estimate_time_haploid {junctions}

estimate time using likelihood for a single chromosome

Description

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
)

Arguments

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

Value

The number of generations passed since the onset of hybridization