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

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

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

Author(s)

[e-mail]

References

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

Examples

# example genepop file
f1 <- function(f) system.file("extdata", f,package="HierDpart")
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(f1("Island.gen"),ncode=3,level1$region,permutations=999)
hiertest

xinghuq/HierDpart documentation built on March 21, 2023, 6:43 p.m.