Genetic Distance Calculation

This function calculates Nei's genetic distance (Nei 1972) between populations or individuals

Usage

stamppNeisD(geno, pop = TRUE, measure = "standard")

Arguments

geno

a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels

pop

logical. True if genetic distance should be calculated between populations, false if it should be calculated between individual

measure

a character string defining the distance measure to use: "standard" for the Neis standard genetic distance 1972 or "DA" for Neis DA distance 1983.

Value

A object of class matrix which contains the genetic distance between each population or individual

References

Nei M (1972) Genetic Distance between Populations. The American Naturalist 106, 283-292.

Author

Luke Pembleton <lpembleton at barenbrug.com>

Examples

# import genotype data and convert to allele frequecies
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")
# Calculate genetic distance between individuals
potato.D.ind <- stamppNeisD(potato.freq, FALSE, "standard")
# Calculate genetic distance between populations
potato.D.pop <- stamppNeisD(potato.freq, TRUE, "standard")