hweustat {hwep}

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

Description

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.

Usage

hweustat(nvec, thresh = NULL, effdf = TRUE)

Arguments

nvec

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

thresh

The threshold for ignoring the genotype. We keep genotypes such that nvec >= thresh. Setting this to 0 uses all genotypes. Setting this to NULL uses a heuristic that works well in practice.

effdf

A logical. Should we use the ad-hoc "effective degrees of freedom" (TRUE) or not (FALSE)?

Details

This is a two-step estimator, where we first obtain a consistent estimate of the double reduction parameter, use this to estimate the covariance of estimators, then use this to obtain our final estimate of the double reduction parameter.

Value

A list with some or all of the following elements:

alpha

The estimated double reduction parameter(s). In diploids, this value is NULL.

chisq_hwe

The chi-square test statistic for testing against the null of equilibrium.

df_hwe

The degrees of freedom associated with chisq_hwe.

p_hwe

The p-value against the null of equilibrium.

Author(s)

David Gerard

Examples

set.seed(1)
ploidy <- 6
size <- 1000
r <- 0.1
alpha <- 0.1
qvec <- hwefreq(r = r, alpha = alpha, ploidy = ploidy)
nvec <- c(rmultinom(n = 1, size = size, prob = qvec))
hweustat(nvec = nvec)