taxondist: Clarke's Taxonomic Community Dissimilarity

In jarioksa/natto: An Extreme 'vegan' Package of Experimental Code

Clarke's Taxonomic Community Dissimilarity

Description

Taxonomic dissimilarity takes into account related species when there is no exact species match in compared communities. This function returns generalizations of Bray-Curtis and Kulczynski indices (Clarke _et al._ 2006).

Usage

taxondist(x, d, method = c("gamma", "theta"), dmax)

Arguments

x	Community data; will be treated as binary presence/absence matrix.
d	Taxonomic, phylogenetic or other dissimilarities among species (columns of x).
method	Type of returned dissimilarity index. Gamma is generalized Bray-Curtis, and Theta generalized Kulczynski index.
dmax	Scale dissimilarities by dmax (if dmax > max(d)) or truncate dissimilarities at dmax (if dmax < max(d)).

Details

When a species occurs only in one of two compared communities, the species will increase dissimilarity of two communities with one species. However, if the other communities contains related species, the increase will be less depending on the relatedness of species (Clarke _et al._ 2006). The degree of relatedness is defined by taxonomic or other taxon dissimilarities.

The current function generalizes Bray-Curtis and Kulczynski indices (see canneddist) for binary (presence-absence) data by taking the dissimilarity to most closely related species as the increase of dissimilarity, instead of 1 of basic index. If species dissimilarities have any values over 1, they will be scaled by observed maximum. Alternatively, user can specify maximum species dissimilarity (argument 'dmax') for scaling, and if it is lower than data maximum, higher values will be truncated to scaled value 1. This allows imposing stricter concept of relatedness so that, say, taxa in different orders will be regarded as completely unrelated.

Although the function was proposed and is named as taxonomic dissimilarity, the function can be used with phylogenetic, functional or trait dissimilarities.

Function distrao provides an alternative index that can handle quantitative data and produce indices related to Euclidean distance.

Value

Clarke's taxonomic dissimilarity index as defined in method.

References

Clarke, K.R., Somerfield, P.J. & Chapman, M.G. (2006). On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages. _J. Exp. Marine Biol. & Ecol._ 330, 55-80.

See Also

distrao is an alternative taxonomic distance measure. The index is closely related to Clarke's taxonomic diversity indices which are available in vegan function taxondive. Vegan function taxa2dist can be used to find taxonomic dissimilarities from classification table.

Examples

if (require(vegan)) {
data(dune, dune.phylodis)
## phylogenetic data, but regard lineaages completely distict
## beyond K/T (K/Pg) age limit
d <- taxondist(dune, dune.phylodis, dmax = 65.2)
polarord(d)
}

jarioksa/natto documentation built on Feb. 20, 2025, 3:29 p.m.