R Observatory: Metrics for metadeconfoundR version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metadeconfoundR

1.0.5Package record

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

0packages depend

4.2Kdownloads / year

97.6%test coverage

13/13flavors OK

Overview

About

Maintained by Till BirknerCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.0.5

"confounded confounders" will now be removed from the status label of a confounded variable.
Example: If the association of D with feature Y is confounded by C1 and C2, but the association of C1 with Y is in turn confounded by C2, then only C2 will be listed as confounder of Y~D
improvments in some logging messages
featureMat is now checked for non-numeric columns at start-up.

From NEWS in the release

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. 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-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). 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: 10.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5

READMEYes · 196 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.5Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to metadeconfoundR

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #16,923 · ~11/day · ~346/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

74890 days

4.2K1 year

Compare downloads with other packages →

Also on98 r2u6 autocran

How downloads are counted

Repository

tillbirkner/metadeconfoundr ↗Account: TillBirkner

22Stars

6Forks

0Open issues

0Open PRs

2Releases

212Commits

7Commit identities

212 commits · Last activity 2026-07-23 · +4.8% stars, 30d · Default branch at 1.0.7, ahead of CRAN 1.0.5 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 189
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-04 · 202026-10-20 · 22

How these are measured

PracticesBeta

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

Checks run against github.com/tillbirkner/metadeconfoundr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Issue templates

Coverage (1)

Coverage reporting

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing metadeconfoundR adds 83 packages (47 with compiled code, 69 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Till Birkner

Author, Maintainer since 1.0.2 (2024)

Sofia Kirke Forslund-Startceva

Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.5Latest
record
2026-02-04 · current release · diff ↗ ·
added 2 exports
BuildConfounderMap, GetPartialEfSizes
R
R 4.5.0 released · 2025-04-11
1.0.2
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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