[phylocom-user] icomdist in R

Steven Kembel steve.kembel at gmail.com
Mon Aug 10 09:29:15 PDT 2009


Hi Nicola,

the icomdist function is unfortunately not available in picante yet  
and I'm not sure how you could obtain similar output.

The only thing I can suggest at this point is to try exporting your  
data from R to phylocom format (i.e. using the write.tree and  
writesample functions) and run the analysis in phylocom.

Cheers,
Steve

On Jul 26, 2009, at 12:19 PM, Nicola van Wilgen wrote:

> Dear phylocom list users
>
> I would like to know whether the function "icomdist" which is  
> available
> in phylocom is also available under the package 'picante' in R? I  
> can't
> seem to find it. There is a function 'comdist', but this gives a
> different output from the one I am interested in.
>
> I would appreciate it if anyone could give me some advice on this.
> Perhaps there are a number of other functions which together can  
> give a
> simialr output to icomdist.
>
> Many thanks!
>
> Nicola
>
> "icomdist
> Outputs the mean pairwise distance matrix between each taxon and all
> members of other samples. In the output, AV refers to mean distance,  
> NN
> refers to mean nearest neighbor distance."
>
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> phylocom-user at lists.phylodiversity.net
> http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net




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