# Spatial autocorrelation coefficient calculations

`utils.spautocor.Rd`

Carries out calculation for spatial autocorrelation coefficient starting from a genetic and geogaphic distance matrix.

## Arguments

- GD
Genetic distance matrix.

- GGD
Geographic distance matrix.

- permutation
Whether permutation calculations for the null hypothesis of no spatial structure should be carried out [default TRUE].

- bootstrap
Whether bootstrap calculations to compute the 95% confidence intervals around r should be carried out [default TRUE].

- bins
The number of bins for the distance classes (i.e.

`length(bins) == 1)`

or a vectors with the break points. See details [default 5].- reps
The number to be used for permutation and bootstrap analyses [default 100].

## Value

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

if both `bootstap`

and `permutation`

are `FALSE`

otherwise only
`r`

estimates are returned

## Details

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.

## 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.