pwag.permutest: Permutation test for allelic differentiation (Delta D) among...

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

Description

This test examines the allelic differentiation (Delta D) among subaggregates within aggregate. The permutation works on the pairwise allelic differentiation between subaggregates within different aggregates.

Usage

pwag.permutest(f, ncode, group, permutations)

Arguments

f	Genepop file
ncode	The number coding genotypes
group	The group or level of the aggregates
permutations	Number of permutations

Value

pwpermutest.detail	Permutation test detail of the pairwise difference between aggregates
pwtest.aggregate	Pairwise permutation P-value between aggregates

Author(s)

[e-mail]

References

Anderson, M. J. (2014). Permutational multivariate analysis of variance (PERMANOVA). Wiley StatsRef: Statistics Reference Online, 1-15.

Examples

f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
region1=paste("region",rep(1,time=6))
region2=paste("region",rep(2,time=6))
region3=paste("region",rep(3,time=2))
region4=paste("region",rep(4,time=2))

level1=data.frame(matrix(data=0,nrow=16,ncol=1))
level1[1:6,1]=region1
level1[7:12,1]=region2
level1[13:14,1]=region3
level1[15:16,1]=region4
colnames(level1)=c("region")
pwag.permutest(infile, ncode=3, group=level1$region, permutations=999)

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