MutationMatrix-class

A mutation matrix is used to simulate mutations that affect loci. An object
of the class <code>MutationMatrix</code> does not only contain a (haplotypic)
mutation matrix. It also contains the attributes necessary for the
construction and easy-to-read display of this matrix.

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

MutationMatrix-class function

<dl>
<dt><code>mutHapLoci</code></dt>
<dd>a list of haploid locus by locus allelic mulation matrices.</dd></dl>
<dt><code>mutDipLoci</code></dt>
<dd>a list of diploid locus by locus allelic mulation matrices.</dd>
<dt><code>mutLoci</code></dt>
<dd>a list concatenating <code>mutHapLoci</code> and <code>mutDipLoci</code></dd>
<dt><code>nbAlDL</code></dt>
<dd>a vector of the number(s) of alleles at each haploid locus</dd>
<dt><code>nbAlHL</code></dt>
<dd>a vector of the number(s) of alleles at each diploid locus</dd>
<dt><code>mutationMatrix</code></dt>
<dd>the haplotypic mutation matrix</dd>
<dt><code>nbHaplo</code></dt>
<dd>the number of haplotypes</dd>
<dt><code>nbDL</code></dt>
<dd>the number of diploid loci</dd>
<dt><code>nbHL</code></dt>
<dd>the number of haploid loci</dd>
<dt><code>haplotypes</code></dt>
<dd>the enumeration of haplotypes</dd>
<dt><code>IDgenome</code></dt>
<dd>ID of the associated genome</dd>

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Mutation matrix — MutationMatrix-class

<dl>
<dt><code>mutHapLoci</code></dt>
<dd>a list of haploid locus by locus allelic mulation matrices.</dd>


<dt><code>mutDipLoci</code></dt>
<dd>a list of diploid locus by locus allelic mulation matrices.</dd>


<dt><code>mutLoci</code></dt>
<dd>a list concatenating <code>mutHapLoci</code> and <code>mutDipLoci</code></dd>


<dt><code>nbAlDL</code></dt>
<dd>a vector of the number(s) of alleles at each haploid locus</dd>


<dt><code>nbAlHL</code></dt>
<dd>a vector of the number(s) of alleles at each diploid locus</dd>


<dt><code>mutationMatrix</code></dt>
<dd>the haplotypic mutation matrix</dd>


<dt><code>nbHaplo</code></dt>
<dd>the number of haplotypes</dd>


<dt><code>nbDL</code></dt>
<dd>the number of diploid loci</dd>


<dt><code>nbHL</code></dt>
<dd>the number of haploid loci</dd>


<dt><code>haplotypes</code></dt>
<dd>the enumeration of haplotypes</dd>


<dt><code>IDgenome</code></dt>
<dd>ID of the associated genome</dd>


</dl>

MutationMatrix-class: Mutation matrix

Description

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