poppr (version 2.1.0)

bitwise.ia: Calculate the index of association between samples in a genlight object.

Description

This function parses over a genlight object to calculate and return the index of association for those samples.

Usage

bitwise.ia(x, missing_match = TRUE, differences_only = FALSE, threads = 0)

Arguments

x

a genlight object.

missing_match

a boolean determining whether missing data should be considered a match. If TRUE (default) missing data at a locus will match with any data at that locus in each comparison. If FALSE, missing data at a locus will cause all comparisons to return the maximu

differences_only

a boolean determining how distance should be counted for diploids. Whether TRUE or FALSE the distance between a heterozygous locus and a homozygous locus is 1. If FALSE (default) the distance between opposite homozygous loci is 2. If TRUE that distance co

threads

The maximum number of parallel threads to be used within this function. A value of 0 (default) will attempt to use as many threads as there are available cores/CPUs. In most cases this is ideal. A value of 1 will force the function to run serially, which

Value

• Index of association representing the samples in this genlight object.