R Observatory: Metrics for metabodeconplus version 0.22.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metabodeconplus

0.22.0Package record

Deconvolution, Alignment and Model Fitting of 1d NMR Spectra

0packages depend

751downloads / year

40.5%test coverage

13/13flavors OK

Overview

About

Maintained by Tobias SchmidtCRAN page ↗GitHub ↗Website ↗Issues ↗

An integrated framework for deconvolution, alignment and postprocessing of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, extended with end-to-end model fitting that turns the resulting matrix of aligned signal integrals into classification models. The deconvolution part uses the algorithm described in Koh et al. (2009) doi:10.1016/j.jmr.2009.09.003. The alignment part is based on functions from the 'speaq' package, described in Beirnaert et al. (2018) doi:10.1371/journal.pcbi.1006018 and Vu et al. (2011) doi:10.1186/1471-2105-12-405. A detailed description and evaluation of an early version of the package can be found in Haeckl et al. (2021) doi:10.3390/metabo11070452. 'metabodeconplus' is the actively developed successor to the 'metabodecon' package and introduces backwards-incompatible API changes.

Changes in 0.22.4

Added a citation entry: citation("metabodeconplus") now returns Schmidt et al. (2026), Metabolites 16(9):604, <doi:10.3390/metabo16090604>, and Haeckl et al. (2021) for the original algorithm.
The package description, README and Model Fitting article now reference Schmidt et al. (2026).
README now presents CRAN as the stable source and GitHub as the development version, and links the Model Fitting and Datasets articles.
Documentation fixes: titles and vignettes now say metabodeconplus instead of Metabodecon, and the Contributing article describes how to run the tests, install the package and prepare a release.
CI: bumped GitHub Actions versions and allowed manual runs of R-CMD-check.
Fixed the internal test helper run_tests(), which aborted because it tried to mock the no longer existing function assert().

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("metabodeconplus", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("spang-lab/metabodeconplus")

Development version from spang-lab/metabodeconplus. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-metabodeconplus

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-metabodeconplus

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-metabodeconplus

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.0 min · r-devel-windows-x86_64

Status changes

OK13 OKNow
OK8 OK2026-08-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.22.4

Release 0.22.0 has not been analysed yet.

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.22.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 38 (1 internal)includes a package overview page
Examples that run: 100%33 run in a plain check (1 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 91%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

751

CRAN downloads in the past year

Rank #16,984 · ~2/day · ~63/mo

Releases R versions

Daily download trend is not available in this view yet.

24230 days

75190 days

7511 year

Compare downloads with other packages →

Also on31 r2u6 autocran

How downloads are counted

Repository

spang-lab/metabodeconplus ↗Organization: spang-lab

1Stars

0Forks

0Open issues

0Open PRs

4Releases

19Commits

1Commit identities

License file reads as GPL-3.0 · 19 commits · Last activity 2026-10-05 · 0% stars, 30d · Default branch at 0.22.4, ahead of CRAN 0.22.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2026-08-10 · 02026-09-08 · 1

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/spang-lab/metabodeconplus on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-05 · The repository has a site deploy workflow

pkgdown site last built 2026-10-05

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (2)

data-raw/Dockerfile

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

lintr

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-07-09
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: CLAUDE.md

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

38 external dependencies (excludes base and recommended)

Installing metabodeconplus adds 15 packages (9 with compiled code, 22 MB of source tarballs). Heaviest: stringi 11 MB, mathjaxr 3.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (5)

mathjaxr ranger readJDX toscutil withr

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Tobias Schmidt

Wolfram Gronwald

Author, Copyright holder

Martina Haeckl

Author, Copyright holder

Yanren Linda Hu

Contributor

Releases (2)

Pick two releases to compare their code metrics.

0.22.4Latest
record
2026-10-24 · current release · diff ↗
0.22.0
record
2026-08-09
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-08-09
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Additional repositories: spang-lab.r-universe.dev
Minimum R: ≥ 3.5.0
Bundled data: 3.1 MB / 3 files
Download size: 5.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metabodeconplus")

Format

Schmidt, T., Gronwald, W., Haeckl, M., & Hu, Y. L. (2026). metabodeconplus: Deconvolution, Alignment and Model Fitting of 1d NMR Spectra (Version 0.22.0) [Computer software]. https://doi.org/10.32614/CRAN.package.metabodeconplus

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for metabodeconplus version 0.22.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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