d50 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20233,3 +20233,35 @@ nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
 infit and outfit measures, ICC and other plots, automated stepwise item
 elimination, simulation module for various binary data matrices.")
     (license license:gpl3)))
+
+(define-public r-irtoys
+  (package
+    (name "r-irtoys")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "irtoys" version))
+        (sha256
+          (base32
+            "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
+    (properties `((upstream-name . "irtoys")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-ltm" ,r-ltm) ("r-sm" ,r-sm)))
+    (home-page
+      "https://cran.r-project.org/package=irtoys")
+    (synopsis
+      "Collection of Functions Related to Item Response Theory (IRT)")
+    (description
+      "This package provides a collection of functions useful in learning and
+practicing IRT, which can be combined into larger programs.  Provides basic CTT
+analysis, a simple common interface to the estimation of item parameters in IRT
+models for binary responses with three different programs (ICL, BILOG-MG, and
+ltm), ability estimation (MLE, BME, EAP, WLE, plausible values), item and
+person fit statistics, scaling methods (MM, MS, Stocking-Lord, and the complete
+Hebaera method), and a rich array of parametric and non-parametric (kernel)
+plots.  Estimates and plots Haberman's interaction model when all items are
+dichotomously scored.")
+    (license license:gpl2+)))
+
-- 
2.20.1

[bug#39416] Bulk import of R packages

[Ricardo Wurmus]

Hi Lars,

> this patch series adds 34 packages from CRAN imported using `guix import cran
> -r`.

Thank you!

Could you please also do the following:

* modify the description to contain only complete sentences
* adjust the letter case in the synopsis (CRAN uppercases all initials)
* adjust the indentation with etc/indent-code.el
* use @dfn{Some Long Term} (SLT) in descriptions where necessary
* wrap URLs in the description in Texinfo syntax (especially all the
  <doi:...> things.

-- 
Ricardo

[bug#39416] Bulk import of R packages

[Lars-Dominik Braun]

[-- Attachment #1: Type: text/plain, Size: 450 bytes --]

Hi Ricardo,

> Could you please also do the following:
> 
> * modify the description to contain only complete sentences
> * adjust the letter case in the synopsis (CRAN uppercases all initials)
> * adjust the indentation with etc/indent-code.el
> * use @dfn{Some Long Term} (SLT) in descriptions where necessary
> * wrap URLs in the description in Texinfo syntax (especially all the
>   <doi:...> things.
done, I hope I did not miss anything.

Lars


[-- Attachment #2: 0001-gnu-Add-package-r-fracdiff.patch --]
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From 3abb7b9d4d94793aacf11ad5784c3908ecc9c752 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:01:03 +0100
Subject: [v2 01/34] gnu: Add package r-fracdiff

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 58ceed06d0..2e3f397bcf 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19259,3 +19259,27 @@ are followed and which ones are not) from one package and use it to check
 another.  This makes it easier to find and correct the most important problems
 first.")
     (license license:gpl3)))
+
+(define-public r-fracdiff
+  (package
+    (name "r-fracdiff")
+    (version "1.5-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fracdiff" version))
+       (sha256
+        (base32
+         "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
+    (properties `((upstream-name . "fracdiff")))
+    (build-system r-build-system)
+    (home-page
+     "https://github.com/mmaechler/fracdiff")
+    (synopsis
+     "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
+    (description
+     "Maximum likelihood estimation of the parameters of a fractionally
+differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
+including inference and basic methods.  Some alternative algorithms to estimate
+\"H\".")
+    (license license:gpl2+)))
-- 
2.20.1


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[-- Type: text/x-diff, Size: 1969 bytes --]

From c76c0d46f23ea3a3a789aa8a0dba51b7617769af Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:04:16 +0100
Subject: [v2 02/34] gnu: Add package r-forecast

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2e3f397bcf..c82049aa18 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19283,3 +19283,40 @@ differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
 including inference and basic methods.  Some alternative algorithms to estimate
 \"H\".")
     (license license:gpl2+)))
+
+(define-public r-forecast
+  (package
+    (name "r-forecast")
+    (version "8.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "forecast" version))
+       (sha256
+        (base32
+         "0jccr2wg7sii38lyqrs58fkxf2az7nw6v0jya27hpbz9bg8ib3kr"))))
+    (properties `((upstream-name . "forecast")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colorspace" ,r-colorspace)
+       ("r-fracdiff" ,r-fracdiff)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lmtest" ,r-lmtest)
+       ("r-magrittr" ,r-magrittr)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-timedate" ,r-timedate)
+       ("r-tseries" ,r-tseries)
+       ("r-urca" ,r-urca)
+       ("r-zoo" ,r-zoo)
+       ;; needed for vignettes
+       ("r-knitr" ,r-knitr)))
+    (home-page "http://pkg.robjhyndman.com/forecast/")
+    (synopsis
+     "Forecasting functions for time series and linear models")
+    (description
+     "Methods and tools for displaying and analysing univariate time series
+forecasts including exponential smoothing via state space models and automatic
+ARIMA modelling.")
+    (license license:gpl3)))
-- 
2.20.1


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From 7016a2fa966ca15710cf2abfe8354b4dff33c92f Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:06:29 +0100
Subject: [v2 03/34] gnu: Add package r-xmisc

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c82049aa18..01a6b5dad8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19320,3 +19320,25 @@ including inference and basic methods.  Some alternative algorithms to estimate
 forecasts including exponential smoothing via state space models and automatic
 ARIMA modelling.")
     (license license:gpl3)))
+
+(define-public r-xmisc
+  (package
+    (name "r-xmisc")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Xmisc" version))
+       (sha256
+        (base32
+         "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
+    (properties `((upstream-name . "Xmisc")))
+    (build-system r-build-system)
+    (home-page
+     "http://cran.r-project.org/package=Xmisc")
+    (synopsis
+     "Xiaobei's miscellaneous classes and functions")
+    (description
+     "Xiaobei's miscellaneous classes and functions, which are useful when
+developing R packages for OOP using R Reference Class.")
+    (license license:gpl2+)))
-- 
2.20.1


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From e0d330ab328c1adcb0674b9a739840bdff9ffb0d Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:55:46 +0100
Subject: [v2 04/34] gnu: Add package r-proxyc

