estimate_time_diploid: estimates the time since admixture, given diploid ancestry...
In junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

estimate_time_diploid

R Documentation

estimates the time since admixture, given diploid ancestry data.

Description

Calculates the time since admixture, given unphased ancestry data.

Usage

estimate_time_diploid(
  ancestry_information,
  analysis_type = "individuals",
  phased = FALSE,
  pop_size = 1000,
  freq_ancestor_1 = 0.5,
  lower_lim = 2,
  upper_lim = 2000,
  num_threads = 1,
  verbose = FALSE
)

Arguments

`ancestry_information`	a matrix with five columns: column 1) indicator of individual, column 2) indicator of chromosome, 3) location of marker in Morgan, 4) ancestry at chromosome 5) ancestry at chromosome 2.
`analysis_type`	how should the data be broken down? there are multiple options: "individuals" - time is inferred for each individual separately, grouping all chromosomes together that belong to the same individual. "chromosomes" - time is inferred for each chromosome separately, grouping chromosomes together belonging from separate individuals. "separate" - time is inferred for each chromosome from each individual separately, "all" - time is inferred jointly for all chromosomes and individuals, grouping all chromosomes and individuals together.
`phased`	is the data phased?
`pop_size`	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 hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
`num_threads`	num_threads, default is all threads. 5 threads is recommended.
`verbose`	display intermediate output? Default = FALSE