extract distance from betadisp {vegan}
The distance to centroid for a site isn't a measure of that site's alpha diversity. It is a reflection (an approximation) of the compositional similarity of the sample to the other samples; distances between sites reflect compositional dissimilarity. The value you want are in the `$distances` component of the object returned by `betadisper`. I should add those as one of the options that `scores.betadisper` extracts for you. But I'm not convinced from what you write in your email that this comparison is warranted nor that it will be fruitful nor enlightening. HTH G
On Mon, 2013-04-22 at 22:17 +0000, Mitchell, Kendra wrote:
I've run betadisp on a set of communities and would now like to compare the distance for each sample from it's centroid to other measures such as alpha diversity. Basically I want to check that increased dispersion isn't simply a reflection of overall diversity. It seems like I should be able to pull that out of the disp object but I haven't figured out how. thanks Kendra -- Kendra Maas Mitchell, Ph.D. Post Doctoral Research Fellow University of British Columbia [[alternative HTML version deleted]]
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Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology [f] +1 306 337 2410 Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada