Fstat.output {Geneland}R Documentation

Computes F statistics on the output of an inference by MCMC simulation

Description

Computes F statistics according to Weir and Cockerham's estimators. Missing values are allowed but as of today, the NA code is only treated as an extra allele which might bias the result. This function should not be used on haploid data.

Usage

Fstat.output(coordinates,genotypes,ploidy,burnin,path.mcmc)

Arguments

coordinates Matrix with one line per individual and two columns
genotypes Genotypes of individuals. A matrix with one line per individual and 2 columns per locus
burnin Integer: number of saved iterations to discard.
ploidy Integer: 1 or 2 (default is 2). Do not use for haploid data.
path.mcmc Path to output files directory

Value

A list with components

Pairwise.Fis A matrix of real numbers estimating the pairwise Fis
Pairwise.Fst A matrix of real numbers estimating the pairwise Fst

Author(s)

Arnaud Estoup for original code in Turbo Pascal.

Translation in Fortran and interface with R by Gilles Guillot

References

Weir, B.S. and C.C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, 1984, vol. 38, 1358-1370.


[Package Geneland version 3.1.4 Index]