Rarefaction

[oko...@gmail.com]

Hi there,

does anyone know if I can use Poppr to do a rarefaction of genotypic diversity if genotypic diversity is already known? 

I already determined that there are clones in my dataset of two populations, calculated number of genotypes in each population. The sample sizes are unequal and I would like to also estimate eMLG corrected to the smallest sample size. The original paper by Hurlbert 1971 is over my head and I struggle to find a separate tool for this.

Will be grateful for any suggestions.

Thanks,

Olga

[Zhian Kamvar]

Hi Olga,

If you have a table of the MLGs and know the dosage of each MLG (e.g. the results of mlg.table() in poppr), then you can pass it to vegan::rarefy() and specify a minimum sample size to rarefy to. 

This is the procedure that the poppr() function uses to calculate eMLG.

I hope that helps,

Zhian

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