I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")
I have two questions:
- What does "error" stand for?
- How do I calculate Fst? Which values do I have to use?
A genind object in R is an object which contains allelic information about a set of individuals.
This is the table that I get:
Analysis of Molecular Variance Call: amova(formula = plantula.dist ~ g, nperm = 100) SSD MSD df g 354992.9 354992.9297 1 Error 310814.9 693.7834 448 Total 665807.9 1482.8683 449 Variance components: sigma2 P.value g 1574.69 0 Error 693.78 Variance coefficients: a 224.9956