R Observatory: Metrics for MicrobiomeStat version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MicrobiomeStat

1.4Package record

Statistical Methods for Microbiome Compositional Data

0packages dependsuggested by 1

14.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jun ChenCRAN 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. 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-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). 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: 4.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 38%3 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 78%

How these are measured

Downloads

14.4K

CRAN downloads in the past year

Rank #3,387 · ~39/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

3.2K90 days

14.4K1 year

Compare downloads with other packages →

Also on570 r2u7 autocran1.8K conda_forge

How downloads are counted

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing MicrobiomeStat adds 77 packages (41 with compiled code, 54 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, lme4 4.1 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

ggpicrust2

How these are counted

Code & Tests

Datasets

People & History

People (4)

Jun Chen

Author, Maintainer since 1.0 (2021)

Xianyang Zhang

Author

Linsui Deng

Contributor · added in 1.3

Huijuan Zhou

Contributor

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4Latest
record
2026-03-03 · current release · diff ↗
1.3
record
2026-01-09 · diff ↗ ·
added 5 exports
cscca, cscca.CV, DGP_OC, bmdd, bmdd.nlopt
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2
record
2024-04-02 · diff ↗ ·
added 1 export
linda.wald.test
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1
record
2022-01-24 · diff ↗
1.0
record
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

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 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 MicrobiomeStat version 1.4 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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