PopGenReport (version 1.01)

gd_smouse: 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).

Usage

gd_smouse(population, verbose = TRUE)

Value

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

References

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

See Also

popgenreport

Examples

data(bilby)
#here we use only the first 50 individuals to speep up the example
popgenreport(bilby[1:50], 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)