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)
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.
coanc_to_kinship to easily obtain kinship matrices from coancestry matrices.