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

In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

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

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.

Value

pwDeltaD.obs	The observed value of allelic differentiation Delta D
pwalltests	The test results of pairwise Delta D

Author(s)

[e-mail]

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

f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
permutate.DeltaD=function(infile,ncode=3,permutations=999)

HierDpart documentation built on March 31, 2021, 5:09 p.m.