R Observatory: Metrics for BRCore version 2.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BRCore

2.0.7

A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers

0packages depend

1.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Bolívar Aponte RolónFirst published 2026-05-053 releasesCRAN page ↗GitHub ↗

A unified framework for identification and ecological interpretation of core microbiomes across time and space, enhancing robustness and reproducibility in microbiome data analysis. 'BRCore' implements the workflow proposed by Shade and Stopnisek (2019) and incorporates additional rarefaction steps. The proposed workflow aims to identify persistent microbiomes using abundance-occupancy distributions and neutral community model fitting. For more details on abundance-occupancy distributions see Shade A, Stopnisek N (2019) doi:10.1016/j.mib.2019.09.008, for neutral models, see Sloan et al. (2006) doi:10.1111/j.1462-2920.2005.00956.x and Burns et al. (2015) doi:10.1038/ismej.2015.142.

Install

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

install.packages("BRCore", 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("germs-lab/BRCore")

Development version from germs-lab/BRCore. 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-brcore

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: 14.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.55

not tracked

Coverage

92%

Documentation · exports

15

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
OK2026-05-19
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-05-06
5 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMEYes · 220 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 100%
Return-value docs: 100%
References docs: 42%

Downloads

1.4K

CRAN downloads in the past year

Rank #7,791 · ~4/day · ~114/mo

Releases R versions

Daily download trend is not available in this view yet.

24330 days

1.1K90 days

1.4K1 year

Compare downloads with other packages →

Also on40 r2u

Repository

GitHub ↗ germs-lab/brcore

1Stars

1Forks

5Open issues

0Open PRs

10Releases

512Commits

5Contributors

512 commits · Last activity 2026-05-20 · 0% stars, 30d

Stars over time

2026-06-29 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/germs-lab/brcore on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (3)

AirVS CodeRStudio project

Show all practices

Coverage (1)

Codecov

Governance and community (1)

Issue templates

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 2025-12-22

copilot

Most recent: copilot on 2025-12-22

Evidence

copilot: on 2025-12-22 · evidence A, PR · sole bot-author seen

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4

Imports (15)

cli dplyr ggplot2 ggpubr ggrepel Hmisc magrittr (>= 2.0.4)minpack.lm phyloseq rlang scalesstats4tibble tidyr vegan

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat tidyverse viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Bolívar Aponte Rolón

Author, Maintainer

Authors (6)

Bolívar Aponte Rolón

Author, Maintainer

Gian Maria Niccolò Benucci

Author

Author

Author

Author

Author

Copyright holders (2)

Center for Advanced Bioenergy and Bioproducts Innovation

Copyright holder, Funder

Great Lakes Bioenergy Research Center

Copyright holder, Funder

Funders (2)

Center for Advanced Bioenergy and Bioproducts Innovation

Copyright holder, Funder

Great Lakes Bioenergy Research Center

Copyright holder, Funder

Package Timeline

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

2.0.7Latest
2026-05-20 · current release · diff ↗
2.0.5
2026-05-19 · diff ↗
2.0.4
2026-05-05
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-05
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.4
Bundled data: 882 KB / 5 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BRCore")

Format

Aponte Rolón, B., Center for Advanced Bioenergy and Bioproducts Innovation, Great Lakes Bioenergy Research Center, Benucci, G. M. N., Howe, A., Kristy, B., Shade, A., & Stopnisek, N. (2026). BRCore: A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers (Version 2.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.BRCore

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 BRCore version 2.0.7 [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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