R Observatory: Metrics for MicrobiomeStat version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MicrobiomeStat

1.4

Statistical Methods for Microbiome Compositional Data

1packages depend

13.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jun ChenFirst published 2021-11-195 releasesCRAN page ↗

A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects. Includes the LinDA method for differential abundance analysis (Zhou et al. (2022)doi:10.1186/s13059-022-02655-5), the BMDD (Bimodal Dirichlet Distribution) method for accurate modeling and imputation of zero-inflated microbiome sequencing data (Zhou et al. (2025)doi:10.1371/journal.pcbi.1013124) and compositional sparse CCA methods for microbiome multi-omics data integration (Deng et al. (2024) <doi: 10.3389/fgene.2024.1489694>).

Install

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

install.packages("MicrobiomeStat", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-microbiomestat

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-MicrobiomeStat

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-MicrobiomeStat

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

Health

CRAN checks

13OK

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

18

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 38%
Documented parameters: 100%
Return-value docs: 100%
References docs: 78%

Downloads

13.9K

CRAN downloads in the past year

Rank #3,330 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.2K90 days

13.9K1 year

Compare downloads with other packages →

Also on464 r2u18 autocran1.7K conda_forge

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (18)

ggplot2 matrixStatsparallelstatsutilsMatrixstatmodMASSggrepel lmerTest foreach modeest dplyr Rcpp mlr3 mlr3mbo bbotk paradox

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

DiceKriging randomForest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

ggpicrust2

Code & Tests

People & History

People (4)

Maintainer (1)

Jun Chen

Author, Maintainer

Authors (2)

Jun Chen

Author, Maintainer

Xianyang Zhang

Author

Contributors (2)

Linsui Deng

Contributor · added in 1.3

Huijuan Zhou

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.4Latest
2026-03-03 · current release · diff ↗
1.3
2026-01-09 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2
2024-04-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1
2022-01-24 · diff ↗
1.0
2021-11-19
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-19
Total releases: 5 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 106 KB / 1 file
Download size: 150 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Compositional Data Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MicrobiomeStat")

Format

Chen, J., Deng, L., Zhang, X., & Zhou, H. (2026). MicrobiomeStat: Statistical Methods for Microbiome Compositional Data (Version 1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.MicrobiomeStat

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 MicrobiomeStat version 1.4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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