estimate_time_haploid: estimate time using likelihood for a single chromosome

In junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

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

junctions documentation built on May 29, 2024, 6:26 a.m.