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 01a6b5dad8..dcdba09f85 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19342,3 +19342,33 @@ ARIMA modelling.")
      "Xiaobei's miscellaneous classes and functions, which are useful when
 developing R packages for OOP using R Reference Class.")
     (license license:gpl2+)))
+
+(define-public r-proxyc
+  (package
+    (name "r-proxyc")
+    (version "0.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "proxyC" version))
+       (sha256
+        (base32
+         "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
+    (properties `((upstream-name . "proxyC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rcppparallel" ,r-rcppparallel)))
+    (home-page
+     "https://cran.r-project.org/package=proxyC")
+    (synopsis
+     "Computes proximity in large sparse matrices")
+    (description
+     "Computes proximity between rows or columns of large matrices efficiently
+in C++.  Functions are optimised for large sparse matrices using the Armadillo
+and Intel TBB libraries.  Among several built-in similarity/distance measures,
+computation of correlation, cosine similarity and Euclidean distance is
+particularly fast.")
+    (license license:gpl3)))
-- 
2.20.1


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From 2a647c53cb6f68ddf3c61e0de6287faeb9a5a5ca Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:57:10 +0100
Subject: [v2 05/34] gnu: Add package r-isocodes

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index dcdba09f85..a3f09317aa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19372,3 +19372,26 @@ and Intel TBB libraries.  Among several built-in similarity/distance measures,
 computation of correlation, cosine similarity and Euclidean distance is
 particularly fast.")
     (license license:gpl3)))
+
+(define-public r-isocodes
+  (package
+    (name "r-isocodes")
+    (version "2019.12.22")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ISOcodes" version))
+       (sha256
+        (base32
+         "1k2f2258bwzs0b3nxma9kcw395qkljvk514a7047rx4dn0iwd874"))))
+    (properties `((upstream-name . "ISOcodes")))
+    (build-system r-build-system)
+    (home-page
+     "https://cran.r-project.org/package=ISOcodes")
+    (synopsis "Selected ISO codes")
+    (description
+     "ISO language, territory, currency, script and character codes.  Provides
+ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO
+15924 script codes, and the ISO 8859 character codes as well as the UN M.49
+area codes.")
+    (license license:gpl2)))
-- 
2.20.1


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From 53b489d5ee620e8168df868d727e72afe83e3256 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:57:46 +0100
Subject: [v2 06/34] gnu: Add package r-stopwords

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a3f09317aa..144fd97f7e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19395,3 +19395,25 @@ ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO
 15924 script codes, and the ISO 8859 character codes as well as the UN M.49
 area codes.")
     (license license:gpl2)))
+
+(define-public r-stopwords
+  (package
+    (name "r-stopwords")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "stopwords" version))
+       (sha256
+        (base32
+         "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
+    (properties `((upstream-name . "stopwords")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-isocodes" ,r-isocodes)))
+    (home-page
+     "https://github.com/quanteda/stopwords")
+    (synopsis "Multilingual stopword lists")
+    (description
+     "This package provides multiple sources of stopwords, for use in text
+analysis and natural language processing.")
+    (license license:expat)))
-- 
2.20.1


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From 94b2aba6fd69dd59d8236caf350fbae490dfb119 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:58:57 +0100
Subject: [v2 07/34] gnu: Add package r-spacyr

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 144fd97f7e..8eb595e29d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19417,3 +19417,26 @@ area codes.")
      "This package provides multiple sources of stopwords, for use in text
 analysis and natural language processing.")
     (license license:expat)))
+
+(define-public r-spacyr
+  (package
+    (name "r-spacyr")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "spacyr" version))
+       (sha256
+        (base32
+         "1xsiz6zx89vs6ykrkkp011d8fz4ksdgnf5nyaq5ynjr6zv865vks"))))
+    (properties `((upstream-name . "spacyr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-reticulate" ,r-reticulate)))
+    (home-page "https://spacyr.quanteda.io")
+    (synopsis "Wrapper to the 'spaCy' NLP library")
+    (description
+     "An R wrapper to the Python @code{spaCy} NLP library, from
+@url{http://spacy.io}.")
+    (license license:gpl3)))
-- 
2.20.1


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From 837228796294044a49b0ecbf823308f98e6d0164 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 16:59:39 +0100
Subject: [v2 08/34] gnu: Add package r-snowballc

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8eb595e29d..788601b894 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19440,3 +19440,28 @@ analysis and natural language processing.")
      "An R wrapper to the Python @code{spaCy} NLP library, from
 @url{http://spacy.io}.")
     (license license:gpl3)))
+
+(define-public r-snowballc
+  (package
+    (name "r-snowballc")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SnowballC" version))
+       (sha256
+        (base32
+         "0b7pqdavf5jbf8si4ybnii5fff39p3b1rb5rym05j8s48hs7sqb1"))))
+    (properties `((upstream-name . "SnowballC")))
+    (build-system r-build-system)
+    (home-page
+     "https://r-forge.r-project.org/projects/r-temis/")
+    (synopsis
+     "Snowball stemmers based on the C 'libstemmer' UTF-8 library")
+    (description
+     "An R interface to the C @code{libstemmer} library that implements Porter's
+word stemming algorithm for collapsing words to a common root to aid comparison
+of vocabulary.  Currently supported languages are Danish, Dutch, English,
+Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian,
+Russian, Spanish, Swedish and Turkish.")
+    (license license:bsd-3)))
-- 
2.20.1


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From a9c4d12e7a19b209dcb2969e8918a5ac5123eccf Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 17:00:45 +0100
Subject: [v2 09/34] gnu: Add package r-quanteda

