R Observatory: Metrics for batchtma version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

batchtma

0.2.0Package record

Batch Effect Adjustments

0packages depend

3.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Konrad StopsackCRAN page ↗GitHub ↗Website ↗

Different adjustment methods for batch effects in biomarker data, such as from tissue microarrays. Some methods attempt to retain differences between batches that may be due to between-batch differences in "biological" factors that influence biomarker values.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("batchtma", 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("stopsack/batchtma")

Development version from stopsack/batchtma. 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-batchtma

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.7 min · r-oldrel-macos-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 0.2.0

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWS· In the repository, left out of the releaseCitation fileNoWebsiteYes · pkgdown

Help pages: 4includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 75%

Vignettes (1)

Get Started: Methods to address batch effects HTML

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #8,972 · ~11/day · ~326/mo

Releases R versions

Daily download trend is not available in this view yet.

40130 days

1.1K90 days

3.9K1 year

Compare downloads with other packages →

Also on122 r2u

How downloads are counted

Repository

stopsack/batchtma ↗Account: stopsack

1Stars

2Forks

0Open issues

0Open PRs

2Releases

114Commits

5Commit identities

batch-effectstissue-microarray-analysismeasurement-error

License file reads as GPL-3.0 · 114 commits · Last activity 2026-02-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 25
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-08-03 · 12026-07-07 · 1

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/stopsack/batchtma on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-23 · The repository has a site deploy workflow

pkgdown site last built 2026-02-23

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing batchtma adds 35 packages (19 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (12)

broom dplyr geepack ggplot2 limmannetpurrr quantreg rlang stringr tibble tidyr

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Konrad Stopsack

Author, Maintainer since 0.1.6 (2021)

Travis Gerke

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
record
2026-02-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.6
record
2021-12-06
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-06
Total releases: 2 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 696 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("batchtma")

Format

Stopsack, K., & Gerke, T. (2026). batchtma: Batch Effect Adjustments (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.batchtma

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 batchtma version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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