HierDpart (version 1.5.0)

Hierpertest: Test the significance among aggregates (regions, ecosystems...)

Description

Permutation test of the significance among aggregates,e.g., test the significance of the allelic differentiation within ecosystem among different regions

Usage

Hierpertest(f, ncode, level, permutations)

Arguments

f

Input file, genepop format

ncode

Genotype coding type, whether 2 digital or 3 digital

level

The hierarchical level you want to test

permutations

permutations

Value

pertest

Permutation test result for the level you specified

%% ~Describe the value returned %% If it is a LIST, use %% \item{comp1 }{Description of 'comp1'} %% \item{comp2 }{Description of 'comp2'} %% ...

References

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

Examples

# NOT RUN {
# example genepop file
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")

hiertest=Hierpertest(infile,ncode=3,level1$region,permutations=999)
hiertest
# }