R Observatory: Metrics for breakaway version 4.8.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

breakaway

4.8.4Package record

Species Richness Estimation and Modeling

0packages depend

7.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Amy D WillisCRAN page ↗GitHub ↗Website ↗Issues ↗

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) doi:10.1111/biom.12332, Willis et al. (2017) doi:10.1111/rssc.12206, and Willis (2016) arXiv:1604.02598, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) doi:10.1214/10-BA527.

Install

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

install.packages("breakaway", 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("adw96/breakaway")

Development version from adw96/breakaway. 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-breakaway

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Amy D Willis <adwillis@uw.edu>’

The Description field contains
  <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

CRAN check page ↗

Slowest check: 13.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-08-20
ERROR11 OK, 1 NOTE, 1 ERROR2026-08-18
NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-16

Show 3 earlier changesHide 3 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-03-13
NOTE12 OK, 2 NOTE2026-03-12
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.8.4

READMEYes · 385 wordsVignettesYes · 6 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 59 (1 internal)
Examples that run: 95%19 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 42%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 24%

Vignettes (6)

How these are measured

Downloads

7.1K

CRAN downloads in the past year

Rank #5,367 · ~20/day · ~594/mo

Releases R versions

Daily download trend is not available in this view yet.

54030 days

1.5K90 days

7.1K1 year

Compare downloads with other packages →

Also on186 r2u397 conda_forge365 bioconda

How downloads are counted

Repository

adw96/breakaway ↗Account: adw96

69Stars

19Forks

5Open issues

0Open PRs

0Releases

424Commits

16Commit identities

424 commits · Last activity 2026-06-25 · +1.5% stars, 30d · Default branch at 5.0.1, ahead of CRAN 4.8.4 (checked 2026-10-18) · Discussions: 9 posts

Responsiveness

How these are sampled

PRs merged (all time): 70%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-08-26 · 672026-09-23 · 69

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/adw96/breakaway on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-06-25

pkgdown site last built 2026-06-25

Coverage (1)

Coverage reporting

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing breakaway adds 30 packages (16 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, lme4 4.1 MB, nloptr 2.1 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.5.0

Imports (9)

ggplot2graphicslme4 magrittrMASSphyloseqstatstibbleutils

LinkingTo (0)

none

Suggests (7)

devtools knitr plyr RCurl rmarkdown testthat dplyr

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 (7)

Amy D Willis

Author, Maintainer · added in 4.8.2

Kathryn Barger

Author · added in 4.7.8

John Bunge

Author

David Clausen

Author · added in 4.7.8

Bryan D Martin

Author · added in 4.7.8

Sarah Teichman

Author · added in 4.7.8

Pauline Trinh

Author · added in 4.7.8

Maintainer since 1.0 (2014)

Listed in earlier versions (1)

Amy Willis

no longer listed · 1.0 to 4.7.9

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-11-22
4.8.4Latest
record
2022-11-22 · current release · diff ↗
archivedRemoved from CRAN
2022-11-14
issues were not corrected in time
unarchivedReturned to CRAN
2022-10-29
4.8.2
record
2022-10-29 · diff ↗ ·
added 2 exports
%>%, objective_bayes_negbin
archivedRemoved from CRAN
2022-09-30
issues were not corrected in time Does not use suggested package 'corncob' conditionally
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-03-09
4.7.9
record
2022-03-09 · diff ↗ ·
removed 1 export
objective_bayes_negbin
archivedRemoved from CRAN
2022-02-28
check problems were not corrected in time
unarchivedReturned to CRAN
2022-02-11
4.7.8
record
2022-02-11 · diff ↗ ·
removed 2 exports
apples, hawaii

added 34 exports
F_test, alpha_estimate, alpha_estimates, betta_lincom, build_frequency_count_tables, chao_shen, convert, good_turing, kemp, make_design_matrix, make_frequency_count_table, objective_bayes_geometric, objective_bayes_mixedgeo, objective_bayes_negbin, objective_bayes_poisson, poisson_model, poisson_model_nof1, proportions_instead, rnbinomtable, rztnbinomtable, sample_inverse_simpson, sample_richness, sample_shannon, sample_shannon_e, sample_simpson, sample_size_estimate, sample_size_figure, test_submodel, true_gini, true_hill and 4 more

Show 12 earlier eventsHide 12 earlier events

R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-03-07
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
3.0
record
2016-03-30 · diff ↗ ·
added 6 exports
betta_random, chao1, chao1_bc, chao_bunge, wlrm_transformed, wlrm_untransformed
2.0
record
2015-10-02 · diff ↗ ·
removed 1 export
betta_basic

added 3 exports
betta, betta_pic, hawaii
R
R 3.2.0 released · 2015-04-16
1.0
record
2014-08-04
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-08-04
Total releases: 7 / 12 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 691 KB / 7 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("breakaway")

Format

Willis, A. D., Barger, K., Bunge, J., Clausen, D., Martin, B. D., Teichman, S., & Trinh, P. (2022). breakaway: Species Richness Estimation and Modeling (Version 4.8.4) [Computer software]. https://doi.org/10.32614/CRAN.package.breakaway

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 breakaway version 4.8.4 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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