poppr (version 2.1.1)

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 or snpclone 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 maxi

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 c

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.

See Also

win.ia, samp.ia