freqnext {hwep}

Update genotype frequencies after one generation

Description

After one generation of random mating, update the genotype frequencies.

Usage

freqnext(freq, alpha, segmat = NULL, more = FALSE, check = TRUE)

Arguments

freq

The current genotype frequencies. This should be a vector of length K+1, where K is the ploidy of the species. freq[i] could contain the proportion of individuals that have genotype i-1.

alpha

A numeric vector containing the double reduction parameter(s). This should be a vector of length floor(ploidy/4) where alpha[i] is the probability of exactly i pairs of IBDR alleles being in the gamete. Note that sum(alpha) should be less than 1, as 1 - sum(alpha) is the probability of no double reduction.

segmat

You can provide your own segregation matrix. segmat[i, j] is the probability that a parent with dosage i-1 produces a gamete with dosage j-1.

more

A logical. Should we return more output (TRUE) or less (FALSE). See the Value section for details.

check

Should we correct for minor numerical issues? Defaults to TRUE.

Value

If more = FALSE, then returns a vector of length length(freq) that contains the updated genotype frequencies after one generation of random mating. If more = TRUE, then returns a list with these genotype frequencies (q) as well as the parental gamete frequencies (p).

Author(s)

David Gerard

Examples

freq <- c(0.5, 0, 0, 0, 0.5)
freqnext(freq = freq, alpha = 0)