Simulate Genotypes from the BN-PSD Admixture Model

Documentation for package ‘bnpsd’ version 1.3.13

bnpsd-package	A package for modeling and simulating an admixed population
admix_prop_1d_circular	Construct admixture proportion matrix for circular 1D geography
admix_prop_1d_linear	Construct admixture proportion matrix for 1D geography
admix_prop_indep_subpops	Construct admixture proportion matrix for independent subpopulations
bnpsd	A package for modeling and simulating an admixed population
coanc_admix	Construct the coancestry matrix of an admixture model
coanc_to_kinship	Transform coancestry matrix to kinship matrix
coanc_tree	Calculate coancestry matrix corresponding to a tree
draw_all_admix	Simulate random allele frequencies and genotypes from the BN-PSD admixture model
draw_genotypes_admix	Draw genotypes from the admixture model
draw_p_anc	Draw random Uniform or Beta ancestral allele frequencies
draw_p_subpops	Draw allele frequencies for independent subpopulations
draw_p_subpops_tree	Draw allele frequencies for subpopulations related by a tree
fit_tree	Fit a tree structure to a coancestry matrix
fixed_loci	Identify fixed loci
fst_admix	Calculate FST for the admixed individuals
make_p_ind_admix	Construct individual-specific allele frequency matrix under the PSD admixture model
scale_tree	Scale a coancestry tree
tree_additive	Calculate additive edges for a coancestry tree, or viceversa
tree_reindex_tips	Reindex tree tips in order of appearance in edges
tree_reorder	Reorder tree tips to best match a desired order
undiff_af	Undifferentiate an allele distribution