estimate time using likelihood for a single chromosome — estimate_time

Estimate the time since the onset of hybridization, for a haploid genome

Usage

estimate_time_haploid(
  ancestry_matrix,
  N = 1000,
  freq_ancestor_1 = 0.5,
  lower_lim = 2,
  upper_lim = 1000,
  verbose = FALSE
)

ancestry_matrix: matrix with 3 columns, column 1 = chromosome, column 2 = location in Morgan, column 3 = ancestry.
N: Population Size
freq_ancestor_1: Frequency of ancestor 1 at t = 0
lower_lim: lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
upper_lim: upper limit of the optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
verbose: return verbose output

The number of generations passed since the onset of hybridization