gd.smouse: Individual genetic distance calculation based on Smouse and...
In PopGenReport: A Simple Framework to Analyse Population and Landscape Genetic Data

gd.smouse

R Documentation

Individual genetic distance calculation based on Smouse and Peakall 1999

Description

Calculate pairwise genetic distances between all individuals using the individual genetic distance measure of Smouse and Peakall (1999). This function should produce the same results as the individual genetic distances calculated using GenAlEx and choosing the interpolate missing data option. Note that depending on your computers capabilities, you may run into memory errors when this function is used on datasets with large numbers of individuals (>1000). Additionally, the time for this function to run can be quite lengthy. Using a PC with a 3.5 GHz processor to calculate pairwise genetic distances between individuals with 36 diploid loci it took 2 seconds for 100 individuals, 51 seconds for 500 individuals, 200 seconds for 1000 individuals, 836 seconds (~14 minutes) for 2000 individuals, and 1793 seconds (~30 minutes) for 3000 individuals. Please note that for each of your population groupings there must be at least one individual with genotyped alleles for each locus (it doesn't have to be the same individual for every locus). If a population doesn't meet this requirement, it will be dropped from the analysis and a warning message will be generated.

Usage

gd.smouse(population, verbose = TRUE)

Arguments

`population`	this is the `genind` object that the analysis will be based on.
`verbose`	information on progress. For large data sets this could be informative as it allows the user to estimate the amount of time remaining until the function is complete. The counter shows the number of the population for which genetic distances are currently being determined.

Value

Returns pairwise individual genetic distances for each individual within a population.

Author(s)

Aaron Adamack, aaron.adamack@canberra.edu.au

References

Smouse PE, Peakall R. 1999. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82: 561-573.

Examples


## Not run: 
data(bilby)
popgenreport(bilby, mk.gd.smouse = TRUE, mk.pdf=FALSE)
#to get a pdf output you need to have a running Latex version installed on your system.
#popgenreport(bilby, mk.gd.smouse = TRUE, mk.pdf=TRUE)

## End(Not run)

PopGenReport documentation built on Oct. 11, 2023, 9:07 a.m.