calculate the log likelihood of observing diploid ancestry data.

Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture

Usage

log_likelihood_diploid(
  local_anc_matrix,
  pop_size,
  freq_ancestor_1 = 0.5,
  t,
  phased = FALSE,
  num_threads = 1
)

local_anc_matrix: a matrix with four columns: column 1) chromosome indicator, 2) location of marker in Morgan on respective chromosome 3) ancestry at chromosome 4) ancestry at chromosome 2.
pop_size: population size
freq_ancestor_1: Frequency of ancestor 1 at t = 0
t: time since admixture
phased: is the data phased or not? default is false.
num_threads: number of threads, default is one thread. Set to -1 to use all available threads.

log likelihood