R Observatory: Metrics for pedtricks version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pedtricks

0.5.0Package record

Visualize, Summarize and Simulate Data from Pedigrees

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Julien MartinCRAN page ↗GitHub ↗Website ↗Issues ↗

Sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for visualizing pedigrees. This is a reboot of the methods developed by Morrissey and Wilson (2010) <doi: 10.1111/j.1755-0998.2009.02817.x>.

Changes in 0.5.0

ped_stats
Added more relationships; cousins and aunts/uncles, returned in cousinNums and auNums slots in ped_stats object
Removed relatedness categories (cumulativeRelatedness and relatednessCategories from output
Instead now directly outputs mean and variances of relatedness, and proportion >= 0.125, 0.25 and 0.5, which are returned in relatednessDistribution slot in ped_stats object
summary.ped_stats
New relationships in ped_stats function not output from summary.ped_stats by default. Use extended=TRUE for them to be included in the output
plot.ped_stats
plotting relatedness distribution now slightly different, due to removing relatednessCategories from ped_stats object. Will plot if A matrix is present on ped_stats object
h2_samp_var
Added new function to calculate expected sampling variance for $h^2$ from Visscher and Goddard 2016

From NEWS.md in the release

Install

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

install.packages("pedtricks", 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("JulienGAMartin/pedtricks")

Development version from JulienGAMartin/pedtricks. 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-pedtricks

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-pedtricks

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-pedtricks

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: 3.5 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 421 wordsVignettesNoNEWSYes · 67% structured · mentions 0.5.0Citation fileNoWebsiteYes · pkgdown

Help pages: 18 (4 internal)includes a package overview page
Examples that run: 82%9 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 92%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 6%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #21,532 · ~7/day · ~198/mo

Releases R versions

Daily download trend is not available in this view yet.

24230 days

62290 days

2.4K1 year

Compare downloads with other packages →

Also on78 r2u5 autocran

How downloads are counted

Repository

juliengamartin/pedtricks ↗Account: JulienGAMartin

4Stars

0Forks

6Open issues

0Open PRs

4Releases

94Commits

4Commit identities

94 commits · Last activity 2026-03-01

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

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/juliengamartin/pedtricks on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-03-01 · The repository has a site deploy workflow

pkgdown site last built 2026-03-01

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing pedtricks adds 51 packages (28 with compiled code, 44 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

R >= 4.0

Imports (11)

ggplot2 dplyr kinship2 tidyrMatrixmvtnorm MCMCglmm nadiv geneticsmethodsigraph

LinkingTo (0)

none

Suggests (0)

none

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 (5)

Julien Martin

Author, Maintainer since 0.4.2 (2024)

Susan Johnston

Author

Michael Morrissey

Author

Joel Pick

Author · added in 0.5.0

Matthew Wolak

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
2026-03-01 · current release · diff ↗ ·
added 1 export
h2_samp_var
R
R 4.5.0 released · 2025-04-11
0.4.2
record
2024-09-09
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-09
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 36 KB / 2 files
Download size: 84 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pedtricks")

Format

Martin, J., Johnston, S., Morrissey, M., Pick, J., & Wolak, M. (2026). pedtricks: Visualize, Summarize and Simulate Data from Pedigrees (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.pedtricks

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 pedtricks version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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