hweboot {hwep}

Bootstrap procedure to test for equilibrium

Description

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

Usage

hweboot(n, nboot = 2000, more = FALSE)

Arguments

n

One of two forms

A vector of length ploidy + 1

Element i is the number of individuals with genotype i.

A matrix with nsamp rows and ploidy+1 columns

Element (i, j) is the posterior probability that individual i has ploidy j-1.

nboot

The number of bootstrap samples to run.

more

A logical. Should we return the bootstrap replicates (FALSE) or just the p-value, with 95% confidence interval of the p-value (TRUE).

Value

A list with some or all of the following elements

p_hwe

The bootstrap p-value against the null of equilibrium.

p_ci

The 95% confidence interval of p_hwe.

alpha_boot

The bootstrap samples of the double reduction parameter.

u_boot

The bootstrap samples of the U-statistic.

Author(s)

David Gerard

Examples

set.seed(1)
ploidy <- 6
size <- 100
r <- 0.5
alpha <- 0.1
qvec <- hwefreq(r = r, alpha = alpha, ploidy = ploidy)
nvec <- c(rmultinom(n = 1, size = size, prob = qvec))
bout <- hweboot(n = nvec, more = TRUE, nboot = 1000)
bout$p_hwe
bout$p_ci
hist(bout$test_boot)
abline(v = bout$test_stat, lty = 2, col = 2)