initialize,Population-method

Initialize method for the <code>Population</code> class

Implementation in a simple and efficient way of fully customisable population genetics simulations,
considering multiple loci that have epistatic interactions. Specifically suited to the modelling of
multilocus nucleocytoplasmic systems (with both diploid and haploid loci), it is nevertheless possible
to simulate purely diploid (or purely haploid) genetic models.
Examples of models that can be simulated with Ease are numerous, for example models of genetic
incompatibilities as presented by Marie-Orleach et al. (2022) <doi:10.1101/2022.07.25.501356>.
Many others are conceivable, although few are actually explored, Ease having been developed
in particular to provide a solution so that these kinds of models can be simulated simply.

Ehouarn Faou

Ease

Simulating Explicit Population Genetics Models

initialize,Population-method function

<dl><dt>.Object</dt>
<dd>a <code>Population</code> object</dd>
<dt>name</dt>
<dd>the name of the population.</dd>
<dt>size</dt>
<dd>the size of the population.</dd>
<dt>dioecy</dt>
<dd>logical indicating whether the population is dioecious or not
(hermaphrodite).</dd>
<dt>selfRate</dt>
<dd>the selfing rate of the population</dd>
<dt>demography</dt>
<dd>logical indicating whether the population has stochastic
demography (this does not include migration), i.e. non-constant size and
potentially population growth or decay, depending on the situation it is in.</dd>
<dt>growthRate</dt>
<dd>growth rate of the population.</dd>
<dt>initGenoFreq</dt>
<dd>A row matrix of the size of the genotype number
describing the initial allele frequencies common to all simulations</dd>
<dt>genomeObj</dt>
<dd>a <code>Genome</code> object</dd>
<dt>initPopSize</dt>
<dd>initial population size, knowing that if the demography
is extinct, the initial population size will automatically be set equal to
the population size.</dd>
<dt>selectionObj</dt>
<dd>a <code>Selection</code> object</dd>
<dt>mutMatrixObj</dt>
<dd>a <code>MutationMatrix</code> object</dd></dl>

Arguments

Author

Initialize method for the Population class — initialize,Population-method

<dl>

<dt>.Object</dt>
<dd>a <code>Population</code> object</dd>


<dt>name</dt>
<dd>the name of the population.</dd>


<dt>size</dt>
<dd>the size of the population.</dd>


<dt>dioecy</dt>
<dd>logical indicating whether the population is dioecious or not
(hermaphrodite).</dd>


<dt>selfRate</dt>
<dd>the selfing rate of the population</dd>


<dt>demography</dt>
<dd>logical indicating whether the population has stochastic
demography (this does not include migration), i.e. non-constant size and
potentially population growth or decay, depending on the situation it is in.</dd>


<dt>growthRate</dt>
<dd>growth rate of the population.</dd>


<dt>initGenoFreq</dt>
<dd>A row matrix of the size of the genotype number
describing the initial allele frequencies common to all simulations</dd>


<dt>genomeObj</dt>
<dd>a <code>Genome</code> object</dd>


<dt>initPopSize</dt>
<dd>initial population size, knowing that if the demography
is extinct, the initial population size will automatically be set equal to
the population size.</dd>


<dt>selectionObj</dt>
<dd>a <code>Selection</code> object</dd>


<dt>mutMatrixObj</dt>
<dd>a <code>MutationMatrix</code> object</dd>

</dl>

initialize,Population-method: Initialize method for the `Population` class

Description

Usage

Value

Arguments

Author