R help - Mar 2009 - CCA - manual selection

Hello,

I am trying to obtain f-values for response (independent) variables from a
CCA  performed in vegan package, to see which ones of them have
significative influence in my dependent variables (like the manual selection
in canoco), but I can't find any function (or package) that do such a thing.
The dependents variables are species data, and the independents are
ambiental data.

Than you.

        Fabricius

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Fabricius Domingos <fabriciusm <at> gmail.com> writes:
> 
> Hello,
> 
> I am trying to obtain f-values for response (independent) variables from a
> CCA  performed in vegan package, to see which ones of them have
> significative influence in my dependent variables (like the manual
selection
> in canoco), but I can't find any function (or package) that do such a
thing.
> The dependents variables are species data, and the independents are
> ambiental data.
> 
> Than you.
> 
Dear Fabricius Domingos,

Use add1/drop1 for the vegan object with argument test =
"permutation". For
adding constraints, you need a 'scope' of variables considered for
adding to the
model. 

The following example shows how to do this with vegan package and one of its
standard data sets:
> library(vegan)
> data(mite)
> data(mite.env)
> mbig <- cca(mite ~ ., mite.env)
> m0 <- cca(mite ~ 1, mite.env)
> add1(m0, scope = formula(mbig), test="perm")
> m0 <- update(m0, . ~ . + Topo)
> add1(m0, scope = formula(mbig), test="perm")
> m0 <- update(m0, . ~ . + WatrCont)
You can also see if some of the included variables should be dropped:
> drop1(m0, test="perm")
The usage of add1.cca is explained on its help page (see ?add1.cca).

Cheers, Jari Oksanen