[bug#59908] [PATCH] gnu: Add r-rcppde, r-ptw, r-pepsnmr and r-asics.

[bug#59908] [PATCH] gnu: Add r-rcppde, r-ptw, r-pepsnmr and r-asics.

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 129 bytes --]

* gnu/packages/bioconductor.scm (r-pepsnmr, r-asics): New variables.
* gnu/packages/cran.scm (r-rcppde, r-ptw): New variables.

[-- Attachment #2: Type: text/html, Size: 975 bytes --]

[bug#59908] [PATCH 1/4] gnu: Add r-rcppde.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-rcppde): 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 5c5258d6e0..016eeb4821 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4569,6 +4569,32 @@ (define-public r-rcpp
 @code{citation(\"Rcpp\")} for details on these last two.")
     (license license:gpl2+)))
 
+(define-public r-rcppde
+  (package
+    (name "r-rcppde")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "RcppDE" version))
+              (sha256
+               (base32
+                "1i9jj595nqpb16y22z2b8fcf0gq1fg0pbiisbd837p1cyw4nff69"))))
+    (properties `((upstream-name . "RcppDE")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-rcpp
+           r-rcpparmadillo))
+    (home-page "https://cran.r-project.org/package=RcppDE")
+    (synopsis "Global optimization by differential evolution in C++")
+    (description
+     "This package provides an iteration of the @code{DEoptim} function.  It
+performs global optimization by differential evolution.  The implementation
+employs the @code{Rcpp} package.  The last one provides tools for integration
+of R objects at the C++ level—and vice versa.  @code{R-rcppde} uses the @code{
+RcppArmadillo} package.  This one provides an interface from R to the Armadillo
+linear algebra package written in C++.")
+    (license license:gpl2+)))
+
 (define-public r-rcppml
   (package
     (name "r-rcppml")

base-commit: 81191e3410cc00c6438f532599dd0b96d521982f
-- 
2.38.1

[bug#59908] [PATCH 2/4] gnu: Add r-ptw.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-ptw): 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 016eeb4821..4561d50e02 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4858,6 +4858,32 @@ (define-public r-powerlaw
     ;; Any of these GPL versions.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-ptw
+  (package
+    (name "r-ptw")
+    (version "1.9-16")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ptw" version))
+              (sha256
+               (base32
+                "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy"))))
+    (properties `((upstream-name . "ptw")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcppde))
+    (home-page "https://github.com/rwehrens/ptw")
+    (synopsis "Parametric time warping")
+    (description
+     "Parametric time warping aligns patterns.  It aims to put corresponding
+features at the same locations.  The algorithm searches for an optimal polynomial
+describing the warping.  It is possible to align one sample to a reference, several
+samples to the same reference, or several samples to several references.  One can
+choose between calculating individual warpings, or one global warping for a set
+of samples and one reference.  Two optimization criteria are implemented: @acronym{
+RMS, Root Mean Square} error and @acronym{WCC, Weighted Cross Correlation}.  Both
+warping of peak profiles and of peak lists are supported.")
+    (license license:gpl2+)))
+
 (define-public r-compare
   (package
     (name "r-compare")
-- 
2.38.1

[bug#59908] [PATCH 3/4] gnu: Add r-pepsnmr.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c62c5970b8..740ec4b84b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8323,6 +8323,35 @@ (define-public r-perfmeas
 a given recall, F-score for single and multiple classes are available.")
     (license license:gpl2+)))
 
+(define-public r-pepsnmr
+  (package
+    (name "r-pepsnmr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "PepsNMR" version))
+              (sha256
+               (base32
+                "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5"))))
+    (properties `((upstream-name . "PepsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-gridextra
+           r-matrix
+           r-matrixstats
+           r-ptw
+           r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ManonMartin/PepsNMR")
+    (synopsis "Pre-process 1H-NMR FID signals")
+    (description
+     "This package provides R functions for common pre-processing steps that are
+applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data.  It also
+provides a function to read the @acronym{FID, free induction decay} signals
+directly in the Bruker format.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package.
 (define-public r-codedepends
   (package
-- 
2.38.1

[bug#59908] [PATCH 4/4] gnu: Add r-asics.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 740ec4b84b..64dbea97d0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2720,6 +2720,40 @@ (define-public r-asgsca
 model as latent variables.")
     (license license:gpl3)))
 
+(define-public r-asics
+  (package
+    (name "r-asics")
+    (version "2.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASICS" version))
+              (sha256
+               (base32
+                "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7"))))
+    (properties `((upstream-name . "ASICS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-ggplot2
+           r-glmnet
+           r-gridextra
+           r-matrix
+           r-mvtnorm
+           r-pepsnmr
+           r-plyr
+           r-quadprog
+           r-ropls
+           r-summarizedexperiment
+           r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASICS")
+    (synopsis "Automatic statistical identification in complex spectra")
+    (description
+     "@code{ASICS} quantifies concentration of metabolites in a complex spectrum.
+The identification of metabolites is performed by fitting a mixture model to the
+spectra of the library with a sparse penalty.")
+    (license license:gpl2+)))
+
 (define-public r-aspli
   (package
     (name "r-aspli")
-- 
2.38.1

bug#59908: [PATCH 1/4] gnu: Add r-rcppde.

[Ricardo Wurmus]

Thanks for the patches.  I applied them with negligible formatting
changes.

-- 
Ricardo