spautocor: Spatial autocorrelation following Smouse and Pekall 1999

Description

Global spatial autocorrelation is a multivariate approach combining all loci into a single analysis. The autocorrelation coefficient r is calculated for each pairwise genetic distance pairs for all specified distance classes. For more information see Smouse and Peakall 1999, Peakall et a. 2003 and Smouse et al. 2008.

Usage

spautocor(gen.m, eucl.m, shuffle=FALSE, bins=10)

Arguments

gen.m

a matrix of individual pairwise genetic distances. Easiest to use gd_smouse or gd_kosman to create such a matrix, but in priniciple any other squared distance matrix can be used. see example

eucl.m

A euclidean distance matrix, based on the coordinates of individuals. see example

shuffle

used internally for the permutation calculation

bins

number of bins for the distance classes. Currently only even bins are supported.

Value

Returns a data frame with r values and number of distances within each distance class.

References

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

Double, MC, et al. 2005. Dispersal, philopatry and infidelity: dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus). Evolution 59, 625-635.

Peakall, R, et al. 2003. Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat, Rattus fuscipes. Evolution 57, 1182-1195.

Smouse, PE, et al. 2008. A heterogeneity test for fine-scale genetic structure. Molecular Ecology 17, 3389-3400.

Gonzales, E, et al. 2010. The impact of landscape disturbance on spatial genetic structure in the Guanacaste tree, Enterolobium cyclocarpum(Fabaceae). Journal of Heredity 101, 133-143.

Beck, N, et al. 2008. Social constraint and an absence of sex-biased dispersal drive fine-scale genetic structure in white-winged choughs. Molecular Ecology 17, 4346-4358.

Examples

Run this code

#not run:
#data(bilby)
#popgenreport(bilby, mk.spautocor=TRUE, mk.pdf=FALSE)
#to get a pdf output you need to have a running Latex version installed on your system.
#popgenreport(bilby[1:50], mk.spautocor=TRUE, mk.pdf=TRUE)