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 [aut, cre] (<https://orcid.org/0000-0003-4928-3403>), John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
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:

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