[bug#55239] [PATCH 1/4] gnu: Add r-forestplot.

[bug#55239] [PATCH 1/4] gnu: Add r-forestplot.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-forestplot): New variable.
X-Debbugs-Cc: rekado@elephly.net
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 91c54bac9a..864540adf1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24377,6 +24377,33 @@ (define-public r-forecast
 space models and automatic ARIMA modelling.")
     (license license:gpl3)))
 
+(define-public r-forestplot
+  (package
+    (name "r-forestplot")
+    (version "2.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "forestplot" version))
+              (sha256
+               (base32
+                "0bzwi6ws0qjq1pqiadssynbkxxd4zjp974jfdplmv16fcyszqhyi"))))
+    (properties `((upstream-name . "forestplot")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-checkmate
+           r-magrittr))
+    (native-inputs (list r-knitr))
+    (home-page "https://gforge.se/packages/")
+    (synopsis "Advanced forest plot using @code{grid} graphics")
+    (description
+     "This package provides a forest plot that allows for multiple confidence
+intervals per row, custom fonts for each text element, custom confidence
+intervals, text mixed with expressions, and more.  The aim is to extend the use
+of forest plots beyond meta-analyses.  This is a more general version of the
+original @code{rmeta} package's @code{forestplot()} function and relies heavily
+on the @code{grid} package.")
+    (license license:gpl2)))
+
 (define-public r-formattable
   (package
     (name "r-formattable")

base-commit: 098f2eea331121905e3c867f478b22cea3510841
-- 
2.36.0

[bug#55238] [PATCH 2/4] gnu: Add r-catdata.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-catdata): 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 864540adf1..63e2b71cd3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8191,6 +8191,28 @@ (define-public r-catdap
 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
     (license license:gpl2+)))
 
+(define-public r-catdata
+  (package
+    (name "r-catdata")
+    (version "1.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "catdata" version))
+              (sha256
+               (base32
+                "14kx7yi0cv6dyh9wjasb8gn6cp1bhglgwql7dc2a7lqvdcp0d5vj"))))
+    (properties `((upstream-name . "catdata")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass))
+    (home-page "https://cran.r-project.org/package=catdata")
+    (synopsis
+     "Datasets and examples used in the book @emph{Regression for Categorical Data}")
+    (description
+     "This R package contains examples from the book @emph{Regression for
+Categorical Data}, Tutz 2012, Cambridge University Press.  The names of the
+examples refer to the chapter and the data set that is used.")
+    (license license:gpl2)))
+
 (define-public r-arules
   (package
     (name "r-arules")
-- 
2.36.0

[bug#55238] [PATCH 2/4] gnu: Add r-catdata.

[Ricardo Wurmus]

Applied, thanks!

-- 
Ricardo

[bug#55241] [PATCH 3/4] gnu: Add r-smurf.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 63e2b71cd3..099bfb8002 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5907,6 +5907,48 @@ (define-public r-sm
 and density estimation")
     (license license:gpl2+)))
 
+(define-public r-smurf
+  (package
+    (name "r-smurf")
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "smurf" version))
+              (sha256
+               (base32
+                "00q54pg42anilhcshhjvv277mkszbpzpkf1g7srs7cjd5skjvsaf"))))
+    (properties `((upstream-name . "smurf")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-catdata
+           r-glmnet
+           r-mass
+           r-matrix
+           r-mgcv
+           r-rcolorbrewer
+           r-rcpp
+           r-rcpparmadillo
+           r-speedglm))
+    (native-inputs (list r-knitr))
+    (home-page "https://gitlab.com/TReynkens/smurf")
+    (synopsis "Sparse multi-type regularized feature modeling")
+    (description
+     "The @code{smurf} package contains the implementation of the @dfn{Sparse
+Multi-type Regularized Feature} (SMuRF) modeling algorithm to fit
+@dfn{generalized linear models} (GLMs) with multiple types of predictors via
+regularized maximum likelihood.  Next to the fitting procedure, following
+functionality is available:
+
+@itemize @bullet
+@item
+Selection of the regularization tuning parameter lambda using three different
+approaches: in-sample, out-of-sample or using cross-validation.
+@item
+S3 methods to handle the fitted object including visualization of the coefficients
+and a model summary.
+@end itemize")
+    (license license:gpl2+)))
+
 (define-public r-venndiagram
   (package
     (name "r-venndiagram")
-- 
2.36.0

[bug#55240] [PATCH 4/4] gnu: Add r-airpart.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-airpart): New variable.
---
 gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a78903becc..2967c5016b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1877,6 +1877,52 @@ (define-public r-agilp
     ;; GPLv3.
     (license license:gpl3)))
 
+(define-public r-airpart
+  (package
+    (name "r-airpart")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "airpart" version))
+              (sha256
+               (base32
+                "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06"))))
+    (properties `((upstream-name . "airpart")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-apeglm
+           r-clue
+           r-complexheatmap
+           r-dplyr
+           r-dynamictreecut
+           r-emdbook
+           r-forestplot
+           r-ggplot2
+           r-lpsolve
+           r-matrixstats
+           r-mclust
+           r-pbapply
+           r-plyr
+           r-rcolorbrewer
+           r-rlang
+           r-s4vectors
+           r-scater
+           r-singlecellexperiment
+           r-smurf
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/airpart")
+    (synopsis "Differential cell-type-specific allelic imbalance")
+    (description
+     "The @code{airpart} package identifies sets of genes displaying differential
+cell-type-specific allelic imbalance across cell types or states, utilizing
+single-cell allelic counts.  It makes use of a generalized fused lasso with
+binomial observations of allelic counts to partition cell types by their allelic
+imbalance.  Alternatively, a nonparametric method for partitioning cell types
+is offered.  The package includes a number of visualizations and quality control
+functions for examining single cell allelic imbalance datasets.")
+    (license license:gpl2)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.36.0

bug#55239: [PATCH 1/4] gnu: Add r-forestplot.

[Ricardo Wurmus]

Applied, thanks!

-- 
Ricardo