* [bug#55239] [PATCH 1/4] gnu: Add r-forestplot.
@ 2022-05-03 6:53 Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55238] [PATCH 2/4] gnu: Add r-catdata Mădălin Ionel Patrașcu
` (3 more replies)
0 siblings, 4 replies; 6+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-05-03 6:53 UTC (permalink / raw)
To: 55239
* 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
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [bug#55238] [PATCH 2/4] gnu: Add r-catdata.
2022-05-03 6:53 [bug#55239] [PATCH 1/4] gnu: Add r-forestplot Mădălin Ionel Patrașcu
@ 2022-05-03 6:53 ` Mădălin Ionel Patrașcu
2022-10-31 19:12 ` Ricardo Wurmus
2022-05-03 6:53 ` [bug#55241] [PATCH 3/4] gnu: Add r-smurf Mădălin Ionel Patrașcu
` (2 subsequent siblings)
3 siblings, 1 reply; 6+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-05-03 6:53 UTC (permalink / raw)
To: 55238
* 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
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [bug#55241] [PATCH 3/4] gnu: Add r-smurf.
2022-05-03 6:53 [bug#55239] [PATCH 1/4] gnu: Add r-forestplot Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55238] [PATCH 2/4] gnu: Add r-catdata Mădălin Ionel Patrașcu
@ 2022-05-03 6:53 ` Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55240] [PATCH 4/4] gnu: Add r-airpart Mădălin Ionel Patrașcu
2022-10-31 19:10 ` bug#55239: [PATCH 1/4] gnu: Add r-forestplot Ricardo Wurmus
3 siblings, 0 replies; 6+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-05-03 6:53 UTC (permalink / raw)
To: 55241
* 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
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [bug#55240] [PATCH 4/4] gnu: Add r-airpart.
2022-05-03 6:53 [bug#55239] [PATCH 1/4] gnu: Add r-forestplot Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55238] [PATCH 2/4] gnu: Add r-catdata Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55241] [PATCH 3/4] gnu: Add r-smurf Mădălin Ionel Patrașcu
@ 2022-05-03 6:53 ` Mădălin Ionel Patrașcu
2022-10-31 19:10 ` bug#55239: [PATCH 1/4] gnu: Add r-forestplot Ricardo Wurmus
3 siblings, 0 replies; 6+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-05-03 6:53 UTC (permalink / raw)
To: 55240
* 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
^ permalink raw reply related [flat|nested] 6+ messages in thread
* bug#55239: [PATCH 1/4] gnu: Add r-forestplot.
2022-05-03 6:53 [bug#55239] [PATCH 1/4] gnu: Add r-forestplot Mădălin Ionel Patrașcu
` (2 preceding siblings ...)
2022-05-03 6:53 ` [bug#55240] [PATCH 4/4] gnu: Add r-airpart Mădălin Ionel Patrașcu
@ 2022-10-31 19:10 ` Ricardo Wurmus
3 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2022-10-31 19:10 UTC (permalink / raw)
To: 55239-done
Applied, thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#55238] [PATCH 2/4] gnu: Add r-catdata.
2022-05-03 6:53 ` [bug#55238] [PATCH 2/4] gnu: Add r-catdata Mădălin Ionel Patrașcu
@ 2022-10-31 19:12 ` Ricardo Wurmus
0 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2022-10-31 19:12 UTC (permalink / raw)
To: 55238-done
Applied, thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
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2022-10-31 19:12 ` Ricardo Wurmus
2022-05-03 6:53 ` [bug#55241] [PATCH 3/4] gnu: Add r-smurf Mădălin Ionel Patrașcu
2022-05-03 6:53 ` [bug#55240] [PATCH 4/4] gnu: Add r-airpart Mădălin Ionel Patrașcu
2022-10-31 19:10 ` bug#55239: [PATCH 1/4] gnu: Add r-forestplot Ricardo Wurmus
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