hweboot

Iteratively resample individuals/genotypes, calculating the U-statistic
for each resample, and use these resamples to test against the null
of no equilibrium.

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 

hweboot function

<dl><dt>n</dt>
<dd>One of two forms<dl>
<dt>A vector of length ploidy + 1</dt>
<dd>Element i is the number of
individuals with genotype i.</dd></dl></dd><dt>A matrix with nsamp rows and ploidy+1 columns</dt>
<dd>Element (i, j)
is the posterior probability that individual i has ploidy j-1.</dd>
</dl>
<dt>nboot</dt>
<dd>The number of bootstrap samples to run.</dd>
<dt>more</dt>
<dd>A logical. Should we return the bootstrap replicates
(<code>FALSE</code>) or just the p-value, with 95% confidence interval
of the p-value (<code>TRUE</code>).</dd>

Arguments

Author

Bootstrap procedure to test for equilibrium — hweboot

<dl>

<dt>n</dt>
<dd>One of two forms<dl>
<dt>A vector of length ploidy + 1</dt>
<dd>Element i is the number of
individuals with genotype i.</dd>

<dt>A matrix with nsamp rows and ploidy+1 columns</dt>
<dd>Element (i, j)
is the posterior probability that individual i has ploidy j-1.</dd>


</dl></dd>


<dt>nboot</dt>
<dd>The number of bootstrap samples to run.</dd>


<dt>more</dt>
<dd>A logical. Should we return the bootstrap replicates
(<code>FALSE</code>) or just the p-value, with 95% confidence interval
of the p-value (<code>TRUE</code>).</dd>

</dl>

hweboot: Bootstrap procedure to test for equilibrium

Description

Usage

Value

Arguments

Author

Examples