R: Simulate Genotypes from the BN-PSD Admixture Model

# Simulate Genotypes from the BN-PSD Admixture Model

## Documentation for package ‘bnpsd’ version 1.3.13

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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