allel.rich: Calculates the allelic richness for a genind object

Description

The function calculates the allelic richness for each combination of population and locus for a genind object. To account for differences in sample sizes and genotyping success, rarefication is used in the calculation. The sample size for each combination of population and locus was set equal to the smallest number of alleles seen in a sample across all combinations of population and locus. Allelic richness was calculated using the methods of Mousadik and Petit (1996) which are in turn based upon the work of Hurlbert (1971).

This function is similar to the allelic.richness function in hiefstat. The main differences between the two packages are that allel.rich works on a genind object while allelic richness works on a data frame and allel.rich is capable of determining allelic richness for species with most ploidies while allelic.richness only works for haploid and diploid species.

Usage

allel.rich(population, min.alleles = NULL)

Arguments

population

a genind object (from package adegenet)

min.alleles

the minimum number of alleles that will be sampled for calculating allelic richness. If min.alleles is set to NULL the min.alleles sampled will be determined automatically (see description)

Value

Returns a list with the following entries:all.richness is the allelic richness for each combination of population and locus sum.richness is the sum of the allelic richnesses for each population mean.richness is the mean allelic richness across all loci alleles.sampled is the smallest number of individuals sampled across all combinations of population and locus multiplied by the ploidy of the species. pop.sizes is a matrix with the total number of alleles counted for each combination of population and locus.

References

El Mousadik A, Petit RJ. (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco

Examples

Run this code

 #not run:
 #data(bilby)
 #here we use only the first 50 individuals to speep up the example
 #popgenreport(bilby, mk.allel.rich=TRUE, mk.pdf=FALSE)
 
#to get a pdf output you need to have a running Latex version installed on your system.
#popgenreport(bilby, mk.allel.rich=TRUE, mk.pdf=TRUE)

#data(bilby)
#allel.rich(bilby)