R Observatory: Metrics for LOCOM2 version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LOCOM2

1.0

A Logistic Regression Model for Testing Microbial Differential Abundance

0packages depend

734downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yi-Juan HuFirst published 2026-05-041 releasesCRAN page ↗GitHub ↗

Testing differential abundance at individual taxa and in a whole microbial community. The tests are based on the log-ratio of relative abundances. The tests accommodate continuous, discrete (binary, categorical), and multivariate traits, and allow adjustment of confounders. For more details see He (2026) doi:10.64898/2026.04.07.716976.

Install

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

install.packages("LOCOM2", 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("yijuanhu/LOCOM2")

Development version from yijuanhu/LOCOM2. 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-locom2

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: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

not tracked

Coverage

100%

Documentation · exports

8

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-05
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 200 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 75%

Downloads

734

CRAN downloads in the past year

Rank #18,495 · ~2/day · ~61/mo

Releases R versions

Daily download trend is not available in this view yet.

20030 days

59390 days

7341 year

Compare downloads with other packages →

Also on96 r2u

Repository

GitHub ↗ yijuanhu/locom2

2Stars

0Forks

0Open issues

0Open PRs

0Releases

1Commits

1Contributors

1 commits · Last activity 2026-04-26 · 0% stars, 30d

Stars over time

2026-05-12 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

Checks run against github.com/yijuanhu/locom2 on 2026-08-09.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (8)

RcppstatspermuteparallelBiocParallel matrixStats abind car

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

testthatsurvival

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Yi-Juan Hu

Author, Maintainer

Authors (1)

Yi-Juan Hu

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

1.0Latest
2026-05-04 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-04
Total releases: 1 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 34 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LOCOM2")

Format

Hu, Y. (2026). LOCOM2: A Logistic Regression Model for Testing Microbial Differential Abundance (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.LOCOM2

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 LOCOM2 version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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