BiodiversityR (version 1.5)

dist.eval: 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".

Value

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

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.

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/resources/databases/tree-diversity-analysis

Examples

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