[bug#60877] [PATCH] gnu: Add r-baseline, r-missforest, r-speaq and r-alpsnmr

[bug#60877] [PATCH] gnu: Add r-baseline, r-missforest, r-speaq and r-alpsnmr

[MadalinIonel.Patrascu]

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[bug#60877] [PATCH 1/4] gnu: Add r-baseline.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-baseline): New variable.
---
 gnu/packages/cran.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3fcbd3b9f6..53f3ebbcf5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
-;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -9241,6 +9241,31 @@ (define-public r-base64url
 systems.")
     (license license:gpl3)))
 
+(define-public r-baseline
+  (package
+    (name "r-baseline")
+    (version "1.3-4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "baseline" version))
+              (sha256
+               (base32
+                "1kl68zvyi2zd73jy3axrvrymwn4y6l4pd62nz0fciwbgkjhz3yyx"))))
+    (properties `((upstream-name . "baseline")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-limsolve r-sparsem))
+    (home-page "https://github.com/khliland/baseline/")
+    (synopsis "Baseline correction of spectra")
+    (description
+     "This package is a collection of baseline correction algorithms.  Beside
+those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline
+algorithm parameters.  Typical use is the removal of the background effects from
+spectra, which are originating from various types of spectroscopy and spectrometry.
+Also, there is a possibility of optimizing this with regard to regression or
+classification results.  Correction methods include polynomial fitting, weighted
+local smoothers and many more.")
+    (license license:gpl2)))
+
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")

base-commit: 789d73234d5b6bbd83bb054146d5bbd1d374d51a
-- 
2.38.1

[bug#60877] [PATCH 2/4] gnu: Add r-missforest.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-missforest): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 53f3ebbcf5..6ae5b96eb2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15227,6 +15227,36 @@ (define-public r-misc3d
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
 
+(define-public r-missforest
+  (package
+    (name "r-missforest")
+    (version "1.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "missForest" version))
+              (sha256
+               (base32
+                "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21"))))
+    (properties `((upstream-name . "missForest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dorng
+           r-foreach
+           r-iterators
+           r-itertools
+           r-randomforest))
+    (home-page "https://github.com/stekhoven/missForest")
+    (synopsis "Nonparametric missing value imputation using Random Forest")
+    (description
+     "The function @code{missForest} in this package is used to impute missing
+values, particularly in the case of mixed-type data.  It uses a random forest
+trained on the observed values of a data matrix to predict the missing values.
+It can be used to impute continuous and/or categorical data, including complex
+interactions and non-linear relations.  It yields an @acronym{OOB, out-of-bag}
+imputation error estimate without the need of a test set or elaborate cross-
+validation.  It can be run in parallel to save computation time.")
+    (license license:gpl2+)))
+
 (define-public r-ks
   (package
     (name "r-ks")
-- 
2.38.1

[bug#60877] [PATCH 3/4] gnu: Add r-speaq.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-speaq): New variable.
---
 gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c2fa26cb59..7498c3a767 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
@@ -7624,6 +7624,46 @@ (define-public r-slingshot
 graph construction.")
    (license license:artistic2.0)))
 
+;; This is a CRAN package but it depends on a bionconductor package.
+(define-public r-speaq
+  (package
+    (name "r-speaq")
+    (version "2.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "speaq" version))
+              (sha256
+               (base32
+                "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk"))))
+    (properties `((upstream-name . "speaq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cluster
+           r-data-table
+           r-dosnow
+           r-foreach
+           r-ggplot2
+           r-gridextra
+           r-impute
+           r-massspecwavelet
+           r-missforest
+           r-reshape2
+           r-rfast
+           r-rvest
+           r-xml2))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=speaq")
+    (synopsis "Tools for nuclear magnetic resonance spectra alignment")
+    (description
+     "This package helps with @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy
+data analysis as easy as possible.  It only requires a small set of functions to
+perform an entire analysis.  Speaq offers the possibility of raw spectra alignment
+and quantitation but also an analysis based on features whereby the spectra are
+converted to peaks which are then grouped and turned into features.  These features
+can be processed with any number of statistical tools either included in speaq
+or available elsewhere on CRAN.")
+    (license license:asl2.0)))
+
 (define-public r-stager
   (package
     (name "r-stager")
-- 
2.38.1

[bug#60877] [PATCH 4/4] gnu: Add r-alpsnmr.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-alpsnmr): New variable.
---
 gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7498c3a767..118f218f4b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2598,6 +2598,59 @@ (define-public r-alpine
 data.")
     (license license:gpl2+)))
 
+(define-public r-alpsnmr
+  (package
+    (name "r-alpsnmr")
+    (version "4.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AlpsNMR" version))
+              (sha256
+               (base32
+                "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl"))))
+    (properties `((upstream-name . "AlpsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-baseline
+           r-biocparallel
+           r-dplyr
+           r-fs
+           r-future
+           r-generics
+           r-ggplot2
+           r-glue
+           r-htmltools
+           r-magrittr
+           r-matrixstats
+           r-mixomics
+           r-pcapp
+           r-purrr
+           r-readxl
+           r-reshape2
+           r-rlang
+           r-rmarkdown
+           r-scales
+           r-signal
+           r-speaq
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-vctrs))
+    (native-inputs (list r-knitr))
+    (home-page "https://sipss.github.io/AlpsNMR/")
+    (synopsis "Automated spectral processing system for NMR")
+    (description
+     "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data
+directories both zipped and unzipped.  It provides automated and efficient signal
+processing for untargeted NMR metabolomics.  It is able to interpolate the samples,
+detect outliers, exclude regions, normalize, detect peaks, align the spectra,
+integrate peaks, manage metadata and visualize the spectra.  After spectra
+proccessing, it can apply multivariate analysis on extracted data.  Efficient
+plotting with 1-D data is also available.  Basic reading of 1D ACD/Labs exported
+JDX samples is also available.")
+    (license license:expat)))
+
 (define-public r-altcdfenvs
   (package
     (name "r-altcdfenvs")
-- 
2.38.1

bug#60877: [PATCH 1/4] gnu: Add r-baseline.

[Ricardo Wurmus]

Hi Mădălin,

> * gnu/packages/cran.scm (r-baseline): New variable.

Thanks for the patches.

The r-baseline package actually needs an additional input for the GUI.
I packaged gWidgets2tcltk and added it as an input.  (The GTK variant
has been archived on CRAN because RGtk has been abandoned.)

I fixed a typo in a description and pushed.  Thanks!

-- 
Ricardo