* gnu/packages/cran.scm (r-quanteda): New variable.
---
 gnu/packages/cran.scm | 48 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 788601b894..3096739012 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19465,3 +19465,51 @@ of vocabulary.  Currently supported languages are Danish, Dutch, English,
 Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian,
 Russian, Spanish, Swedish and Turkish.")
     (license license:bsd-3)))
+
+(define-public r-quanteda
+  (package
+    (name "r-quanteda")
+    (version "1.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quanteda" version))
+       (sha256
+        (base32
+         "0iv25rpx5cl9ansazjs0qb97pniajrxf4mqsnb5q98y2hil9ipd3"))))
+    (properties `((upstream-name . "quanteda")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-extrafont" ,r-extrafont)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-lubridate" ,r-lubridate)
+       ("r-magrittr" ,r-magrittr)
+       ("r-matrix" ,r-matrix)
+       ("r-network" ,r-network)
+       ("r-proxyc" ,r-proxyc)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rcppparallel" ,r-rcppparallel)
+       ("r-rspectra" ,r-rspectra)
+       ("r-sna" ,r-sna)
+       ("r-snowballc" ,r-snowballc)
+       ("r-spacyr" ,r-spacyr)
+       ("r-stopwords" ,r-stopwords)
+       ("r-stringi" ,r-stringi)
+       ("r-xml2" ,r-xml2)
+       ("r-yaml" ,r-yaml)))
+    (home-page "https://quanteda.io")
+    (synopsis
+     "Quantitative analysis of textual data")
+    (description
+     "This package provides a fast, flexible, and comprehensive framework for
+quantitative text analysis in R.  Provides functionality for corpus management,
+creating and manipulating tokens and ngrams, exploring keywords in context,
+forming and manipulating sparse matrices of documents by features and feature
+co-occurrences, analyzing keywords, computing feature similarities and
+distances, applying content dictionaries, applying supervised and unsupervised
+machine learning, visually representing text and text analyses, and more.")
+    (license license:gpl3)))
-- 
2.20.1


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From 52bd26df655b2f921cfef11e613fc0bca9eebedd Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 17:55:05 +0100
Subject: [v2 10/34] gnu: Add package r-topicmodels

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3096739012..38cab6f179 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19513,3 +19513,33 @@ co-occurrences, analyzing keywords, computing feature similarities and
 distances, applying content dictionaries, applying supervised and unsupervised
 machine learning, visually representing text and text analyses, and more.")
     (license license:gpl3)))
+
+(define-public r-topicmodels
+  (package
+    (name "r-topicmodels")
+    (version "0.2-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "topicmodels" version))
+       (sha256
+        (base32
+         "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
+    (properties `((upstream-name . "topicmodels")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-modeltools" ,r-modeltools)
+       ("r-slam" ,r-slam)
+       ("r-tm" ,r-tm)))
+    (home-page
+     "https://cran.r-project.org/package=topicmodels")
+    (synopsis "Topic models")
+    (description
+     "This package provides an interface to the C code for @dfn{Latent
+Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
+David M.  Blei and co-authors and the C++ code for fitting @abbr{LDA} models
+using Gibbs sampling by Xuan-Hieu Phan and co-authors.")
+    (license license:gpl2)))
+
-- 
2.20.1


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From 132331d2b31c792e56dfa9c365b32a9dbce08102 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 17:57:12 +0100
Subject: [v2 11/34] gnu: Add package r-stm

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 38cab6f179..a2c7ca2e71 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19543,3 +19543,41 @@ David M.  Blei and co-authors and the C++ code for fitting @abbr{LDA} models
 using Gibbs sampling by Xuan-Hieu Phan and co-authors.")
     (license license:gpl2)))
 
+(define-public r-stm
+  (package
+    (name "r-stm")
+    (version "1.3.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "stm" version))
+       (sha256
+        (base32
+         "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
+    (properties `((upstream-name . "stm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-glmnet" ,r-glmnet)
+       ("r-lda" ,r-lda)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-quadprog" ,r-quadprog)
+       ("r-quanteda" ,r-quanteda)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-slam" ,r-slam)
+       ("r-stringr" ,r-stringr)))
+    (home-page "http://www.structuraltopicmodel.com/")
+    (synopsis
+     "Estimation of the Structural Topic Model")
+    (description
+     "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
+topic models with document-level covariates.  The package also includes tools
+for model selection, visualization, and estimation of topic-covariate
+regressions.  Methods developed in Roberts et al (2014)
+@url{doi:10.1111/ajps.12103} and Roberts et al (2016)
+@url{doi:10.1080/01621459.2016.1141684}.  Vignette is Roberts et al (2019)
+@url{doi:10.18637/jss.v091.i02}.")
+    (license license:expat)))
+
-- 
2.20.1


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From 740ea214eeaf46c0d4caed97cb9127f8d666bb71 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 18:27:31 +0100
Subject: [v2 12/34] gnu: Add package r-polycor

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a2c7ca2e71..9c1e56bf33 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19581,3 +19581,27 @@ regressions.  Methods developed in Roberts et al (2014)
 @url{doi:10.18637/jss.v091.i02}.")
     (license license:expat)))
 
+(define-public r-polycor
+  (package
+    (name "r-polycor")
+    (version "0.7-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "polycor" version))
+       (sha256
+        (base32
+         "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
+    (properties `((upstream-name . "polycor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm)))
+    (home-page
+     "https://r-forge.r-project.org/projects/polycor/")
+    (synopsis
+     "Polychoric and polyserial correlations")
+    (description
+     "Computes polychoric and polyserial correlations by quick \"two-step\"
+methods or ML, optionally with standard errors; tetrachoric and biserial
+correlations are special cases.")
+    (license license:gpl2+)))
-- 
2.20.1


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From d6c574f2a3a2afbf115b59684cdcc89075262c20 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 18:32:17 +0100
Subject: [v2 13/34] gnu: Add package r-msm

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9c1e56bf33..2d8e2f6f7d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19605,3 +19605,32 @@ regressions.  Methods developed in Roberts et al (2014)
 methods or ML, optionally with standard errors; tetrachoric and biserial
 correlations are special cases.")
     (license license:gpl2+)))
+
+(define-public r-msm
+  (package
+    (name "r-msm")
+    (version "1.6.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "msm" version))
+       (sha256
+        (base32
+         "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
+    (properties `((upstream-name . "msm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-expm" ,r-expm)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-survival" ,r-survival)))
+    (home-page "https://github.com/chjackson/msm")
+    (synopsis
+     "Multi-state Markov and hidden Markov models in continuous time")
+    (description
+     "This package provides functions for fitting continuous-time Markov and
+hidden Markov multi-state models to longitudinal data.  Designed for processes
+observed at arbitrary times in continuous time (panel data) but some other
+observation schemes are supported.  Both Markov transition rates and the hidden
+Markov output process can be modelled in terms of covariates, which may be
+constant or piecewise-constant in time.")
+    (license license:gpl2+)))
-- 
2.20.1


