log_likelihood_haploid

log likelihood of the time since admixture for a set of single
chromosomes (for ex. in Yeast).

Individual based simulations of hybridizing populations,
where the accumulation of junctions is tracked. Furthermore,
mathematical equations are provided to verify simulation outcomes.
Both simulations and mathematical equations are based on Janzen
(2018, <doi:10.1101/058107>) and Janzen (2022,
<doi:10.1111/1755-0998.13519>).

Thijs Janzen

junctions

The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

log_likelihood_haploid function

<dl><dt>ancestry_matrix</dt>
<dd>matrix with 3 columns, column 1 = chromosome,
column 2 = location in Morgan, column 3 = ancestry.</dd>
<dt>N</dt>
<dd>Population Size</dd>
<dt>freq_ancestor_1</dt>
<dd>Frequency of ancestor 1 at t = 0</dd>
<dt>t</dt>
<dd>time since admixture</dd></dl>

Arguments

log likelihood of the time since admixture for a haploid genome — log_likelihood_haploid

<dl>

<dt>ancestry_matrix</dt>
<dd>matrix with 3 columns, column 1 = chromosome,
column 2 = location in Morgan, column 3 = ancestry.</dd>


<dt>N</dt>
<dd>Population Size</dd>


<dt>freq_ancestor_1</dt>
<dd>Frequency of ancestor 1 at t = 0</dd>


<dt>t</dt>
<dd>time since admixture</dd>

</dl>

log_likelihood_haploid: log likelihood of the time since admixture for a haploid genome

Description

Usage

Value

Arguments