habitat_clustering: Do genotypes cluster by microhabitat?

In ellisztamas/simmiad: Simulations of Emmer wheat at the Ammiad kibbutz

Do genotypes cluster by microhabitat?

Description

Calculates how many pairs of plants of the same genotype are also in the same microhabitat.

Usage

habitat_clustering(genotype, habitat)

Arguments

genotype	Vector of genotype labels.
habitat	Vector of habitat labels of the same length as genotype.

Details

This calculates Fst as

\frac{f_0-\bar{f}}{1-\bar{f}}

where f_0 is the probability that two individuals in the same habitat are identical and f \bar{f} is the probability that two individuals from the total population are identical.

Value

Proportion of pairs of individuals in the same habitat that are identical.

Author(s)

Tom Ellis

ellisztamas/simmiad documentation built on Dec. 12, 2023, 5:32 a.m.