R Observatory: Metrics for castgen version 1.0.2

Balamuta, James Joseph

castgen

1.0.2

Estimate Sample Size for Population Genomic Studies

0packages depend

2.4Kdownloads / year

84.5%test coverage

13/13checks pass

Overview

About

Maintained by Alexander M. SandercockFirst published 2025-04-021 releasesCRAN page ↗GitHub ↗

Estimate sample sizes needed to capture target levels of genetic diversity from a population (multivariate allele frequencies) for applications like germplasm conservation and breeding efforts. Compares bootstrap samples to a full population using linear regression, employing the R-squared value to represent the proportion of diversity captured. Iteratively increases sample size until a user-defined target R-squared is met. Offers a parallelized R implementation of a previously developed 'python' method. All ploidy levels are supported. For more details, see Sandercock et al. (2024) doi:10.1073/pnas.2403505121.

Install

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

install.packages("castgen", 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("alex-sandercock/castgen")

Development version from alex-sandercock/castgen. 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-castgen

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-castgen

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.40

84.5%

Coverage · measured lines

100%

Documentation · exports

8

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

Documentation

READMEYes · 175 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.4K

CRAN downloads in the past year

Rank #16,632 · ~7/day · ~199/mo

Releases R versions

Daily download trend is not available in this view yet.

18330 days

63090 days

2.4K1 year

Compare downloads with other packages →

Also on114 r2u

Repository

GitHub ↗ alex-sandercock/castgen

1Stars

0Forks

0Open issues

0Open PRs

2Releases

25Commits

1Contributors

breedingconservationcran-rgenomics

License Apache-2.0 · 25 commits · Last activity 2025-04-02

Stars over time

2024-09-10 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/alex-sandercock/castgen on 2026-08-03.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

VS CodeRStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (8)

doParallel dplyr foreachparallelRdpackstatsutilsvcfR (>= 1.15.0)

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Alexander M. Sandercock

Author, Maintainer

Authors (1)

Alexander M. Sandercock

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-02
Total releases: 1 / 1 yrs
License: Apache License (>= 2)
Download size: 8.1 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("castgen")

CRAN DOI

https://doi.org/10.32614/CRAN.package.castgen

BibTeX, derived from DESCRIPTION

@Manual{castgen,
  title  = {castgen: Estimate Sample Size for Population Genomic Studies},
  author = {Sandercock, Alexander M.},
  year   = {2025},
  note   = {R package version 1.0.2},
  doi    = {10.32614/CRAN.package.castgen},
  url    = {https://CRAN.R-project.org/package=castgen}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatorycastgen,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {castgen} version 1.0.2},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/castgen},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for castgen version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/castgen

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for castgen version 1.0.2
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/castgen
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/castgen.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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