Calculate Allele Frequencies

Calculates population allele frequencies from data, adjusting for COI.

Usage

calcAfreq(dsmp, coi, tol = 1e-04, qstart = 0.5)

Arguments

dsmp

a list with each element corresponding to one sample.

coi

a vector containing complexity of infection for each sample.

tol

convergence tolerance for frequency estimates.

qstart

a starting value for frequencies.

Value

A list of allele frequencies, where each element is a numeric vector containing frequencies for a single locus.

Examples

coi   <- getCOI(dsmp, lrank = 2)           # estimate COI first
afreq <- calcAfreq(dsmp, coi, tol = 1e-5)