R Observatory: Metrics for radEmu version 2.3.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

radEmu

2.3.2.0Package record

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

0packages depend

1.8Kdownloads / year

79.7%test coverage

13/13flavors OK

Overview

About

Maintained by Amy D WillisCRAN page ↗GitHub ↗Website ↗

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. 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-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). 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: 14.3 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 1 NOTE2026-04-04
ERROR6 OK, 1 NOTE, 1 ERROR2026-03-27

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.2.0

READMEYes · 827 wordsVignettesYes · 7 · dynamicNEWSYes · 100% structured · does not mention 2.3.2.0Citation fileNoWebsiteYes · pkgdown

Help pages: 26 (1 internal)includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 23%

Vignettes (7)

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #20,169 · ~5/day · ~153/mo

Releases R versions

Daily download trend is not available in this view yet.

27030 days

66190 days

1.8K1 year

Compare downloads with other packages →

Also on53 r2u7 autocran

How downloads are counted

Repository

statdivlab/rademu ↗Organization: statdivlab

67Stars

10Forks

10Open issues

0Open PRs

2Releases

478Commits

8Commit identities

statisticsdamicrobiomemetagenomics

478 commits · Last activity 2026-10-12 · +1.5% stars, 30d · Default branch at 2.4.0.0, ahead of CRAN 2.3.2.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 19
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-17 · 572026-10-19 · 67

How these are measured

PracticesBeta

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

Checks run against github.com/statdivlab/rademu on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on macOS and Windows

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-12 · The repository has a site deploy workflow

pkgdown site last built 2026-10-12

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-09-30
Commits: at least 1 crediting it in the message

Models named in its commits

Claude Opus 5.51 commit · Sep 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing radEmu adds 2 packages (2 with compiled code, 1.0 MB of source tarballs). Heaviest: rlang 766 KB, magrittr 275 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Amy D Willis

Author, Maintainer since 2.3.1.0 (2026)

David Clausen

Author

Sarah Teichman

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.3.2.0Latest
record
2026-04-03 · current release · diff ↗
2.3.1.0
record
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

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 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 radEmu version 2.3.2.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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