bnpsd

Installation

install.packages("bnpsd")

install.packages("devtools")# if neededlibrary(devtools)install_github('StoreyLab/bnpsd',build_vignettes=TRUE)

vignette('bnpsd')

Example

library(bnpsd)# dimensions of data/model# number of locim_loci<-10# number of individualsn_ind<-5# number of intermediate subpopsk_subpops<-2# define population structure# FST values for k=2 subpopulationsinbr_subpops<- c(0.1,0.3)# admixture proportions from 1D geographyadmix_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 matrixcoancestry<- coanc_admix(admix_proportions,inbr_subpops)# FST of admixed individualsFst<- fst(admix_proportions,inbr_subpops)

# draw all random allele freqs and genotypesout<- draw_all_admix(admix_proportions,inbr_subpops,m_loci)# genotypesX<-out$X# ancestral allele frequencies (AFs)p_anc<-out$p_anc# OR... draw each vector or matrix separately# provided for additional flexibility# ancestral AFsp_anc<- draw_p_anc(m_loci)# independent subpops (intermediate) AFsp_subpops<- draw_p_subpops(p_anc,inbr_subpops)# individual-specific AFsp_ind<- make_p_ind_admix(p_subpops,admix_proportions)# genotypesX<- draw_genotypes_admix(p_ind)

Examples with a tree for intermediate subpopulations

# best to start by specifying tree in Newick string formattree_str<-'(S1:0.1,(S2:0.1,S3:0.1)N1:0.1)T;'# and turn it into `phylo` object using the `ape` packagelibrary(ape)tree_subpops<- read.tree(text=tree_str )# true coancestry matrix corresponding to this treecoanc_subpops<- coanc_tree(tree_subpops )# admixture proportions from 1D geography# (constructed again but for k=3 tree)k_subpops<- nrow(coanc_subpops )admix_proportions<- admix_prop_1d_linear(n_ind,k_subpops,sigma=0.5 )# get pop structure parameters of the admixed individuals# the coancestry matrixcoancestry<- coanc_admix(admix_proportions,coanc_subpops )# FST of admixed individualsFst<- fst_admix(admix_proportions,coanc_subpops )# draw all random allele freqs and genotypes, tree versionout<- draw_all_admix(admix_proportions,tree_subpops=tree_subpops,m_loci=m_loci )# genotypesX<-out$X# ancestral allele frequencies (AFs)p_anc<-out$p_anc# OR... draw tree subpops (intermediate) AFs separatelyp_subpops_tree<- draw_p_subpops_tree(p_anc,tree_subpops )

Citations