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CCA - manual selection
2 messages · Fabricius Domingos, Jari Oksanen
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