bnpsd: Simulate Genotypes from the BN-PSD Admixture Model

The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. This simulation approach is now extended to subpopulations related by a tree. Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Version: 1.3.13
Imports: stats, ape, nnls
Suggests: popkin (≥ 1.3.9), testthat, knitr, rmarkdown, RColorBrewer
Published: 2021-08-25
Author: Alejandro Ochoa ORCID iD [aut, cre], John D. Storey ORCID iD [aut]
Maintainer: Alejandro Ochoa <alejandro.ochoa at duke.edu>
BugReports: https://github.com/StoreyLab/bnpsd/issues
License: GPL (≥ 3)
URL: https://github.com/StoreyLab/bnpsd/
NeedsCompilation: no
Citation: bnpsd citation info
Materials: README NEWS
CRAN checks: bnpsd results

Documentation:

Reference manual: bnpsd.pdf
Vignettes: Simulate Admixed Populations with 'bnpsd'

Downloads:

Package source: bnpsd_1.3.13.tar.gz
Windows binaries: r-devel: bnpsd_1.3.13.zip, r-release: bnpsd_1.3.13.zip, r-oldrel: bnpsd_1.3.13.zip
macOS binaries: r-release (arm64): bnpsd_1.3.13.tgz, r-release (x86_64): bnpsd_1.3.13.tgz, r-oldrel: bnpsd_1.3.13.tgz
Old sources: bnpsd archive

Reverse dependencies:

Reverse suggests: ggmix, popkin, simfam, simtrait

Linking:

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