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From 694b581020d5b82ffb2ef3fe2a6a05bf0f703c05 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 31 Jan 2020 18:32:48 +0100
Subject: [v2 14/34] gnu: Add package r-ltm

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2d8e2f6f7d..ad4cf0bb0b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19634,3 +19634,30 @@ observation schemes are supported.  Both Markov transition rates and the hidden
 Markov output process can be modelled in terms of covariates, which may be
 constant or piecewise-constant in time.")
     (license license:gpl2+)))
+
+(define-public r-ltm
+  (package
+    (name "r-ltm")
+    (version "1.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ltm" version))
+       (sha256
+        (base32
+         "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
+    (properties `((upstream-name . "ltm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-msm" ,r-msm)
+       ("r-polycor" ,r-polycor)))
+    (home-page "https://github.com/drizopoulos/ltm")
+    (synopsis "Latent trait models under IRT")
+    (description
+     "Analysis of multivariate dichotomous and polytomous data using latent
+trait models under the Item Response Theory approach.  It includes the Rasch,
+the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded
+Response, and the Generalized Partial Credit Models.")
+    (license license:gpl2+)))
+
-- 
2.20.1


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From 432030ab35533f974358b0fdd580c3f2658978b8 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 13:30:50 +0100
Subject: [v2 15/34] gnu: Add package r-mi

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ad4cf0bb0b..25c3057bea 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19661,3 +19661,30 @@ the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded
 Response, and the Generalized Partial Credit Models.")
     (license license:gpl2+)))
 
+(define-public r-mi
+  (package
+    (name "r-mi")
+    (version "1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "mi" version))
+        (sha256
+          (base32
+            "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
+    (properties `((upstream-name . "mi")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-arm" ,r-arm) ("r-matrix" ,r-matrix)))
+    (home-page
+      "http://www.stat.columbia.edu/~gelman/")
+    (synopsis
+      "Missing data imputation and model checking")
+    (description
+	  "The mi package provides functions for data manipulation, imputing
+missing values in an approximate Bayesian framework, diagnostics of the models
+used to generate the imputations, confidence-building mechanisms to validate
+some of the assumptions of the imputation algorithm, and functions to analyze
+multiply imputed data sets with the appropriate degree of sampling
+uncertainty.")
+    (license license:gpl2+)))
-- 
2.20.1


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From 166cc18121bd3e5859b1b8c5404b56a44f83525d Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 13:31:48 +0100
Subject: [v2 16/34] gnu: Add package r-matrixcalc

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 25c3057bea..7807bdb7aa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19688,3 +19688,29 @@ some of the assumptions of the imputation algorithm, and functions to analyze
 multiply imputed data sets with the appropriate degree of sampling
 uncertainty.")
     (license license:gpl2+)))
+
+(define-public r-matrixcalc
+  (package
+    (name "r-matrixcalc")
+    (version "1.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "matrixcalc" version))
+       (sha256
+        (base32
+         "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
+    (properties `((upstream-name . "matrixcalc")))
+    (build-system r-build-system)
+    (home-page
+     "https://cran.r-project.org/web/packages/matrixcalc")
+    (synopsis
+     "Collection of functions for matrix calculations")
+    (description
+     "This package provides a collection of functions to support matrix
+calculations for probability, econometric and numerical analysis.  There are
+additional functions that are comparable to APL functions which are useful for
+actuarial models such as pension mathematics.  This package is used for
+teaching and research purposes at the Department of Finance and Risk
+Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.")
+    (license license:gpl2+)))
-- 
2.20.1


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From d7f34322d1a96a56bb63e4387a381bd061e5837e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:07:00 +0100
Subject: [v2 17/34] gnu: Add package r-sem

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7807bdb7aa..63a2a8dd2e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19714,3 +19714,30 @@ actuarial models such as pension mathematics.  This package is used for
 teaching and research purposes at the Department of Finance and Risk
 Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.")
     (license license:gpl2+)))
+
+(define-public r-sem
+  (package
+    (name "r-sem")
+    (version "3.1-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sem" version))
+       (sha256
+        (base32
+         "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
+    (properties `((upstream-name . "sem")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-mass" ,r-mass)
+       ("r-matrixcalc" ,r-matrixcalc)
+       ("r-mi" ,r-mi)))
+    (home-page "https://cran.r-project.org/package=sem")
+    (synopsis "Structural equation models")
+    (description
+     "This package provides functions for fitting general linear structural
+equation models (with observed and latent variables) using the RAM approach,
+and for fitting structural equations in observed-variable models by two-stage
+least squares.")
+    (license license:gpl2+)))
-- 
2.20.1


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From f6b6d4b85612dd717758fc33f778bf9a76772824 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:07:41 +0100
Subject: [v2 18/34] gnu: Add package r-semtools

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 63a2a8dd2e..1e643d0baa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19741,3 +19741,25 @@ equation models (with observed and latent variables) using the RAM approach,
 and for fitting structural equations in observed-variable models by two-stage
 least squares.")
     (license license:gpl2+)))
+
+(define-public r-semtools
+  (package
+    (name "r-semtools")
+    (version "0.5-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "semTools" version))
+       (sha256
+        (base32
+         "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
+    (properties `((upstream-name . "semTools")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-lavaan" ,r-lavaan)))
+    (home-page
+     "https://github.com/simsem/semTools/wiki")
+    (synopsis
+     "Useful tools for structural equation modeling")
+    (description
+     "This package provides useful tools for structural equation modeling.")
+    (license license:gpl2+)))
-- 
2.20.1


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From 3702fa7f53f63b6a67ea744ee78c49fa65725136 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:08:09 +0100
Subject: [v2 19/34] gnu: Add package r-regsem

