[R-sig-eco] Phylogenetic turnover using large datasets

[Jens Ringelberg]

Dear list,

Does anyone happen to have experience with calculating Simpson's pair-wise
phylogenetic dissimilarity for large datasets?

I have tried using betapart’s phylo.beta.pair function to calculate
phylogenetic turnover for a globally-distributed clade with about 1500
taxa, but my machine, which has 125 GB RAM, quickly runs out of memory
while doing so.

Other than increasing RAM, does anyone have any suggestions for calculating
Simpson’s dissimilarity for large datasets? I'm aware of the PhyloMeasures
package, which was designed to work with large datasets, but as far as I
can tell it does not allow one to partition the resulting dissimilarity
index into the true turnover (i.e., Simpson's dissimilarity) and richness
components.

Many thanks in advance.


Jens

PhD student
University of Zurich

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