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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

Source: R/estimate_time_one_chrom.R
estimate_time_one_chrom.Rd

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 unpublished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

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
#> [1] 200