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1e643d0baa..5c0b323d21 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19763,3 +19763,33 @@ least squares.")
     (description
      "This package provides useful tools for structural equation modeling.")
     (license license:gpl2+)))
+
+(define-public r-regsem
+  (package
+    (name "r-regsem")
+    (version "1.3.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "regsem" version))
+       (sha256
+        (base32
+         "1klml4bp76mplipxaca7fk653cjxgdmmiciksxgiglxkzmf2bdps"))))
+    (properties `((upstream-name . "regsem")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lavaan" ,r-lavaan)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rsolnp" ,r-rsolnp)))
+    (home-page
+     "https://cran.r-project.org/package=regsem")
+    (synopsis
+     "Regularized structural equation modeling")
+    (description
+     "Uses both ridge and lasso penalties (and extensions) to penalize
+specific parameters in structural equation models.  The package offers
+additional cost functions, cross validation, and other extensions beyond
+traditional structural equation models.  Also contains a function to perform
+@dfn{exploratory mediation} (XMed).")
+    (license license:gpl2+)))
-- 
2.20.1


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From 0ee20f94d933d0d065fd192c5a914ab5d02ea0fd Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:08:37 +0100
Subject: [v2 20/34] gnu: Add package r-stanheaders

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c0b323d21..d3d382761a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19793,3 +19793,38 @@ additional cost functions, cross validation, and other extensions beyond
 traditional structural equation models.  Also contains a function to perform
 @dfn{exploratory mediation} (XMed).")
     (license license:gpl2+)))
+
+(define-public r-stanheaders
+  (package
+    (name "r-stanheaders")
+    (version "2.19.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "StanHeaders" version))
+       (sha256
+        (base32
+         "0kyka130sin4nbji7p840394ynhmaynv9jyi94ddbplj83i2nhx3"))))
+    (properties `((upstream-name . "StanHeaders")))
+    (build-system r-build-system)
+    (inputs `(("pandoc" ,ghc-pandoc)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://mc-stan.org/")
+    (synopsis "C++ header files for Stan")
+    (description
+     "The C++ header files of the Stan project are provided by this package,
+but it contains no R code or function documentation.  There is a shared object
+containing part of the @code{CVODES} library, but it is not accessible from R.
+@code{r-stanheaders} is only useful for developers who want to utilize the
+@code{LinkingTo} directive of their package's DESCRIPTION file to build on the
+Stan library without incurring unnecessary dependencies.  The Stan project
+develops a probabilistic programming language that implements full or
+approximate Bayesian statistical inference via Markov Chain Monte Carlo or
+variational methods and implements (optionally penalized) maximum likelihood
+estimation via optimization.  The Stan library includes an advanced automatic
+differentiation scheme, templated statistical and linear algebra functions that
+can handle the automatically differentiable scalar types (and doubles, ints,
+etc.), and a parser for the Stan language.  The @code{r-rstan} package provides
+user-facing R functions to parse, compile, test, estimate, and analyze Stan
+models.")
+    (license license:bsd-3)))
-- 
2.20.1


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From 0f0669e6437b46097f27eb9c2bda520635d72af2 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:09:10 +0100
Subject: [v2 21/34] gnu: Add package r-rpf

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d3d382761a..3934f2085f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19828,3 +19828,29 @@ etc.), and a parser for the Stan language.  The @code{r-rstan} package provides
 user-facing R functions to parse, compile, test, estimate, and analyze Stan
 models.")
     (license license:bsd-3)))
+
+(define-public r-rpf
+  (package
+    (name "r-rpf")
+    (version "0.62")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rpf" version))
+       (sha256
+        (base32
+         "1vgqhwi676bi9jjxljnxblw65b5szjwbp87wnsabc11vfjzc9wki"))))
+    (properties `((upstream-name . "rpf")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mvtnorm" ,r-mvtnorm)
+       ("r-rcppeigen" ,r-rcppeigen)))
+    (home-page "https://github.com/jpritikin/rpf")
+    (synopsis "Response probability functions")
+    (description
+     "The purpose of this package is to factor out logic and math common to
+Item Factor Analysis fitting, diagnostics, and analysis.  It is envisioned as
+core support code suitable for more specialized IRT packages to build upon.
+Complete access to optimized C functions are made available with
+@code{R_RegisterCCallable()}.")
+    (license license:gpl3+)))
-- 
2.20.1


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From b7a15fc07667c90b1c7dde9a119dfab192715cb4 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:09:42 +0100
Subject: [v2 22/34] gnu: Add package r-openmx

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3934f2085f..310089e81f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19854,3 +19854,36 @@ core support code suitable for more specialized IRT packages to build upon.
 Complete access to optimized C functions are made available with
 @code{R_RegisterCCallable()}.")
     (license license:gpl3+)))
+
+(define-public r-openmx
+  (package
+    (name "r-openmx")
+    (version "2.15.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "OpenMx" version))
+       (sha256
+        (base32
+         "1wbzhmyb1lnk39dkcyccmblxvniwsghh0jd94x05pk6yrcq8im5v"))))
+    (properties `((upstream-name . "OpenMx")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-digest" ,r-digest)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-rpf" ,r-rpf)
+       ("r-stanheaders" ,r-stanheaders)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://openmx.ssri.psu.edu")
+    (synopsis
+     "Extended structural equation modelling")
+    (description
+     "Allows estimation of a wide variety of advanced multivariate statistical
+models and consists of a library of functions and optimizers that allow you to
+quickly and flexibly define an SEM model and estimate parameters given observed
+data.")
+    (license license:asl2.0)))
-- 
2.20.1


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From 5576d64e965947d1ec0d4bebc7aef84ea4e35f16 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:10:25 +0100
Subject: [v2 23/34] gnu: Add package r-kutils

