R Observatory: Metrics for radEmu version 2.3.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

radEmu

2.3.2.0

Using Relative Abundance Data to Estimate of Multiplicative Differences in Mean Absolute Abundance

0packages depend

1.3Kdownloads / year

79.7%test coverage

13/13checks pass

Overview

About

Maintained by Amy D WillisFirst published 2026-03-262 releasesCRAN page ↗GitHub ↗

A differential abundance method for the analysis of microbiome data. 'radEmu' estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) doi:10.1093/biomet/asag009.

Install

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

install.packages("radEmu", 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("statdivlab/radEmu")

Development version from statdivlab/radEmu. 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-rademu

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-radEmu

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-radEmu

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

Health

CRAN checks

13OK

Slowest check: 14.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.10

79.7%

Coverage · measured lines

100%

Documentation · exports

5

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-04
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-27
6 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 827 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 23%

Downloads

1.3K

CRAN downloads in the past year

Rank #19,315 · ~4/day · ~109/mo

Releases R versions

Daily download trend is not available in this view yet.

13830 days

58490 days

1.3K1 year

Compare downloads with other packages →

Also on45 r2u22 autocran

Repository

GitHub ↗ statdivlab/rademu

66Stars

10Forks

9Open issues

0Open PRs

2Releases

473Commits

8Contributors

statisticsdamicrobiomemetagenomics

473 commits · Last activity 2026-04-14 · 0% stars, 30d

Stars over time

2025-07-03 · 552026-07-07 · 66

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/statdivlab/rademu on 2026-08-23.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (6)

R >= 2.10MASSMatrixmethodsmagrittr rlang

Imports (0)

none

LinkingTo (0)

none

Suggests (12)

testthat numDeriv phyloseq TreeSummarizedExperiment SummarizedExperiment SingleCellExperiment knitr dplyr ggplot2 stringrparallelrmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Amy D Willis

Author, Maintainer

Authors (3)

Amy D Willis

Author, Maintainer

David Clausen

Author

Sarah Teichman

Author

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
2.3.2.0Latest
2026-04-03 · current release · diff ↗
2.3.1.0
2026-03-26
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-26
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 747 KB / 6 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("radEmu")

Format

Willis, A. D., Clausen, D., & Teichman, S. (2026). radEmu: Using Relative Abundance Data to Estimate of Multiplicative Differences in Mean Absolute Abundance (Version 2.3.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.radEmu

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 radEmu version 2.3.2.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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