[bug#44683] [PATCH] Miscellaneous R packages

[bug#44683] [PATCH] Miscellaneous R packages

[Lars-Dominik Braun]

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Hi,

I’ve imported several R packages from CRAN using the importer. Descriptions
have been edited slightly.

Cheers,
Lars

-- 
Lars-Dominik Braun
Wissenschaftlicher Mitarbeiter/Research Associate

www.leibniz-psychology.org
ZPID - Leibniz-Institut für Psychologie /
ZPID - Leibniz Institute for Psychology
Universitätsring 15
D-54296 Trier - Germany
Tel.: +49–651–201-4964

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From 90f282cc5a9fb369cbb650f847917ccf956e8276 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 12:56:25 +0100
Subject: [PATCH 1/9] gnu: Add r-prereg.

* gnu/packages/cran.scm (r-prereg): 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 64e139c243..eb8ce230d4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24657,3 +24657,26 @@ orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
 parabolic or user defined by custom scale factors.")
     (license license:gpl3)))
 
+(define-public r-prereg
+  (package
+    (name "r-prereg")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "prereg" version))
+        (sha256
+          (base32
+            "1jhlgp7ajq6mx7gn4kf3b7wqzs3v0678pa1r6p4mgvvynic8rnqj"))))
+    (properties `((upstream-name . "prereg")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-rmarkdown" ,r-rmarkdown)))
+    (home-page "https://github.com/crsh/prereg")
+    (synopsis
+      "R Markdown Templates to Preregister Scientific Studies")
+    (description
+     "This package provides a collection of templates to author
+preregistration documents for scientific studies in PDF format.")
+    (license license:gpl3)))
+
-- 
2.25.1


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From 87219fced97d6359ac43017804347e79b3d2b0d1 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 12:58:22 +0100
Subject: [PATCH 2/9] gnu: Add r-metafor.

* gnu/packages/cran.scm (r-metafor): 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 eb8ce230d4..59f018c123 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24680,3 +24680,40 @@ parabolic or user defined by custom scale factors.")
 preregistration documents for scientific studies in PDF format.")
     (license license:gpl3)))
 
+(define-public r-metafor
+  (package
+    (name "r-metafor")
+    (version "2.4-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "metafor" version))
+        (sha256
+          (base32
+            "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
+    (properties `((upstream-name . "metafor")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme)))
+    (home-page
+      "https://cran.r-project.org/web/packages/metafor")
+    (synopsis "Meta-Analysis Package for R")
+    (description
+     "This package provides a comprehensive collection of functions for
+conducting meta-analyses in R.  The package includes functions to calculate
+various effect sizes or outcome measures, fit fixed-, random-, and
+mixed-effects models to such data, carry out moderator and meta-regression
+analyses, and create various types of meta-analytical plots (e.g., forest,
+funnel, radial, L'Abbe, Baujat, GOSH plots).  For meta-analyses of binomial and
+person-time data, the package also provides functions that implement
+specialized methods, including the Mantel-Haenszel method, Peto's method, and a
+variety of suitable generalized linear (mixed-effects) models (i.e.,
+mixed-effects logistic and Poisson regression models).  Finally, the package
+provides functionality for fitting meta-analytic multivariate/multilevel models
+that account for non-independent sampling errors and/or true effects (e.g., due
+to the inclusion of multiple treatment studies, multiple endpoints, or other
+forms of clustering).  Network meta-analyses and meta-analyses accounting for
+known correlation structures (e.g., due to phylogenetic relatedness) can also
+be conducted.")
+    (license license:gpl2+)))
+
-- 
2.25.1


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From 0b52713d2c0d9ea38c8d4120ec0a719949064e56 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 12:58:47 +0100
Subject: [PATCH 3/9] gnu: Add r-ez.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 59f018c123..602eec8250 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24717,3 +24717,43 @@ known correlation structures (e.g., due to phylogenetic relatedness) can also
 be conducted.")
     (license license:gpl2+)))
 
+(define-public r-ez
+  (package
+    (name "r-ez")
+    (version "4.4-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "ez" version))
+        (sha256
+          (base32
+            "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
+    (properties `((upstream-name . "ez")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-car" ,r-car)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-lme4" ,r-lme4)
+        ("r-mass" ,r-mass)
+        ("r-matrix" ,r-matrix)
+        ("r-mgcv" ,r-mgcv)
+        ("r-plyr" ,r-plyr)
+        ("r-reshape2" ,r-reshape2)
+        ("r-scales" ,r-scales)
+        ("r-stringr" ,r-stringr)))
+    (home-page "https://github.com/mike-lawrence/ez")
+    (synopsis "Easy Analysis and Visualization of Factorial Experiments")
+    (description
+     "Facilitates easy analysis of factorial experiments, including purely
+within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
+and mixed within-and-between-Ss designs.  The functions in this package aim to
+provide simple, intuitive and consistent specification of data analysis and
+visualization.  Visualization functions also include design visualization for
+pre-analysis data auditing, and correlation matrix visualization.  Finally,
+this package includes functions for non-parametric analysis, including
+permutation tests and bootstrap resampling.  The bootstrap function obtains
+predictions either by cell means or by more advanced/powerful mixed effects
+models, yielding predictions and confidence intervals that may be easily
+visualized at any level of the experiment's design.")
+    (license license:gpl2+)))
+
-- 
2.25.1


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From f7c09f739c894b5e3894eab5f3c832d37cec3ad6 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 12:59:26 +0100
Subject: [PATCH 4/9] gnu: Add r-quantpsyc.