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 310089e81f..8cab74e4b1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19887,3 +19887,36 @@ models and consists of a library of functions and optimizers that allow you to
 quickly and flexibly define an SEM model and estimate parameters given observed
 data.")
     (license license:asl2.0)))
+
+(define-public r-kutils
+  (package
+    (name "r-kutils")
+    (version "1.69")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "kutils" version))
+       (sha256
+        (base32
+         "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
+    (properties `((upstream-name . "kutils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreign" ,r-foreign)
+       ("r-lavaan" ,r-lavaan)
+       ("r-openxlsx" ,r-openxlsx)
+       ("r-plyr" ,r-plyr)
+       ("r-runit" ,r-runit)
+       ("r-xtable" ,r-xtable)))
+    (home-page
+     "https://cran.r-project.org/package=kutils")
+    (synopsis "Project management tools")
+    (description
+     "Tools for data importation, recoding, and inspection that are used at
+the University of Kansas Center for Research Methods and Data Analysis.  There
+are functions to create new project folders, R code templates, create uniquely
+named output directories, and to quickly obtain a visual summary for each
+variable in a data frame.  The main feature here is the systematic
+implementation of the \"variable key\" framework for data importation and
+recoding.")
+    (license license:gpl2)))
-- 
2.20.1


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From 802caedbebe1d3985bed5a40acdf5b76d91ad68f Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:10:55 +0100
Subject: [v2 24/34] gnu: Add package r-rockchalk

* gnu/packages/cran.scm (r-rockchalk): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8cab74e4b1..1ccc237bf1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19920,3 +19920,37 @@ variable in a data frame.  The main feature here is the systematic
 implementation of the \"variable key\" framework for data importation and
 recoding.")
     (license license:gpl2)))
+
+(define-public r-rockchalk
+  (package
+    (name "r-rockchalk")
+    (version "1.8.144")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rockchalk" version))
+       (sha256
+        (base32
+         "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
+    (properties `((upstream-name . "rockchalk")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cardata" ,r-cardata)
+       ("r-kutils" ,r-kutils)
+       ("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)))
+    (home-page
+     "https://cran.r-project.org/package=rockchalk")
+    (synopsis
+     "Regression estimation and presentation")
+    (description
+     "This package provides a collection of functions for interpretation and
+presentation of regression analysis.  These functions are used to produce the
+statistics lectures in @url{http://pj.freefaculty.org/guides}.  Includes
+regression diagnostics, regression tables, and plots of interactions and
+\"moderator\" variables.  The emphasis is on \"mean-centered\" and
+\"residual-centered\" predictors.  The vignette @code{rockchalk} offers a
+fairly comprehensive overview.  The vignette @code{Rstyle} has advice about
+coding in R.  The package title @code{rockchalk} refers to our school motto,
+\"Rock Chalk Jayhawk, Go K.U.\".")
+    (license license:gpl3+)))
-- 
2.20.1


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From 669dbf6dc52cd6349262234625f5b02a3bc4ae60 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:11:25 +0100
Subject: [v2 25/34] gnu: Add package r-lisreltor

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1ccc237bf1..55966d09aa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19954,3 +19954,25 @@ fairly comprehensive overview.  The vignette @code{Rstyle} has advice about
 coding in R.  The package title @code{rockchalk} refers to our school motto,
 \"Rock Chalk Jayhawk, Go K.U.\".")
     (license license:gpl3+)))
+
+(define-public r-lisreltor
+  (package
+    (name "r-lisreltor")
+    (version "0.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lisrelToR" version))
+       (sha256
+        (base32
+         "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
+    (properties `((upstream-name . "lisrelToR")))
+    (build-system r-build-system)
+    (home-page
+     "https://cran.r-project.org/package=lisrelToR")
+    (synopsis "Import output from LISREL into R")
+    (description
+     "This is an unofficial package aimed at automating the import of LISREL
+output in R.  This package or its maintainer is not in any way affiliated with
+the creators of LISREL and SSI, Inc.")
+    (license license:gpl2)))
-- 
2.20.1


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From c320b8ca61babc8f09484e81e5c3965ed4001913 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:11:51 +0100
Subject: [v2 26/34] gnu: Add package r-bdgraph

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 55966d09aa..bb958bb577 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19976,3 +19976,29 @@ coding in R.  The package title @code{rockchalk} refers to our school motto,
 output in R.  This package or its maintainer is not in any way affiliated with
 the creators of LISREL and SSI, Inc.")
     (license license:gpl2)))
+
+(define-public r-bdgraph
+  (package
+    (name "r-bdgraph")
+    (version "2.62")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BDgraph" version))
+       (sha256
+        (base32
+         "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
+    (properties `((upstream-name . "BDgraph")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-igraph" ,r-igraph)))
+    (home-page
+     "https://www.uva.nl/profile/a.mohammadi")
+    (synopsis
+     "Bayesian structure learning in graphical models using birth-death MCMC")
+    (description
+     "Statistical tools for Bayesian structure learning in undirected
+graphical models for continuous, discrete, and mixed data.  The package is
+implemented the recent improvements in the Bayesian graphical models
+literature, including Mohammadi and Wit (2015) @url{doi:10.1214/14-BA889},
+Mohammadi and Wit (2019) @url{doi:10.18637/jss.v089.i03}.")
+    (license license:gpl2+)))
-- 
2.20.1


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From c37a7e8bcf31161c4b70ea1ff0a134e8140910a8 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:12:19 +0100
Subject: [v2 27/34] gnu: Add package r-ggm

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bb958bb577..47af203fa6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20002,3 +20002,26 @@ implemented the recent improvements in the Bayesian graphical models
 literature, including Mohammadi and Wit (2015) @url{doi:10.1214/14-BA889},
 Mohammadi and Wit (2019) @url{doi:10.18637/jss.v089.i03}.")
     (license license:gpl2+)))
+
+(define-public r-ggm
+  (package
+    (name "r-ggm")
+    (version "2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "ggm" version))
+        (sha256
+          (base32
+            "1n4y459x2i0jil8chjjqqjs28a8pzfxrws2fcjkg3il7zy0zwbw3"))))
+    (properties `((upstream-name . "ggm")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-igraph" ,r-igraph)))
+    (home-page
+      "https://cran.r-project.org/package=ggm")
+    (synopsis
+      "Functions for graphical Markov models")
+    (description
+      "This package provides functions and datasets for maximum likelihood
+fitting of some classes of graphical Markov models.")
+    (license license:gpl2+)))
-- 
2.20.1


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From f013c408268628aec67b63998bfe78d91d022a5e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:12:49 +0100
Subject: [v2 28/34] gnu: Add package r-d3network

