[bug#56021] gnu: Add r-nada, r-zcompositions, r-aldex2.

[bug#56021] gnu: Add r-nada, r-zcompositions, r-aldex2.

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #2: Type: text/html, Size: 830 bytes --]

[bug#56021] [PATCH 1/3] gnu: Add r-nada.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b326332bf6..28cd2e7fad 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -27881,6 +27881,26 @@ (define-public r-nabor
 to speed up repeated queries of the same set of target points.")
     (license license:bsd-3)))
 
+(define-public r-nada
+  (package
+    (name "r-nada")
+    (version "1.6-1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "NADA" version))
+              (sha256
+               (base32
+                "0jp4mqr77cx7q5lff84s6wb0dwjy9mi0jyhbjc5fsx50bdczc3v7"))))
+    (properties `((upstream-name . "NADA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-survival))
+    (home-page "https://cran.r-project.org/package=NADA")
+    (synopsis "Nondetects and data analysis for environmental data")
+    (description
+     "This package contains methods described by Dennis Helsel in his book
+@emph{Nondetects and Data Analysis: Statistics for Censored Environmental Data}.")
+    (license license:gpl2+)))
+
 (define-public r-naturalsort
   (package
    (name "r-naturalsort")

base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
-- 
2.36.1

[bug#56021] [PATCH 2/3] gnu: Add r-zcompositions.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-zcompositions): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 28cd2e7fad..945cb5bdce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -836,6 +836,37 @@ (define-public r-dlm
 known as Dynamic Linear Models.")
     (license license:gpl2+)))
 
+(define-public r-zcompositions
+  (package
+    (name "r-zcompositions")
+    (version "1.4.0-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "zCompositions" version))
+              (sha256
+               (base32
+                "1rrhja9iaq123r2gqw1bzrn1ri0s3z4wzq8p0sfcr1yb6pv13vik"))))
+    (properties `((upstream-name . "zCompositions")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-mass
+           r-nada
+           r-truncnorm))
+    (home-page "https://github.com/Japal/zCompositions")
+    (synopsis
+     "Treatment of zeros, left-censored and missing values in compositional data")
+    (description
+     "This package @code{zCompositions} is an @code{R} package for the imputation
+of left-censored data under a compositional approach.  The implemented methods
+consider aspects of relevance for a compositional approach such as scale
+invariance, subcompositional coherence or preserving the multivariate relative
+structure of the data.  Based on solid statistical frameworks, it comprises the
+ability to deal with single and varying censoring thresholds, consistent treatment
+of closed and non-closed data, exploratory tools, multiple imputation, @dfn{MCMC}
+(Markov Chain Monte Carlo), robust and non-parametric alternatives, and recent
+proposals for count data.")
+    (license license:gpl2+)))
+
 (define-public r-zoo
   (package
     (name "r-zoo")
-- 
2.36.1

[bug#56021] [PATCH 3/3] gnu: Add r-aldex2.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-aldex2): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..3abd57359d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,48 @@ (define-public r-agimicrorna
 objects are used so that other packages could be used as well.")
     (license license:gpl3)))
 
+(define-public r-aldex2
+  (package
+    (name "r-aldex2")
+    (version "1.28.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ALDEx2" version))
+              (sha256
+               (base32
+                "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"))))
+    (properties `((upstream-name . "ALDEx2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-genomicranges
+           r-iranges
+           r-multtest
+           r-rfast
+           r-s4vectors
+           r-summarizedexperiment
+           r-zcompositions))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ggloor/ALDEx_bioc")
+    (synopsis
+     "Analysis Of differential abundance taking sample variation into account")
+    (description
+     "This package provides a differential abundance analysis for the comparison
+of two or more conditions.  Useful for analyzing data from standard RNA-seq or
+meta-RNA-seq assays as well as selected and unselected values from in-vitro
+sequence selections.  Uses a Dirichlet-multinomial model to infer abundance from
+counts, optimized for three or more experimental replicates.  The method infers
+biological and sampling variation to calculate the expected false discovery
+rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test
+(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear
+model (via aldex.glm), or a correlation test (via aldex.corr).  All tests report
+p-values and Benjamini-Hochberg corrected p-values.  ALDEx2 also calculates
+expected standardized effect sizes for paired or unpaired study designs.")
+    ;; The code for the function "rdirichlet" which is from the "R" package
+    ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball
+    ;; LICENSE specifies GPL-3.
+    (license (list license:agpl3+ license:gpl2+ license:gpl3))))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.36.1

bug#56021: gnu: Add r-nada, r-zcompositions, r-aldex2.

[Ricardo Wurmus]

Applied, thank you!

-- 
Ricardo