picante: species.dist – R documentation

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picante

species.dist

Species co-occurrence distances

Description

Compute interspecific distances based on patterns of species co-occurrence in communities.

Usage

species.dist(x, metric = c("cij", "jaccard", "checkerboard", "doij"))

Arguments

`x`	Community data matrix
`metric`	Co-occurrence metric to use (see Details section for description)

Details

Currently implemented co-occurrence measures (arguments to metric):

cij: Schoener's index of co-occurrence
jaccard: Jaccard index of co-occurrence
checkerboard: Checkerboard index of co-occurrence
doij: DOij index of co-occurrence

Value

A dist object with co-occurrences among all species pairs

Author(s)

Steven Kembel <steve.kembel@gmail.com>

References

Hardy, O.J. 2008. Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. Journal of Ecology 96:914-926.