estimate_time_one_chrom {junctions} | R Documentation |
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 unpublished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
[Package junctions version 2.1.0 Index]