MadalinIonel.Patrascu@mdc-berlin.de wrote 2 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
e24e3bb057c945438fa5f5668efe7262@mdc-berlin.de
[PATCH] gnu: Add r-baseline, r-missforest, r-speaq and r-alpsnmr
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 1/4] gnu: Add r-baseline.
(address . 60877@debbugs.gnu.org)
20230117122538.41537-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-baseline): New variable.
---
gnu/packages/cran.scm | 27 ++++++++++++++++++++++++++-
1 file changed, 26 insertions(+), 1 deletion(-)
Toggle diff (49 lines)
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
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 2/4] gnu: Add r-missforest.
(address . 60877@debbugs.gnu.org)
20230117122538.41537-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-missforest): New variable.
---
gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
Toggle diff (43 lines)
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
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 3/4] gnu: Add r-speaq.
(address . 60877@debbugs.gnu.org)
20230117122538.41537-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-speaq): New variable.
---
gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++-
1 file changed, 41 insertions(+), 1 deletion(-)
Toggle diff (62 lines)
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
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 4/4] gnu: Add r-alpsnmr.
(address . 60877@debbugs.gnu.org)
20230117122538.41537-4-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-alpsnmr): New variable.
---
gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
Toggle diff (66 lines)
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
Ricardo Wurmus wrote 2 years ago
Re: [bug#60877] [PATCH 1/4] gnu: Add r-baseline.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 60877-done@debbugs.gnu.org)
87sfg3f0ow.fsf@elephly.net
Hi Mădălin,
Toggle quote (2 lines)
> * 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
Closed
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