R Observatory: Metrics for BREADR version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BREADR

1.1.0

Estimates Degrees of Relatedness (Up to the Second Degree) for Extreme Low-Coverage Data

0packages depend

3.8Kdownloads / year

22.2%test coverage

13/13checks pass

Overview

About

Maintained by Jono TukeFirst published 2023-04-075 releasesCRAN page ↗GitHub ↗

The goal of the package is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extreme low-coverage data. The package also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.

Install

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

install.packages("BREADR", 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("jonotuke/BREADR")

Development version from jonotuke/BREADR. 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-breadr

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-BREADR

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-BREADR

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

Health

CRAN checks

13OK

Slowest check: 9.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

22.2%

Coverage · measured lines

93%

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 213 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.8K

CRAN downloads in the past year

Rank #6,142 · ~10/day · ~317/mo

Releases R versions

Daily download trend is not available in this view yet.

24830 days

1.4K90 days

3.8K1 year

Compare downloads with other packages →

Also on134 r2u4 autocran

Repository

GitHub ↗ jonotuke/breadr

0Stars

1Forks

2Open issues

0Open PRs

0Releases

120Commits

2Contributors

120 commits · Last activity 2026-04-16

Forks over time

2025-11-11 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jonotuke/breadr on 2026-08-09.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (2)

README.RmdQuarto project

Show all practices

Research and citation (1)

JOSS paper

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3

Imports (15)

data.table dplyr forcats ggplot2 ggpubr ggstatsplotgrDevicesmagrittrMASSmatrixStats purrr readr stringr tibble tidyr

LinkingTo (0)

none

Suggests (6)

spelling knitr rmarkdown testthatMatrixfs

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Jono Tuke

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2026-04-16 · current release · diff ↗
1.0.3
2025-04-14 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2024-09-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.1
2023-04-12 · diff ↗
1.0.0
2023-04-07
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-04-07
Total releases: 5 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3
Bundled data: 2.0 KB / 2 files
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BREADR")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 BREADR version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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