Hi Dave,

I used the indval function from the package labdsv (your package Dave, I
believe) and confirmed these results with output from the indicspecies
package. I want to use all the species to construct the PCA ordination but
only want to show the species vectors for those 27 species identified as
significant group discriminators.

Andy

On Sun, May 22, 2011 at 1:19 AM, Dave Roberts <
dvrbts@ecology.msu.montana.edu> wrote:

> 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
>>
>
> --
> Andrew,
>
>   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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>



-- 
Andrew Halford Ph.D
Associate Research Scientist
Marine Laboratory
University of Guam
Ph: +1 671 734 2948

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