estimate_time_one_chrom: Estimate the time since the onset of hybridization, using the...

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

Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers on a single chromosome

Description

Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished

Usage

estimate_time_one_chrom(
  J = NA,
  N = Inf,
  H_0 = 0.5,
  marker_distribution = NA,
  lower_lim = 2,
  upper_lim = 1000
)

Arguments

J	The observed number of junctions
N	Population Size
H_0	Frequency of heterozygosity at t = 0
marker_distribution	A vector containing the position of all markers in Morgan.
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.

Value

The number of generations passed since the onset of hybridization

Examples

cat("example estimate time one chrom")
markers <- seq(from = 0, to = 1, length.out = 100)
J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200,
marker_distribution = markers)
estimate_time_one_chrom(J = J,
                        N = 100,
                        H_0 = 0.5,
                        marker_distribution = markers) #should be 200 again

thijsjanzen/junctions documentation built on Feb. 16, 2024, 12:14 p.m.