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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
DOI: 10.32614/CRAN.package.bnpsd
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-oldrel (arm64): bnpsd_1.3.13.tgz, r-release (x86_64): bnpsd_1.3.13.tgz, r-oldrel (x86_64): bnpsd_1.3.13.tgz
Old sources: bnpsd archive

Reverse dependencies:

Reverse suggests: ggmix, popkin, simfam, simtrait

Linking:

Please use the canonical form https://CRAN.R-project.org/package=bnpsd to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.