[R-sig-eco] calculate "dispersion index" (betadisper, vegan)

[Jari Oksanen]

Natalie & Zoltan,

I'd be more worried about the effect of outliers on the area of convex hulls. Here an _ad hoc_ definition of outlier: outlier a single point that has a huge effect on the area of an enclosing convex hull.

That said, two points are certainly on a line, and three points can be (almost) on a line. Four or more points can be on a line, but rarely they are.

In vegan, we have function betadisper() that is suggested to be used to measure the dispersion. It may be interesting to compare this to convex hulls. In vegan, summary() of ordihull() result gives the areas of convex hulls (see ?ordihull), and function ordiaretest() runs a permutation test on the areas of convex hulls.

Cheers, Jari Okanen 

On 30/07/2015, at 08:52 AM, Zoltan Botta-Dukat wrote:

> Hi Natalie,
> 
> Be careful with convex hull volume, because it is zero if points lie on a line (an near to zero, if the configuration is close to this), independently from the amount of distances.
> 
> Zoltan
> 
> 2015.07.29. 19:26 keltezéssel, Natalie írta:
>> hi all
>> 
>> I would like to  calculate a dispersion index or similar from the results of the vegan function betadisper.
>> i would like to know if there is a possibility to e.g. calculate the volume of the community dispersion(area of the hull in the PCoA) from the betadisper results.
>> common is to show the distance to the centroid.but I have the impression the dispersion within communities are not that clear,especially if you have similar variance.
>> The program primer v5 calculates a disperion index based on  the similarity percentage.
>> similarity percentage is not an option since it is mainly based on most counted species.
>> 
>> ideas and help are very much appreciated
>> cheers natalie
>> 
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> 
> 
> -- 
> Botta-Dukát Zoltán
> --------------------------------
> Ökológiai és Botanikai Intézet
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> 
> Zoltán BOTTA-Dukát
> --------------------------------
> Institute of Ecology and Botany
> Hungarian Academy of Sciences
> Centre for Ecological Research
> --------------------------------
> H-2163 Vácrátót, Alkomány u. 2-4.
> HUNGARY
> Phone: +36 28 360122/157
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