[R-sig-eco] controlling the species displayed on a biplot

Dave Roberts dvrbts at ecology.msu.montana.edu
Sat May 21 17:19:16 CEST 2011

On 05/20/2011 11:54 PM, Andrew Halford wrote:
> Hi All,
> I have done a IndVal analysis on a dataset which has identified 27 species
> out of 57 as being significant arbiters of site differences. What I want to
> do is a PCA biplot (data is hellinger transformed prior to this) with only
> these 27 species on the ordination, not all 57, How can I control the
> species I want displayed?
> cheers
> Andy


    We need a little more information.  Which IndVal function did you 
use?  It should return a vector of p-values you can use as a mask [p-val 
<= 0.05,] on your taxon matrix.  But are you saying you want to use all 
57 in constructing the PCA and only identify 27, or that you only want 
to use those 27 in the construction of the PCA?

Dave Roberts

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