* gnu/packages/cran.scm (r-quantpsyc): 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 602eec8250..4e4c6623e4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24757,3 +24757,25 @@ models, yielding predictions and confidence intervals that may be easily
 visualized at any level of the experiment's design.")
     (license license:gpl2+)))
 
+(define-public r-quantpsyc
+  (package
+    (name "r-quantpsyc")
+    (version "1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "QuantPsyc" version))
+        (sha256
+          (base32
+            "1i9bh88r8zxndzjqsj14qw64gnvm5a9kvhjhzk3qsrvl3qzjgh93"))))
+    (properties `((upstream-name . "QuantPsyc")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-boot" ,r-boot) ("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/QuantPsyc/")
+    (synopsis "Quantitative Psychology Tools")
+    (description
+      "Contains functions useful for data screening, testing moderation,
+mediation and estimating power.")
+    (license license:gpl2+)))
+
-- 
2.25.1


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From 00938f70c0e0dcf5303c7eb102e1b7e46813df23 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 13:00:06 +0100
Subject: [PATCH 5/9] gnu: Add r-visnetwork.

* gnu/packages/cran.scm (r-visnetwork): 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 4e4c6623e4..7b6338df0f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24779,3 +24779,29 @@ visualized at any level of the experiment's design.")
 mediation and estimating power.")
     (license license:gpl2+)))
 
+(define-public r-visnetwork
+  (package
+    (name "r-visnetwork")
+    (version "2.0.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "visNetwork" version))
+        (sha256
+          (base32
+            "0854r9znpjd9iy6j5bgrn20vj13dhp606gs3b6iy0rhym71ks2sy"))))
+    (properties `((upstream-name . "visNetwork")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-htmltools" ,r-htmltools)
+        ("r-htmlwidgets" ,r-htmlwidgets)
+        ("r-jsonlite" ,r-jsonlite)
+        ("r-magrittr" ,r-magrittr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "http://datastorm-open.github.io/visNetwork/")
+    (synopsis "Network Visualization using vis.js Library")
+    (description
+      "This package provides an R interface to the vis.js JavaScript charting
+library.  It allows an interactive visualization of networks.")
+    (license license:expat)))
+
-- 
2.25.1


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From ecf9923d276b2a5e2889c1bab049fe6ffbf01957 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 13:01:13 +0100
Subject: [PATCH 6/9] gnu: Add r-diagrammer.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7b6338df0f..e567cc8c2b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24805,3 +24805,48 @@ mediation and estimating power.")
 library.  It allows an interactive visualization of networks.")
     (license license:expat)))
 
+(define-public r-diagrammer
+  (package
+    (name "r-diagrammer")
+    (version "1.0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "DiagrammeR" version))
+        (sha256
+          (base32
+            "0gb7ccdrh7jlyqafdk8zs465ygczxxd25s05whn914in1994qkmy"))))
+    (properties `((upstream-name . "DiagrammeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-downloader" ,r-downloader)
+        ("r-dplyr" ,r-dplyr)
+        ("r-glue" ,r-glue)
+        ("r-htmltools" ,r-htmltools)
+        ("r-htmlwidgets" ,r-htmlwidgets)
+        ("r-igraph" ,r-igraph)
+        ("r-influencer" ,r-influencer)
+        ("r-magrittr" ,r-magrittr)
+        ("r-purrr" ,r-purrr)
+        ("r-rcolorbrewer" ,r-rcolorbrewer)
+        ("r-readr" ,r-readr)
+        ("r-rlang" ,r-rlang)
+        ("r-rstudioapi" ,r-rstudioapi)
+        ("r-scales" ,r-scales)
+        ("r-stringr" ,r-stringr)
+        ("r-tibble" ,r-tibble)
+        ("r-tidyr" ,r-tidyr)
+        ("r-viridis" ,r-viridis)
+        ("r-visnetwork" ,r-visnetwork)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/rich-iannone/DiagrammeR")
+    (synopsis "Graph/Network Visualization")
+    (description
+      "Build graph/network structures using functions for stepwise addition
+and deletion of nodes and edges.  Work with data available in tables for bulk
+addition of nodes, edges, and associated metadata.  Use graph selections and
+traversals to apply changes to specific nodes or edges.  A wide selection of
+graph algorithms allow for the analysis of graphs.  Visualize the graphs and
+take advantage of any aesthetic properties assigned to nodes and edges.")
+    (license license:expat)))
+
-- 
2.25.1


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From 6bf8cfb004441ae75e2ca93075ae7a1d0a9799aa Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 13:01:50 +0100
Subject: [PATCH 7/9] gnu: Add r-lavaanplot.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e567cc8c2b..4a7c1535f4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24850,3 +24850,31 @@ graph algorithms allow for the analysis of graphs.  Visualize the graphs and
 take advantage of any aesthetic properties assigned to nodes and edges.")
     (license license:expat)))
 
