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I have generated a functional trait dendrogram using species x trait and plots x species matrices through dbFD in package FD. I want to randomize the tips of the trait dendrogram to check if community assembly of the trees in my study area is random or if their are functional differences between plots. I have the vectors for functional richeness, evenness, and dispersion from the dbFD output.

Can someone please help me with the next step of how to infer community assembly mechanisms? Could I just randomize the species composition in plots and re-run the analyses. This implies that I shuffle my original dataset, create a new community matrix each time, and run that in dbFD to get indices for functional diversity?

chl
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Meghna Krishnadas
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  • I am no expert on the matter but the basic idea of having a dendrogram is that it induces a non-arbitrary covariance function between your points (eg. OU - the "Hansen" model). A very "rough" way to check if there is "phylogenetic signal" would be to use a second, star-phylogeny, that assumes no complex phylogenetic relations between your tips and compare your phylogenetic means. Additionally you could keep the same dentrogram and mixing the tips at the reading and then estimate their likelihood under your model of evolution. Simplify the terminology you use to get better answers. – usεr11852 Mar 28 '13 at 18:53

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