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. 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.
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
see Gerard (2023a) doi:10.1111/biom.13722
and
Gerard (2023b) doi:10.1111/1755-0998.13856
.
Main Functions
hwefit()
Fit either hwelike()
,
rmlike()
, hweustat()
, or
hwenodr()
across many loci.
Parallelization is supported through the future package.
hwelike()
Likelihood inference for equilibrium.
This function estimates the rate of double reduction given
equilibrium, and tests for at most small deviations from
equilibrium.
rmlike()
Likelihood inference for random
mating in polyploids. This function tests for random mating
and estimates gametic frequencies given random mating.
This function does not assume a model for meiosis.
hweustat()
U-statistic approach for equilibrium
and double reduction. This function tests for equilibrium given
double reduction rates and estimates these rates given equilibrium.
hwenodr()
Implements a likelihood ratio test
that tests for equilibrium in autopolyploids given no double reduction.
hweboot()
Implements a bootstrap approach to test
for equilibrium which is more appropriate for small samples and
uncertain genotypes.
Other Functions
dgamete()
Gamete dosage probability given
parental dosage.
drbounds()
Upper bounds on the rates of double
reduction given the complete equational segregation model.
freqnext()
Update genotype frequencies after one
generation of random mating.
gsegmat()
Gamete dosage probabilities for all
possible parental dosages.
hwefreq()
Generate equilibrium
genotype frequencies.
p_from_alpha()
Obtain gamete frequencies from
the major allele frequency and double reduction rates.
zsegarray()
All zygote dosage distributions
given all possible parental dosages.
zygdist()
Zygote dosage distribution given
one pair of parental dosages.
Citation
If you find the methods in this package useful, please run the following
in R for citation information: citation("hwep")