HierAr: Calculating hierarchical allelic richness
In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	HierAr(x, nreg, r, ncode)

`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.

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.

`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

qinxinghu@gmail.com

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.

HierHe; HierFst; HierD

#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