R Observatory: Metrics for ZIBR version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ZIBR

1.0.3

A Zero-Inflated Beta Random Effect Model

0packages depend

2.6Kdownloads / year

95.5%test coverage

8/13checks pass

Overview

About

Maintained by Charlie BushmanFirst published 2023-10-172 releasesCRAN page ↗GitHub ↗

A two-part zero-inflated Beta regression model with random effects (ZIBR) for testing the association between microbial abundance and clinical covariates for longitudinal microbiome data. Eric Z. Chen and Hongzhe Li (2016) doi:10.1093/bioinformatics/btw308.

Install

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

install.packages("ZIBR", 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("PennChopMicrobiomeProgram/ZIBR")

Development version from PennChopMicrobiomeProgram/ZIBR. 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-zibr

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-ZIBR

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-ZIBR

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 6.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.24

95.5%

Coverage · measured lines

100%

Documentation · exports

1

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 629 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 100%
References docs: 13%

Downloads

2.6K

CRAN downloads in the past year

Rank #19,575 · ~7/day · ~220/mo

Releases R versions

Daily download trend is not available in this view yet.

12030 days

56090 days

2.6K1 year

Compare downloads with other packages →

Also on117 r2u15 autocran

Repository

GitHub ↗ pennchopmicrobiomeprogram/zibr

30Stars

10Forks

0Open issues

0Open PRs

3Releases

141Commits

6Contributors

141 commits · Last activity 2026-03-06 · -3.2% stars, 30d

Stars over time

2025-08-13 · 312026-08-17 · 30

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/pennchopmicrobiomeprogram/zibr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

lintrRStudio project

Show all practices

Coverage (1)

Codecov

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: copilot on 2026-02-04

copilot

Most recent: copilot on 2026-02-04

Evidence

copilot: on 2026-02-04 · evidence A, PR · sole bot-author seen

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.10statmod

Imports (0)

none

LinkingTo (0)

none

Suggests (8)

betareg dplyr lme4nlmeknitr rmarkdown testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Charlie Bushman

Maintainer

Authors (1)

Eric Zhang Chen

Author, Copyright holder

Copyright holders (1)

Eric Zhang Chen

Author, Copyright holder

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
1.0.3Latest
2026-02-05 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.2
2023-10-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-17
Total releases: 2 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 2.8 KB / 1 file
Download size: 602 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ZIBR")

Format

Bushman, C., & Zhang Chen, E. (2026). ZIBR: A Zero-Inflated Beta Random Effect Model (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.ZIBR

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 ZIBR version 1.0.3 [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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