log_likelihood_diploid

Calculates the log likelihood of observing the phased data,
given the population size, initial heterozygosity and time since admixture

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 (2020,
<doi:10.1101/2020.09.10.292441>).

Thijs Janzen

junctions

The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

log_likelihood_diploid function

<dl><dt>local_anc_matrix</dt>
<dd>a matrix with four columns: column 1) chromosome
indicator, 2) location of marker in Morgan on respective chromosome 3)
ancestry at chromosome 4) ancestry at chromosome 2.</dd>
<dt>pop_size</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>
<dt>phased</dt>
<dd>is the data phased or not? default is false.</dd>
<dt>num_threads</dt>
<dd>number of threads, default is one thread. Set to -1 to
use all available threads.</dd></dl>

Arguments

calculate the log likelihood of observing diploid ancestry data. — log_likelihood_diploid

<dl>

<dt>local_anc_matrix</dt>
<dd>a matrix with four columns: column 1) chromosome
indicator, 2) location of marker in Morgan on respective chromosome 3)
ancestry at chromosome 4) ancestry at chromosome 2.</dd>


<dt>pop_size</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>


<dt>phased</dt>
<dd>is the data phased or not? default is false.</dd>


<dt>num_threads</dt>
<dd>number of threads, default is one thread. Set to -1 to
use all available threads.</dd>

</dl>

log_likelihood_diploid: calculate the log likelihood of observing diploid ancestry data.

Description

Usage

Value

Arguments