allelic.richness: Estimates allelic richness

Description Usage Arguments Value Author(s) References Examples

Description

Estimates allelic richness, the rarefied allelic counts, per locus and population

Usage

1

Arguments

data

A data frame, with as many rows as individuals. The first column contains the population to which the individual belongs, the following to the different loci

min.n

The number of alleles down to which the number of alleles should be rarefied. The default is the minimum number of individuals genotyped (times 2 for diploids)

diploid

a boolean specifying wether individuals are diploid (default) or haploid

Value

min.all

The number of alleles used for rarefaction

Ar

A table with as many rows as loci and columns as populations containing the rarefied allele counts

Author(s)

Jerome Goudet jerome.goudet@unil.ch

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

Hurlbert S.H. (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52:577-586

Petit R.J., El Mousadik A. and Pons O. (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology, 12:844-855

Examples

1
2

Example output

$min.all
[1] 10

$Ar
          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7] [,8]
L21.V 1.999799 1.670290 3.533590 2.551478 1.000000 1.000000 1.000000    1
L37.J 2.622531 1.995917 2.561729 2.956688 1.965217 1.000000 1.000000    1
L20.B 1.878261 1.905797 1.961922 1.333333 1.999433 1.000000 1.563218    1
L29.V 1.999799 1.905797 2.763370 1.823207 1.000000 1.000000 1.000000    1
L36.B 1.998492 1.995917 2.913167 2.332967 1.630769 1.000000 1.000000    1
L16.J 1.982609 1.998469 2.438424 2.896635 1.000000 1.995917 1.563218    1
          [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]
L21.V 1.000000 1.000000 1.998452 1.998452 2.349833 2.760993 1.595238 1.563218
L37.J 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.357143 1.934723
L20.B 1.000000 1.563218 1.714286 1.000000 1.630769 1.000000 1.000000 1.000000
L29.V 1.000000 1.000000 2.984520 2.919945 1.996339 2.629249 2.190476 2.714412
L36.B 1.000000 1.000000 2.930681 1.998452 2.015385 3.226756 1.996666 2.332653
L16.J 1.714286 1.000000 1.969925 1.999558 1.878261 1.982609 1.595238 2.757930
         [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
L21.V 1.000000 1.000000 1.998492 1.912821 2.454423 1.000000 1.999385 1.000000
L37.J 1.823207 1.563218 1.784615 1.985921 1.000000 1.000000 1.850549 1.000000
L20.B 1.000000 1.000000 1.000000 1.750916 1.993851 1.000000 1.999343 1.000000
L29.V 1.823207 1.333333 1.996339 1.965217 1.998541 1.000000 1.996666 1.000000
L36.B 2.386426 1.563218 2.261538 1.912821 1.563218 1.992961 2.541696 1.993851
L16.J 1.891205 1.978477 2.622531 1.991762 1.999800 1.000000 1.978477 1.000000
         [,25]    [,26]    [,27] [,28] [,29]
L21.V 1.905797 2.000000 1.894737     2     2
L37.J 1.905797 1.999875 1.983746     2     2
L20.B 1.905797 1.875000 1.500000     2     2
L29.V 2.816069 1.625000 2.981841     3     3
L36.B 1.416667 2.589286 1.994582     2     2
L16.J 1.670290 1.964286 1.983746     2     2

hierfstat documentation built on Nov. 17, 2021, 5:08 p.m.