geco: geco distance matrix

In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

geco distance matrix

Description

Computes geco distances between the columns of a 0-1-matrix, based on a distance matrix between regions (usually, but not necessarily, this is a geographical distance).

Usage

geco(regmat,geodist=as.dist(matrix(as.integer(!diag(nrow(regmat))))),
                   transform="piece",
                   tf=0.1,
                   countmode=ncol(regmat)+1)

Arguments

regmat	0-1-matrix. Columns are species, rows are regions.
geodist	dist-object or symmetric non-negative matrix. Geographical distances between regions.
transform	transformation applied to the distances before computation of geco coefficient, see details. "piece" means piecewise linear, namely distance/(tf*maximum distance) if distance<tf*maximum distance, and 1 otherwise, "log" means log((tf*distance)+1), "sqrt" means sqrt(tf*distance), "none" means no transformation.
tf	tuning constant for transformation. See transform.
countmode	optional positive integer. Every 'countmode' algorithm runs 'geco' shows a message.

Details

The geco distance between two species is 0.5*(mean distance between region where species 1 is present and closest region where species 2 is present plus mean distance between region where species 2 is present and closest region where species 1 is present). 'closest' to a region could be the regions itself. It is recommended (Hennig and Hausdorf, 2006) to transform the distances first, because the differences between large distances are usually not meaningful or at least much less meaningful than differences between small distances for dissimilarity measurement between species ranges. See parameter transform.

If the between-regions distance is 1 for all pairs of non-equal regions, the geco distance degenerates to the Kulczynski distance, see kulczynski.

Value

A symmetrical matrix of geco distances.

Author(s)

Christian Hennig [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

References

Hennig, C. and Hausdorf, B. (2006) A robust distance coefficient between distribution areas incorporating geographic distances. Systematic Biology 55, 170-175.

See Also

kulczynski

Examples

options(digits=4)
data(kykladspecreg)
data(waterdist)
geco(t(kykladspecreg),waterdist)

prabclus documentation built on Sept. 24, 2024, 5:07 p.m.