* gnu/packages/cran.scm (r-d3network): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 47af203fa6..02742e8e74 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20025,3 +20025,29 @@ Mohammadi and Wit (2019) @url{doi:10.18637/jss.v089.i03}.")
       "This package provides functions and datasets for maximum likelihood
 fitting of some classes of graphical Markov models.")
     (license license:gpl2+)))
+
+(define-public r-d3network
+  (package
+    (name "r-d3network")
+    (version "0.5.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "d3Network" version))
+       (sha256
+        (base32
+         "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
+    (properties `((upstream-name . "d3Network")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-plyr" ,r-plyr)
+       ("r-rjson" ,r-rjson)
+       ("r-whisker" ,r-whisker)))
+    (home-page
+     "http://christophergandrud.github.io/d3Network/")
+    (synopsis
+     "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
+    (description
+     "This packages is intended to make it easy to create D3 JavaScript
+network, tree, dendrogram, and Sankey graphs from R using data frames.")
+    (license license:gpl3+)))
-- 
2.20.1


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From aff4464330ba8f983e332b1ee6d17ef1caf9594f Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:15:00 +0100
Subject: [v2 29/34] gnu: Add package r-qgraph

* gnu/packages/cran.scm (r-qgraph): New variable.
---
 gnu/packages/cran.scm | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 02742e8e74..d251278d0c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20051,3 +20051,52 @@ fitting of some classes of graphical Markov models.")
      "This packages is intended to make it easy to create D3 JavaScript
 network, tree, dendrogram, and Sankey graphs from R using data frames.")
     (license license:gpl3+)))
+
+(define-public r-qgraph
+  (package
+    (name "r-qgraph")
+    (version "1.6.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qgraph" version))
+       (sha256
+        (base32
+         "1glg814h7fwl1jfm6dw1d9i80bilmj5jcjjrfln15byrdh4mm1j3"))))
+    (properties `((upstream-name . "qgraph")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-bdgraph" ,r-bdgraph)
+       ("r-colorspace" ,r-colorspace)
+       ("r-corpcor" ,r-corpcor)
+       ("r-d3network" ,r-d3network)
+       ("r-dplyr" ,r-dplyr)
+       ("r-fdrtool" ,r-fdrtool)
+       ("r-ggm" ,r-ggm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggraph" ,r-ggraph)
+       ("r-glasso" ,r-glasso)
+       ("r-gtools" ,r-gtools)
+       ("r-hmisc" ,r-hmisc)
+       ("r-huge" ,r-huge)
+       ("r-igraph" ,r-igraph)
+       ("r-jpeg" ,r-jpeg)
+       ("r-lavaan" ,r-lavaan)
+       ("r-matrix" ,r-matrix)
+       ("r-pbapply" ,r-pbapply)
+       ("r-plyr" ,r-plyr)
+       ("r-png" ,r-png)
+       ("r-psych" ,r-psych)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-tidygraph" ,r-tidygraph)))
+    (home-page "http://sachaepskamp.com/qgraph/")
+    (synopsis
+     "Graph plotting methods, psychometric data visualization and graphical
+model estimation")
+    (description
+     "Weighted network visualization and analysis, as well as Gaussian
+graphical model computation.  See Epskamp et al. (2012)
+@url{doi:10.18637/jss.v048.i04}.")
+    (license license:gpl2)))
-- 
2.20.1


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From 4ae37e50fa2214c44d9c7cc48500ac009a0f8d91 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:15:25 +0100
Subject: [v2 30/34] gnu: Add package r-semplot

* gnu/packages/cran.scm (r-semplot): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d251278d0c..1e09579cb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20100,3 +20100,37 @@ model estimation")
 graphical model computation.  See Epskamp et al. (2012)
 @url{doi:10.18637/jss.v048.i04}.")
     (license license:gpl2)))
+
+(define-public r-semplot
+  (package
+    (name "r-semplot")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "semPlot" version))
+       (sha256
+        (base32
+         "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
+    (properties `((upstream-name . "semPlot")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colorspace" ,r-colorspace)
+       ("r-corpcor" ,r-corpcor)
+       ("r-igraph" ,r-igraph)
+       ("r-lavaan" ,r-lavaan)
+       ("r-lisreltor" ,r-lisreltor)
+       ("r-openmx" ,r-openmx)
+       ("r-plyr" ,r-plyr)
+       ("r-qgraph" ,r-qgraph)
+       ("r-regsem" ,r-regsem)
+       ("r-rockchalk" ,r-rockchalk)
+       ("r-sem" ,r-sem)
+       ("r-xml" ,r-xml)))
+    (home-page
+     "https://github.com/SachaEpskamp/semPlot")
+    (synopsis
+     "Path diagrams and visual analysis of various SEM packages' output")
+    (description
+     "Path diagrams and visual analysis of various SEM packages' output.")
+    (license license:gpl2)))
-- 
2.20.1


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From c176ff89ec75e2d0d201f3815fcfbf9956481168 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:15:51 +0100
Subject: [v2 31/34] gnu: Add package r-cdm

* gnu/packages/cran.scm (r-cdm): New variable.
---
 gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1e09579cb6..62a9dede4e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20134,3 +20134,42 @@ graphical model computation.  See Epskamp et al. (2012)
     (description
      "Path diagrams and visual analysis of various SEM packages' output.")
     (license license:gpl2)))
+
+(define-public r-cdm
+  (package
+    (name "r-cdm")
+    (version "7.4-19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "CDM" version))
+       (sha256
+        (base32
+         "1ln1r3rk004fmk55iy08bjh3vv4wnkb8zg2wj3r9rq7pi8jn8fv4"))))
+    (properties `((upstream-name . "CDM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mvtnorm" ,r-mvtnorm)
+       ("r-polycor" ,r-polycor)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page
+     "https://github.com/alexanderrobitzsch/CDM")
+    (synopsis "Cognitive diagnosis modeling")
+    (description
+     "Functions for cognitive diagnosis modeling and multidimensional item
+response modeling for dichotomous and polytomous item responses.  This package
+enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001,
+@url{doi:10.1177/01466210122032064}), the multiple group (polytomous) GDINA
+model (de la Torre, 2011, @url{doi:10.1007/s11336-011-9207-7}), the multiple
+choice DINA model (de la Torre, 2009, @url{doi:10.1177/0146621608320523}), the
+general diagnostic model (GDM; von Davier, 2008,
+@url{doi:10.1348/000711007X193957}), the structured latent class model (SLCA;
+Formann, 1992, @url{doi:10.1080/01621459.1992.10475229}) and regularized latent
+class analysis (Chen, Li, Liu, & Ying, 2017,
+@url{doi:10.1007/s11336-016-9545-6}).  See George, Robitzsch, Kiefer, Gross,
+and Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
+estimation and the package structure.  For tutorials on how to use the CDM
+package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
+well as Ravand and Robitzsch (2015).")
+    (license license:gpl2+)))
-- 
2.20.1


