simufreqD: Function to simulate allele frequencies for independent loci from a Dirichlet model
Description
The simufreqD function simulate single population allele frequencies for independent loci.
Allele frequencies are generated as random deviates from a Dirichlet distribution, whose parameters control
the mean and the variance of the simulated allele frequencies.
Usage
simufreqD(nloc = 1, nal = 2, alpha = 1)
Arguments
nloc
the number of loci to simulate
nal
the numbers of alleles per locus. Either an integer, if the loci have the same number of
alleles, or an integer vector, if the number of alleles differ between loci
alpha
the parameter used to simulate allele frequencies from the Dirichlet distribution. If the
nloc loci have the same allele number,
alpha can either be the same for all alleles (default is one: uniform distribution), in this
Value
A matrix containing the simulated allele frequencies. The data is presented in the format of the Journal of
Forensic Sciences for genetic data: allele names are given in the first column, and frequencies for a given allele are read in rows for the
different markers in columns. When an allele is not observed for a given locus, the value is coded NA (instead of "-" in the
original format).
encoding
UTF-8
Details
Allele frequencies for independent loci are simulated using a Dirichlet distribution with parameter
alpha. At a given locus L with n alleles, the allele frequencies are modeled as a vector of random
variables
p=(p1, ..., pn), following a Dirichlet distribution with parameters:
alpha = (alpha1, ..., alphan) where p1+...+pn=1 and alpha1,..., alphan > 0.
References
Johnson NL, Kotz S, Balakrishnan N. Continuous Univariate Distributions, vol 2. John Wiley & Sons, 1995.
Wright S. The genetical structure of populations. Ann Eugen 1951;15:323-354.