+(define-public r-lavaanplot
+  (package
+    (name "r-lavaanplot")
+    (version "0.5.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "lavaanPlot" version))
+        (sha256
+          (base32
+            "01bx1snd3zhc8dmq0f407qhw2d00f6d38qpr791qc1mq5kr3d8qj"))))
+    (properties `((upstream-name . "lavaanPlot")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-diagrammer" ,r-diagrammer)
+        ("r-lavaan" ,r-lavaan)
+        ("r-stringr" ,r-stringr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/alishinski/lavaanPlot")
+    (synopsis "Path Diagrams for Lavaan Models via DiagrammeR")
+    (description
+      "Plots path diagrams from models in lavaan using the plotting
+functionality from the DiagrammeR package.  DiagrammeR provides nice path
+diagrams via Graphviz, and these functions make it easy to generate these
+diagrams from a lavaan path model without having to write the DOT language
+graph specification.")
+    (license license:gpl2+)))
+
-- 
2.25.1


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From 3312c0c3754f62222dfe67733f8610aa6e7d687a Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 13:02:28 +0100
Subject: [PATCH 8/9] gnu: Add r-clubsandwich.

* gnu/packages/cran.scm (r-clubsandwich): 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 4a7c1535f4..0caff23582 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24878,3 +24878,36 @@ diagrams from a lavaan path model without having to write the DOT language
 graph specification.")
     (license license:gpl2+)))
 
+(define-public r-clubsandwich
+  (package
+    (name "r-clubsandwich")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "clubSandwich" version))
+       (sha256
+        (base32
+         "1q4kidxcarlazh9zaav6vdc7ixb3hdg3zh5kr6mwkm087gi05nw5"))))
+    (properties `((upstream-name . "clubSandwich")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-sandwich" ,r-sandwich)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jepusto/clubSandwich")
+    (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
+Corrections")
+    (description
+     "Provides several cluster-robust variance estimators (i.e., sandwich
+estimators) for ordinary and weighted least squares linear regression models,
+including the bias-reduced linearization estimator introduced by
+@url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf, Bell
+and McCaffrey (2002)} and developed further by
+@url{DOI:10.1080/07350015.2016.1247004, Pustejovsky and Tipton (2017)}.  The
+package includes functions for estimating the variance- covariance matrix and
+for testing single- and multiple- contrast hypotheses based on Wald test
+statistics.  Tests of single regression coefficients use Satterthwaite or
+saddle-point corrections.  Tests of multiple- contrast hypotheses use an
+approximation to Hotelling's T-squared distribution.")
+    (license license:gpl3)))
+
-- 
2.25.1


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From dd2095db08802c6481903466b58866b2e987eb60 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Mon, 16 Nov 2020 13:03:16 +0100
Subject: [PATCH 9/9] gnu: Add r-puniform.

* gnu/packages/cran.scm (r-puniform): 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 0caff23582..caf8cfbfc1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24911,3 +24911,37 @@ saddle-point corrections.  Tests of multiple- contrast hypotheses use an
 approximation to Hotelling's T-squared distribution.")
     (license license:gpl3)))
 
+(define-public r-puniform
+  (package
+    (name "r-puniform")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "puniform" version))
+       (sha256
+        (base32
+         "1y47y6s76pjvp10m8rvdh7y1iidjw96a4wrr920w0js3rn4fi1fz"))))
+    (properties `((upstream-name . "puniform")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-adgoftest" ,r-adgoftest)
+       ("r-metafor" ,r-metafor)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page
+     "https://cran.r-project.org/web/packages/puniform")
+    (synopsis
+     "Meta-Analysis Methods Correcting for Publication Bias")
+    (description
+     "This package provides meta-analysis methods that correct for publication
+bias and outcome reporting bias.  Four methods and a visual tool are currently
+included in the package.  The p-uniform method as described in
+@url{doi:10.1037/met0000025, van Assen and and van Aert and Wicherts (2015)},
+the p-uniform* method as described in @url{doi:10.31222/osf.io/zqjr9, van Aert
+and van Assen (2019)}, the hybrid method as described in
+@url{doi:10.3758/s13428-017-0967-6, van Aert and van Assen (2017)} and the
+Snapshot Bayesian Hybrid Meta-Analysis Method as described in
+@url{doi:10.1371/journal.pone.0175302, van Aert and van Assen (2018)}.")
+    (license license:gpl2+)))
+
-- 
2.25.1


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bug#44683: [PATCH] Miscellaneous R packages

[Lars-Dominik Braun]

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This patchset is now obsolete, since some of them have been updated in the meantime.

-- 
Lars-Dominik Braun
Wissenschaftlicher Mitarbeiter/Research Associate

www.leibniz-psychology.org
ZPID - Leibniz-Institut für Psychologie /
ZPID - Leibniz Institute for Psychology
Universitätsring 15
D-54296 Trier - Germany
Tel.: +49–651–201-4964

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