R Observatory: Metrics for BRCore version 2.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BRCore

2.0.7Package record

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

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Bolívar Aponte RolónCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Center for Advanced Bioenergy and Bioproducts Innovation and Great Lakes Bioenergy Research Center

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.

Changes in 2.0.7

2026-05-19

a43bc71 Typo and instructions fixes to README and DESCRIPTION files.

From NEWS.md in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 11.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-19

Show 1 earlier changeHide 1 earlier change

ERROR5 OK, 2 ERROR2026-05-06

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.7

READMEYes · 220 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 2.0.7Citation fileNoWebsiteYes · pkgdown

Help pages: 19 (2 internal)
Examples that run: 92%11 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 92%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 42%

Vignettes (1)

Introduction to BRCore

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #4,084 · ~9/day · ~284/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

2.2K90 days

3.4K1 year

Compare downloads with other packages →

Also on64 r2u

How downloads are counted

Repository

germs-lab/brcore ↗Organization: germs-lab

1Stars

2Forks

5Open issues

0Open PRs

10Releases

512Commits

5Commit identities

512 commits · Last activity 2026-05-20 · 0% stars, 30d · Default branch at 2.0.7.9000, ahead of CRAN 2.0.7 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 84%
Median days to close, 50 most recently updated closed issues: 24
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2026-06-29 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/germs-lab/brcore on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (3)

Code of conductContributing guideIssue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-20 · The repository has a site deploy workflow

pkgdown site last built 2026-05-20

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (4)

Lint workflowAirVS CodeRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-12-22
Pull request: opened by its own account
Commits: 11 by its own account · at least 3 crediting it in the message

Review tools

Copilot code review
Commits: at least 9 accepting its review suggestions

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing BRCore adds 98 packages (50 with compiled code, 90 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (8)

Bolívar Aponte Rolón

Author, Maintainer since 2.0.4 (2026)

Gian Maria Niccolò Benucci

Author

Co-maintainer

Author

Author

Author

Author

Center for Advanced Bioenergy and Bioproducts Innovation

Copyright holder, Funder

Great Lakes Bioenergy Research Center

Copyright holder, Funder

Releases (3)

Pick two releases to compare their code metrics.

2.0.7Latest
record
2026-05-20 · current release · diff ↗
2.0.5
record
2026-05-19 · diff ↗
2.0.4
record
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

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 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 BRCore version 2.0.7 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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