castgen: Estimate Sample Size for Population Genomic Studies

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>.

Version: 1.0.2
Imports: doParallel (≥ 1.0.17), dplyr (≥ 1.1.2), foreach (≥ 1.5.2), parallel (≥ 4.0.0), Rdpack (≥ 0.7), stats, utils, vcfR (≥ 1.15.0)
Suggests: testthat (≥ 3.0.0)
Published: 2025-04-02
Author: Alexander M. Sandercock ORCID iD [aut, cre]
Maintainer: Alexander M. Sandercock <ams866 at cornell.edu>
BugReports: https://github.com/alex-sandercock/castgen/issues
License: Apache License (≥ 2)
URL: https://github.com/alex-sandercock/castgen
NeedsCompilation: no
Materials: README, NEWS
CRAN checks: castgen results

Documentation:

Reference manual: castgen.html , castgen.pdf

Downloads:

Package source: castgen_1.0.2.tar.gz
Windows binaries: r-devel: castgen_1.0.2.zip, r-release: castgen_1.0.2.zip, r-oldrel: castgen_1.0.2.zip
macOS binaries: r-release (arm64): castgen_1.0.2.tgz, r-oldrel (arm64): castgen_1.0.2.tgz, r-release (x86_64): castgen_1.0.2.tgz, r-oldrel (x86_64): castgen_1.0.2.tgz

Linking:

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