[R-sig-eco] extract distance from betadisp {vegan}

[Mitchell, Kendra]

Excellent, thank you.  I'm working with soil bacterial communities which have incredibly high diversity so insufficient sampling is often behind what initially looks like an interesting pattern.  If the increased dispersion in certain groups is related to some underlying ecology (such as response to disturbance), I'd expect little relationship between dispersion and alpha diversity.  But if the increased dispersion is just a byproduct of having only 1500 observations of a community that is likely made up of 10^6 organisms, there will likely be a relationship.  at least that's my current hypothesis.


--
Kendra Maas Mitchell, Ph.D.
Post Doctoral Research Fellow
University of British Columbia

________________________________________
From: Gavin Simpson [gavin.simpson at ucl.ac.uk]
Sent: Monday, April 22, 2013 3:41 PM
To: Mitchell, Kendra
Cc: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] 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
>
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>
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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