causalBatch

1.3.0

Causal Batch Effects

0packages depend

2.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Eric W. BridgefordFirst published 2024-01-244 releasesCRAN page ↗GitHub ↗

Software which provides numerous functionalities for detecting and removing group-level effects from high-dimensional scientific data which, when combined with additional assumptions, allow for causal conclusions, as-described in our manuscripts Bridgeford et al. (2024) doi:10.1101/2021.09.03.458920 and Bridgeford et al. (2023) doi:10.48550/arXiv.2307.13868. Also provides a number of useful utilities for generating simulations and balancing covariates across multiple groups/batches of data via matching and propensity trimming for more than two groups.

Install

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

install.packages("causalBatch", 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("neurodata/causal_batch")

Development version from neurodata/causal_batch. 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-causalbatch

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

Health

CRAN checks

13OK

Slowest check: 10.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.30

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 10 earlier snapshots

ERROR2026-06-16
12 OK · 0 NOTE · 0 WARNING · 1 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
OK2026-05-01
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-28
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-21
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-16
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 82%

Downloads

2.7K

CRAN downloads in the past year

Rank #14,876 · ~7/day · ~221/mo

Releases R versions

Daily download trend is not available in this view yet.

27030 days

71390 days

2.7K1 year

Compare downloads with other packages →

Also on128 r2u

Repository

GitHub ↗ neurodata/causal_batch

4Stars

0Forks

0Open issues

0Open PRs

0Releases

137Commits

2Contributors

License GPL-3.0 · 137 commits · Last activity 2025-03-13

Stars over time

2025-01-13 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/neurodata/causal_batch on 2026-07-30.

Reproducibility and dev environment (1)

Dockerfile

Lint, format, editor (1)

RStudio project

Git structural (1)

Submodules

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (9)

cdcsis sva MatchItnnetdplyr magrittr genefilter BiocParallelutils

LinkingTo (0)

none

Suggests (10)

tidyr ggpubr knitr rmarkdownparalleltestthat (>= 3.0.0)covr roxygen2 ks ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Eric W. Bridgeford

Author, Maintainer

Authors (1)

Eric W. Bridgeford

Author, Maintainer

Contributors (3)

Brian Caffo

Contributor

Michael Powell

Contributor

Joshua T. Vogelstein

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.0Latest
2025-01-07 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2024-03-01 · diff ↗
1.1
2024-02-13 · diff ↗
1.0
2024-01-24
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-24
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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