R Observatory: Metrics for metadeconfoundR version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metadeconfoundR

1.0.5

Covariate-Sensitive Analysis of Cross-Sectional High-Dimensional Data

0packages depend

4.8Kdownloads / year

97.6%test coverage

13/13checks pass

Overview

About

Maintained by Till BirknerFirst published 2024-06-252 releasesCRAN page ↗GitHub ↗

Using non-parametric tests, naive associations between omics features and metadata in cross-sectional data-sets are detected. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests, as first described in Forslund, Chakaroun, Zimmermann-Kogadeeva, et al. (2021) doi:10.1038/s41586-021-04177-9. The generated output can be graphically summarized using the built-in plotting function.

Install

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

install.packages("metadeconfoundR", 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("TillBirkner/metadeconfoundR")

Development version from TillBirkner/metadeconfoundR. 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-metadeconfoundr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-metadeconfoundR

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-metadeconfoundR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 10.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.40

97.6%

Coverage · measured lines

100%

Documentation · exports

19

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 196 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.8K

CRAN downloads in the past year

Rank #15,385 · ~13/day · ~402/mo

Releases R versions

Daily download trend is not available in this view yet.

16030 days

68090 days

4.8K1 year

Compare downloads with other packages →

Also on120 r2u17 autocran

Repository

GitHub ↗ tillbirkner/metadeconfoundr

21Stars

6Forks

0Open issues

0Open PRs

2Releases

212Commits

7Contributors

212 commits · Last activity 2026-07-23 · +5% stars, 30d

Stars over time

2025-08-04 · 202026-07-25 · 21

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/tillbirkner/metadeconfoundr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

Show all practices

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0detectseparation

Imports (18)

lmtest foreachparalleldoParallelstatslogger lme4 ggplot2 reshape2methodsrlang circlize dplyr ggraph igraph magrittr scales stringr

LinkingTo (0)

none

Suggests (6)

pander knitr gridExtra kableExtra testthat covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Till Birkner

Author, Maintainer

Authors (1)

Till Birkner

Author, Maintainer

Contributors (1)

Sofia Kirke Forslund-Startceva

Contributor

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.5Latest
2026-02-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2024-06-25
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-25
Total releases: 2 / 2 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 63 KB / 2 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metadeconfoundR")

Format

Birkner, T., & Forslund-Startceva, S. K. (2026). metadeconfoundR: Covariate-Sensitive Analysis of Cross-Sectional High-Dimensional Data (Version 1.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.metadeconfoundR

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 metadeconfoundR version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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