HierDpart (version 1.5.0)

permutate.DeltaD: Permutation test for allelic differentiation (Delta D)

Description

This function performs permutations for pairwise comparison of allelic differentiation.

Usage

permutate.DeltaD(file, ncode, permutations)

Arguments

file

Genepop file

ncode

Genotype coding

permutations

Number of permutations

Value

pwDeltaD.obs

The observed value of allelic differentiation Delta D

pwalltests

The test results of pairwise Delta D

%% ...

Details

This function runs slowly because the permutations work on the random sampling of the individuals from raw data and calculating the statistics every iteration. The permutation test here shuffles the individuals and samples the individuals to calculate the Delta D every permutation. Significance of the allelic differentiation is obtained from Monte-Carlo test.

References

Thioulouse, J., & Dray, S. (2007). Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages. Journal of Statistical Software, 22(5), 1-14.

Examples

# NOT RUN {
f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
permutate.DeltaD=function(infile,ncode=3,permutations=999)
# }