HierDpart (version 1.5.0)

HierAr: Calculating hierarchical allelic richness

Description

This function calculates hierarchical allelic richness for populations structured in any hierarchy.

Usage

HierAr(x, nreg, r, ncode)

Arguments

x

The data file, genepop format.

nreg

Number of aggregate in your hierarchical structure.

r

The number of subaggregate in your hierarchical structure.

ncode

Coding type of genetic data.

Value

Ar_pop

Allelic richness for each population per locus

Hierareco

Total allelic richness

Ar_reg

Allelic richness for each aggregate (eg. region)

Hierar_loc

Allelic richness per locus for each aggregate (eg. region)

Ar_overall

Hierarchical allelic richness at different hierarchical levels

Details

This function calculates the hierarchical allelic richness for metapopulations structured in any hierarchy. In this function, you can input your genepop file (x) and structure (nreg, r) of your data in the arguments, and then returns a matrix of your hierarchical Ar. This is very efficient than other functions.

References

El Mousadik A. and Petit R.J. (1996) High level of genetic differentiation for allelic richness among populations of the argan tree argania spinosa skeels endemic to Morocco. Theoretical and Applied Genetics, 92:832-839

Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5(1), 184-186.

See Also

HierHe; HierFst; HierD

Examples

# NOT RUN {
#we want to calculate the hierarchical allelic richness of
#16 populations structured in a 4 regions.
#Each region contains 7,4,2,3 populations.
# example genepop file
f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
HAr=HierAr(infile, nreg=4, r=c(7,4,2,3), ncode=3)
HAr
# }