[R-sig-eco] Extract residuals from adonis function in vegan package

[Ivailo]

On Tue, Mar 18, 2014 at 5:02 PM, Alicia Valdés
<aliciavaldes1501 at gmail.com> wrote:
...
> However, what I attempt to do is to perform an indicator species analysis
> (ISA) with these residuals. I want to see if I can find species which are
> indicators for different environmental conditions, but first I would like
> to remove the differences in species composition due to the study region
> (which accounts in fact for a big part of the differences in species
> composition). I am using the packages indicspecies and labdsv for ISA but
> in none of the cases did I found a way of including this as, for example, a
> block variable, that's what I attempt to get the residuals.

Alicia,

following up on my previous comment, I think you might use the regions
as a typology on which to base your ISA. So you'll get the
characteristic species for each region and there is no need to
"account" for differences in species composition among regions
(moreover, I fail to understand why one might need to do so).

If you take a look at the help page for multipatt() in indicspecies,
you'll see that you need a community data table (your presence/absence
matrix) and a site classification (your "regions" if these are not
further classified into meaningful clusters; although you didn't
provide more details on how the forest patches relate to the regions
you wrote about) to run the analysis.

HTH,
Ivailo
-- 
"The cure for boredom is curiosity. There is no cure for curiosity." --
Dorothy Parker