dgamete

Estimates the probability of a gamete dosage given the parent dosage
(<code>G</code>), the parent ploidy (<code>ploidy</code>), and the double reduction
parameter (<code>alpha</code>). This is for biallelic loci.

Inference concerning equilibrium and random mating in
autopolyploids. Methods are available to test for equilibrium
and random mating at any even ploidy level (>2) in the presence
of double reduction at biallelic loci. For autopolyploid populations
in equilibrium, methods are available to estimate the degree of
double reduction. We also provide functions to calculate genotype
frequencies at equilibrium, or after one or several rounds of
random mating, given rates of double reduction. The main function is
hwefit(). This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The opinions,
findings, and conclusions or recommendations expressed are those of
the author and do not necessarily reflect the views of the National
Science Foundation. For details of these methods, see
Gerard (2023a) <doi:10.1111/biom.13722> and
Gerard (2023b) <doi:10.1111/1755-0998.13856>.

David Gerard

hwep

Hardy-Weinberg Equilibrium in Polyploids

NSF DBI 2132247 

dgamete function

<dl><dt>x</dt>
<dd>A vector of numerics in <code>seq(0, ploidy/2)</code>. The dosage of the
gametes.</dd>
<dt>alpha</dt>
<dd>A numeric vector containing the double reduction parameter(s).
This should be a
vector of length <code>floor(ploidy/4)</code> where <code>alpha[i]</code>
is the probability of exactly <code>i</code> pairs of IBDR alleles
being in the gamete. Note that <code>sum(alpha)</code> should be less than
1, as <code>1 - sum(alpha)</code> is the probability of no double reduction.</dd>
<dt>G</dt>
<dd>The dosage of the parent. Should be an integer between <code>0</code>
and <code>ploidy</code>.</dd>
<dt>ploidy</dt>
<dd>The ploidy of the species. This should be an even positive
integer.</dd>
<dt>log_p</dt>
<dd>A logical. Should we return the log-probability (<code>TRUE</code>)
or not (<code>FALSE</code>)? Defaults to <code>FALSE</code>.</dd></dl>

Arguments

Author

Gamete dosage probability — dgamete

<dl>

<dt>x</dt>
<dd>A vector of numerics in <code>seq(0, ploidy/2)</code>. The dosage of the
gametes.</dd>


<dt>alpha</dt>
<dd>A numeric vector containing the double reduction parameter(s).
This should be a
vector of length <code>floor(ploidy/4)</code> where <code>alpha[i]</code>
is the probability of exactly <code>i</code> pairs of IBDR alleles
being in the gamete. Note that <code>sum(alpha)</code> should be less than
1, as <code>1 - sum(alpha)</code> is the probability of no double reduction.</dd>


<dt>G</dt>
<dd>The dosage of the parent. Should be an integer between <code>0</code>
and <code>ploidy</code>.</dd>


<dt>ploidy</dt>
<dd>The ploidy of the species. This should be an even positive
integer.</dd>


<dt>log_p</dt>
<dd>A logical. Should we return the log-probability (<code>TRUE</code>)
or not (<code>FALSE</code>)? Defaults to <code>FALSE</code>.</dd>

</dl>

dgamete: Gamete dosage probability

Description

Usage

Value

Arguments

Author

Examples