dist.eval {BiodiversityR}R Documentation

Distance Matrix Evaluation

Description

Provides one test of a distance matrix, and continuous with distconnected (vegan).

Usage

dist.eval(x,dist)

Arguments

x Community data frame with sites as rows, species as columns and species abundance as cell values.
dist Method for calculating ecological distance with function vegdist: partial match to "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "morisita", "horn" or "mountford".

Details

This functions provides two tests of a distance matrix.

The first test checks whether any pair of sites that share some species have a larger distance than any other pair of sites that do not share any species. In case that cases are found, then a warning message is given.

The second test is the one implemented by the distconnected function (vegan). The distconnected test is only calculated for distances that calculate a value of 1 if sites share no species (i.e. not manhattan or euclidean), using the threshold of 1 as an indication that the sites do not share any species. Interpretation of analysis of distance matrices that provided warnings should be cautious.

Value

The function tests whether distance matrices have some desirable properties and provide warnings if this is not the case.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp

Examples

library(vegan)
data(dune)
dist.eval(dune,"euclidean")
dist.eval(dune,"bray")

[Package BiodiversityR version 1.2 Index]