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From deaccf8b2cafa67804a050d7b8c5b43fc058f13e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:16:30 +0100
Subject: [v2 32/34] gnu: Add package r-tam

* gnu/packages/cran.scm (r-tam): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 62a9dede4e..195c6b801e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20173,3 +20173,37 @@ estimation and the package structure.  For tutorials on how to use the CDM
 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
 well as Ravand and Robitzsch (2015).")
     (license license:gpl2+)))
+
+(define-public r-tam
+  (package
+    (name "r-tam")
+    (version "3.3-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "TAM" version))
+       (sha256
+        (base32
+         "1rkjp5x6wrk1dfspp1imvfals0wvy4w1wb8a5mhfbnilc7vgnlbq"))))
+    (properties `((upstream-name . "TAM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cdm" ,r-cdm)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page
+     "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
+    (synopsis "Test analysis modules")
+    (description
+     "Includes marginal maximum likelihood estimation and joint maximum
+likelihood estimation for unidimensional and multidimensional item response
+models.  The package functionality covers the Rasch model, 2PL model, 3PL
+model, generalized partial credit model, multi-faceted Rasch model, nominal
+item response model, structured latent class model, mixture distribution IRT
+models, and located latent class models.  Latent regression models and
+plausible value imputation are also supported.  For details see Adams, Wilson
+and Wang, 1997 @url{doi:10.1177/0146621697211001}, Adams, Wilson and Wu, 1997
+@url{doi:10.3102/10769986022001047}, Formann, 1982
+@url{doi:10.1002/bimj.4710240209}, Formann, 1992
+@url{doi:10.1080/01621459.1992.10475229}.")
+    (license license:gpl2+)))
-- 
2.20.1


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From ee59209affbdab125ff40770482e56689086a3e7 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:16:57 +0100
Subject: [v2 33/34] gnu: Add package r-erm

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 195c6b801e..43ce04f826 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20207,3 +20207,36 @@ and Wang, 1997 @url{doi:10.1177/0146621697211001}, Adams, Wilson and Wu, 1997
 @url{doi:10.1002/bimj.4710240209}, Formann, 1992
 @url{doi:10.1080/01621459.1992.10475229}.")
     (license license:gpl2+)))
+
+(define-public r-erm
+  (package
+    (name "r-erm")
+    (version "1.0-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "eRm" version))
+       (sha256
+        (base32
+         "11p8j61arq1ih2qi33wf0442vcdbp3zvknzm5aknsifwl4mbzzly"))))
+    (properties `((upstream-name . "eRm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page
+     "https://cran.r-project.org/package=eRm")
+    (synopsis "Extended Rasch modeling")
+    (description
+     "Fits @dfn{Rasch models} (RM), @dfn{linear logistic test models} (LLTM),
+@dfn{rating scale model} (RSM), @dfn{linear rating scale models} (LRSM),
+@dfn{partial credit models} (PCM), and @dfn{linear partial credit models}
+(LPCM).  Missing values are allowed in the data matrix.  Additional features
+are the ML estimation of the person parameters, Andersen's LR-test,
+item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests,
+itemfit and personfit statistics including infit and outfit measures, ICC and
+other plots, automated stepwise item elimination, simulation module for various
+binary data matrices.")
+    (license license:gpl3)))
-- 
2.20.1


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From e8683cb87a54b57d857689466809dd87ba7ef2d9 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 4 Feb 2020 14:17:17 +0100
Subject: [v2 34/34] gnu: Add package r-irtoys

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 43ce04f826..5d06b8d452 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20240,3 +20240,35 @@ itemfit and personfit statistics including infit and outfit measures, ICC and
 other plots, automated stepwise item elimination, simulation module for various
 binary data matrices.")
     (license license:gpl3)))
+
+(define-public r-irtoys
+  (package
+    (name "r-irtoys")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "irtoys" version))
+       (sha256
+        (base32
+         "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
+    (properties `((upstream-name . "irtoys")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ltm" ,r-ltm) ("r-sm" ,r-sm)))
+    (home-page
+     "https://cran.r-project.org/package=irtoys")
+    (synopsis
+     "Collection of functions related to Item Response Theory (IRT)")
+    (description
+     "This package provides a collection of functions useful in learning and
+practicing IRT, which can be combined into larger programs.  Provides basic CTT
+analysis, a simple common interface to the estimation of item parameters in IRT
+models for binary responses with three different programs (ICL, BILOG-MG, and
+ltm), ability estimation (MLE, BME, EAP, WLE, plausible values), item and
+person fit statistics, scaling methods (MM, MS, Stocking-Lord, and the complete
+Hebaera method), and a rich array of parametric and non-parametric (kernel)
+plots.  Estimates and plots Haberman's interaction model when all items are
+dichotomously scored.")
+    (license license:gpl2+)))
+
-- 
2.20.1

bug#39416: Bulk import of R packages

[Ricardo Wurmus]

Hi Lars,

>> Could you please also do the following:
>>
>> * modify the description to contain only complete sentences
>> * adjust the letter case in the synopsis (CRAN uppercases all initials)
>> * adjust the indentation with etc/indent-code.el
>> * use @dfn{Some Long Term} (SLT) in descriptions where necessary
>> * wrap URLs in the description in Texinfo syntax (especially all the
>>   <doi:...> things.
> done, I hope I did not miss anything.

Thank you for the updated patches. I’ve just pushed variants of these
patches.

There were still quite a few things to change, which is why this took me
so long.  One of the problems was that the descriptions often included
incomplete sentence fragments.

--
Ricardo