bnpsd (version 1.1.1)

bnpsd: A package for modeling and simulating an admixed population

Description

The underlying model is called the BN-PSD admixture model, which combines the Balding-Nichols (BN) allele frequency model for the intermediate subpopulations with the Pritchard-Stephens-Donnelly (PSD) model of individual-specific admixture proportions. The BN-PSD model enables the simulation of complex population structures, ideal for illustrating challenges in kinship coefficient and \(F_{ST}\) estimation. Simulated loci are drawn independently (in linkage equilibrium).

See Also

Useful links:

• https://github.com/StoreyLab/bnpsd/

• Report bugs at https://github.com/StoreyLab/bnpsd/issues

Examples

# NOT RUN {
# dimensions of data/model
# number of loci
m_loci <- 10
# number of individuals
n_ind <- 5
# number of intermediate subpops
k_subpops <- 2

# define population structure
# FST values for k = 2 subpopulations
inbr_subpops <- c(0.1, 0.3)
# admixture proportions from 1D geography
admix_proportions <- admix_prop_1d_linear(n_ind, k_subpops, sigma = 1)
# also available:
# - admix_prop_1d_circular
# - admix_prop_indep_subpops

# get pop structure parameters of the admixed individuals
# the coancestry matrix
coancestry <- coanc_admix(admix_proportions, inbr_subpops)
# FST of admixed individuals
Fst <- fst_admix(admix_proportions, inbr_subpops)

# draw all random allele freqs and genotypes
out <- draw_all_admix(admix_proportions, inbr_subpops, m_loci)
# genotypes
X <- out$X
# ancestral allele frequencies (AFs)
p_anc <- out$p_anc

# OR... draw each vector or matrix separately
# provided for additional flexibility
# ancestral AFs
p_anc <- draw_p_anc(m_loci)
# independent subpops (intermediate) AFs
p_subpops <- draw_p_subpops(p_anc, inbr_subpops)
# individual-specific AFs
p_ind <- make_p_ind_admix(p_subpops, admix_proportions)
# genotypes
X <- draw_genotypes_admix(p_ind)

# }