genotype.index: Genotype indices
In MarcoAndrello/MetaPopGen-2.0: Simulation of metapopulation genetics

Description Usage Arguments Value Author(s) Examples

Functions giving genotype indices as a function of the number of alleles (for a single locus) or the number of allele at each locus (for multiple loci).

1 2	genotype.index(l) genotype.index.multilocus(allele_vec,r,method)

`l`	Number of alleles
`allele_vec`	Vector giving the number of alleles at each locus
`r`	Recombination rate. A single value between 0 and 0.5. For more than two loci, recombination rate must be set to 0.5.
`method`	A string defining the method used to store the genotypes. One of either `"gamete"` or `"genotype"`. For two loci and `r` < 0.5, method must be `"gamete"`.

For genotype.index, a square matrix whose [i,j] element gives the index of the genotype formed by the i and j alleles.

For genotype.index.multilocus, the value depends on the argument method. If method = "gamete", it is a square matrix whose [i,j] element gives the index of the multilocus genotype formed by the i and j gametes. If method = "genotype", it is an n-dimensional array, where n is the number of loci, giving the index of the multilocus genotype formed by the ith single-locus genotype at the first locus, the jth single-locus genotype at the second locus, etc.

Marco Andrello

# Monolocus case:
genotype.index(2)

# Multilocus case:
allele_vec <- c(2,2)
genotype.index.multilocus(allele_vec,r=0.5,method="gamete")
genotype.index.multilocus(allele_vec,r=0.5,method="genotype")