R Observatory: Metrics for BGmisc version 1.6.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BGmisc

1.6.0.1Package record

An R Package for Extended Behavior Genetics Analysis

2packages dependsuggested by 1

10.8Kdownloads / year

84.5%test coverage

13/13flavors OK

Overview

About

Maintained by S. Mason GarrisonCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) doi:10.1007/s10519-021-10055-x], calculation of relatedness coefficients using path-tracing methods [Wright (1922) doi:10.1086/279872; McArdle & McDonald (1984) doi:10.1111/j.2044-8317.1984.tb00802.x], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2025) doi:10.1007/s10519-025-10225-1]. For a full overview, see [Garrison et al. (2024) doi:10.21105/joss.06203]. For a big data application see [Burt et al. (2025) <doi: 10.1016/j.ebiom.2025.105911>.

Changes in 1.6.0.1

CRAN submission

Add OpenMx pedigree model builders and docs
Added vignette for OpenMx pedigree model builders
Add option for MZ twins in the additive genetic matrix
Add option to select sex for MZ twin generation.
Add option to tweak pedigree with one id provided
Add helper functions for checkParents etc
fixed incorrect direction so that parents are pointing to children in the graphs
Optimize simulatePedigree and helpers for speed and memory usage
Major gains (>x10) in speed for deeper pedigrees
Added more tests for simulatePedigree
Fix error when not enough single people available

From NEWS.md in the release

Install

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

install.packages("BGmisc", 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("R-Computing-Lab/BGmisc")

Development version from R-Computing-Lab/BGmisc. 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-bgmisc

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

# 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-BGmisc

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-BGmisc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.5 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
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.0.1

READMEYes · 445 wordsVignettesYes · 7 · dynamicNEWSYes · 100% structured · mentions 1.6.0.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Cites a JOSS paper

Help pages: 142 (56 internal)includes a package overview page
Examples that run: 43%6 run in a plain check · 8 never run
Exported functions with examples: 28%
Documented parameters: 98%
Return-value docs: 76%
Help pages citing references: 0%

Vignettes (7)

How these are measured

Downloads

10.8K

CRAN downloads in the past year

Rank #4,426 · ~30/day · ~902/mo

Releases R versions

Daily download trend is not available in this view yet.

74730 days

1.9K90 days

10.8K1 year

Compare downloads with other packages →

Also on244 r2u23 autocran

How downloads are counted

Repository

r-computing-lab/bgmisc ↗Organization: R-Computing-Lab

4Stars

3Forks

13Open issues

4Open PRs

14Releases

1,369Commits

11Commit identities

packagecranrr-packagebehavior-genetics

License file reads as GPL-3.0 · 1,369 commits · Last activity 2026-08-05 · 0% stars, 30d · Default branch at 1.9.0, ahead of CRAN 1.6.0.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-05 · 22026-08-09 · 4

How these are measured

PracticesBeta

16 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/r-computing-lab/bgmisc on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (3)

Code of conductContributing guidePR template (inherited from r-computing-lab)

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-05 · The repository has a site deploy workflow

pkgdown site last built 2026-08-05

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-10-14
Seen in the repository: .github/copilot-instructions.md
Pull request: opened by its own account
Commits: 19 by its own account · at least 9 crediting it in the message
Claude Codefirst seen 2026-02-09
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 7 crediting it in the message

Models named in its commits

Claude Sonnet 4.63 commits · Jun 2026

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

17 external dependencies (excludes base and recommended)

Installing BGmisc adds 12 packages (8 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, igraph 4.8 MB.

Depends (1)

R >= 3.5.0

Imports (6)

data.table igraphMatrixstatsstringrmethods

LinkingTo (0)

none

Suggests (14)

corrplot discord dplyr EasyMx ggpedigree ggplot2 kinship2 knitr OpenMx rmarkdown testthat tidyverse mvtnorm withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

ggpedigree tidygedcom

Suggests, most downloaded first

discord

How these are counted

Code & Tests

Datasets

People & History

People (6)

S. Mason Garrison

Author, Maintainer since 1.0 (2023)

S. Alexandra Burt

Author

Michael D. Hunter

Author

Xuanyu Lyu

Author · added in 1.0

Jonathan D. Trattner

Author

Rachel N. Good

Contributor

Previously maintained by Jonathan D. Trattner (0.1).

Listed in earlier versions (4)

Show 4 peopleHide 4 people

S. Alexandra

no longer listed · 0.1 to 1.6.0.1

Jonathan D.

no longer listed · 0.1 to 1.6.0.1

Michael D.

no longer listed · 0.1 to 1.6.0.1

Rachel N.

no longer listed · 1.2.0 to 1.6.0.1

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.6.0.1Latest
record
2026-03-13 · current release · diff ↗ ·
removed 2 exports
evenInsert, insertEven

added 5 exports
buildFamilyGroups, buildOneFamilyGroup, buildPedigreeModelCovariance, buildPedigreeMx, fitPedigreeModel
1.5.2
record
2026-01-11 · diff ↗ ·
added 1 export
ped2gen
1.5.0
record
2025-07-19 · diff ↗ ·
removed 1 export
resample

added 1 export
sliceFamilies
1.4.3.1
record
2025-06-10 · diff ↗ ·
removed 2 exports
assignCoupleIDs, plotPedigree

added 2 exports
addPersonToPed, determineSex
1.4.1
record
2025-05-30 · diff ↗ ·
removed 5 exports
allGens, extractSummaryText, famSizeCal, parseTree, relatedness

added 17 exports
assignCoupleIDs, buildTreeGrid, calcAllGens, calcFamilySize, calculateCIs, checkParentIDs, computeParentAdjacency, getWikiTreeSummary, insertEven, readGed, readgedcom, repairIDs, summariseFamilies, summariseMatrilines, summarisePatrilines, summarisePedigrees, traceTreePaths
R
R 4.5.0 released · 2025-04-11
1.3.5
record
2025-04-03 · diff ↗ ·
added 5 exports
checkPedigreeNetwork, com2links, extractSummaryText, parseTree, readWikifamilytree
1.3.3
record
2025-02-19 · diff ↗
1.3.2
record
2024-06-18 · diff ↗
1.3.1
record
2024-06-16 · diff ↗ ·
removed 1 export
determineSex

added 6 exports
readGedcom, recodeSex, summarizeFamilies, summarizeMatrilines, summarizePatrilines, summarizePedigrees
R
R 4.4.0 released · 2024-04-24
1.2.0
record
2024-02-26 · diff ↗ ·
added 11 exports
checkIDs, checkSex, createGenDataFrame, determineSex, dropLink, makeInbreeding, makeTwins, ped2maternal, ped2paternal, repairSex, resample
1.0.1
record
2023-09-27 · diff ↗
1.0
record
2023-09-20 · diff ↗ ·
added 15 exports
SimPed, allGens, calculateRelatedness, evenInsert, famSizeCal, inferRelatedness, ped2add, ped2ce, ped2cn, ped2com, ped2fam, ped2graph, ped2mit, plotPedigree, simulatePedigree
R
R 4.3.0 released · 2023-04-21

Show 4 earlier eventsHide 4 earlier events

R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1
record
2020-12-04
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-04
Total releases: 13 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 43 KB / 4 files
Download size: 610 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("BGmisc")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.21105/joss.06203.

The repository also keeps a CITATION.cff.

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 BGmisc version 1.6.0.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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