install.packages("bnpsd")

install.packages("devtools") # if needed
library(devtools)
install_github('StoreyLab/bnpsd', build_opts = c())

vignette('bnpsd')

library(bnpsd)
# 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_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)

# best to start by specifying tree in Newick string format
tree_str <- '(S1:0.1,(S2:0.1,S3:0.1)N1:0.1)T;'
# and turn it into `phylo` object using the `ape` package
library(ape)
tree_subpops <- read.tree( text = tree_str )
# true coancestry matrix corresponding to this tree
coanc_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 matrix
coancestry <- coanc_admix( admix_proportions, coanc_subpops )
# FST of admixed individuals
Fst <- fst_admix( admix_proportions, coanc_subpops )

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

# OR... draw tree subpops (intermediate) AFs separately
p_subpops_tree <- draw_p_subpops_tree( p_anc, tree_subpops )