Spatial autocorrelation coefficient calculations
Carries out calculation for spatial autocorrelation coefficient starting from a genetic and geogaphic distance matrix.
Genetic distance matrix.
Geographic distance matrix.
Whether permutation calculations for the null hypothesis of no spatial structure should be carried out [default TRUE].
Whether bootstrap calculations to compute the 95% confidence intervals around r should be carried out [default TRUE].
The number of bins for the distance classes (i.e.
length(bins) == 1)or a vectors with the break points. See details [default 5].
The number to be used for permutation and bootstrap analyses [default 100].
Returns a data frame with the following columns:
Bin The distance classes
N The number of pairwise comparisons within each distance class
r.uc The uncorrected autocorrelation coefficient
FALSE otherwise only
r estimates are returned
The code of this function is based one
spautocorr from the package
PopGenReport, which has been modified to fix a few bugs (as of
PopGenReport v 3.0.4 and allow calculations of bootstraps estimates.
See details from
gl.spatial.autoCorr for a detailed explanation.
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.