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) .


2017-09-11 - bnpsd

  • Public release!

2018-01-15 - bnpsd 1.0.1

  • Minor non-code changes for first CRAN submission.

2018-02-01 - bnpsd

  • now contains instructions for installing from CRAN as well as from GitHub.

2019-02-06 - bnpsd

  • Added option noFixed to function rbnpsd to redraw loci that were drawn fixed for a single allele. These loci are not polymorphic so they would normally not be considered in analyses.

  • Added function fixed_loci to test for fixed loci within rbnpsd.

2019-02-07 - bnpsd

  • Added function coanc_to_kinship to easily obtain kinship matrices from coancestry matrices.

2019-02-11 - bnpsd 1.0.4

  • Second CRAN submission.

Reference manual

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1.3.13 by Alejandro Ochoa, 5 months ago

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Browse source code at

Authors: Alejandro Ochoa [aut, cre] , John D. Storey [aut]

Documentation:   PDF Manual  

GPL (>= 3) license

Imports stats, ape, nnls

Suggests popkin, testthat, knitr, rmarkdown, RColorBrewer

Suggested by ggmix, popkin, simfam, simtrait.

See at CRAN