utils.spautocor: Spatial autocorrelation coefficient calculations

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Spatial autocorrelation coefficient calculations

Description

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

Usage

utils.spautocor(
  GD,
  GGD,
  permutation = FALSE,
  bootstrap = FALSE,
  bins = 10,
  reps
)

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].

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.

Value

Returns a data frame with the following columns:

1. Bin The distance classes

2. N The number of pairwise comparisons within each distance class

3. r.uc The uncorrected autocorrelation coefficient

if both bootstap and permutation are FALSE otherwise only r estimates are returned

Author(s)

Carlo Pacioni & Bernd Gruber

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.

See Also

gl.spatial.autoCorr

Examples

# See gl.spatial.autoCorr

dartR documentation built on June 8, 2023, 6:48 a.m.