hweustat

Estimates double reduction and tests for equilibrium while accounting
for double reduction. It does this using an approach called
"U-process minimization", where we minimize a function of a U-statistic
that should be 0 at equilibrium given the true double reduction rate.

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 

hweustat function

<dl><dt>nvec</dt>
<dd>A vector containing the observed genotype counts,
where <code>nvec[[i]]</code> is the number of individuals with genotype
<code>i-1</code>. This should be of length <code>ploidy+1</code>.</dd>
<dt>thresh</dt>
<dd>The threshold for ignoring the genotype. We keep
genotypes such that <code>nvec &gt;= thresh</code>.
Setting this to <code>0</code> uses all genotypes. Setting this to
<code>NULL</code> uses a heuristic that works well in practice.</dd>
<dt>effdf</dt>
<dd>A logical. Should we use the ad-hoc
"effective degrees of freedom" (<code>TRUE</code>) or not (<code>FALSE</code>)?</dd></dl>

Arguments

Author

U-process minimizer approach to equilibrium testing and double reduction
estimation — hweustat

<dl>

<dt>nvec</dt>
<dd>A vector containing the observed genotype counts,
where <code>nvec[[i]]</code> is the number of individuals with genotype
<code>i-1</code>. This should be of length <code>ploidy+1</code>.</dd>


<dt>thresh</dt>
<dd>The threshold for ignoring the genotype. We keep
genotypes such that <code>nvec &gt;= thresh</code>.
Setting this to <code>0</code> uses all genotypes. Setting this to
<code>NULL</code> uses a heuristic that works well in practice.</dd>


<dt>effdf</dt>
<dd>A logical. Should we use the ad-hoc
"effective degrees of freedom" (<code>TRUE</code>) or not (<code>FALSE</code>)?</dd>

</dl>

hweustat: U-process minimizer approach to equilibrium testing and double reduction estimation

Description

Usage

Value

Arguments

Author

Details

Examples