[Biomod-commits] Predictors automatically dropped from models?

Jonathan Heubes Jonathan.Heubes at senckenberg.de
Mon Aug 8 17:31:44 CEST 2011

I am currently working with R 2.13.0 and Biomod 1.1-6.9.
I discovered that predictors are automatically dropped from GAM/GLM
models, when their importance (via VarImportance) is zero. Is BIOMOD
intended to work like that? Are there any possibilities to suppress the
dropping? I am asking, because the evaluation of variable importance can
be extremely different, pending on the models which are used. Example:
> VarImportance
     Var1 Var2 Var3 Var4
GAM 0.000 0.973 0.000 0.000
GBM 0.192 0.344 0.42 0.015
The GAM model was calibrated with one predictor only (Var2)! All other
variables were automatically dropped from the GAM, including Var3, which
is suggested to be the most important one by GBM. When I used Models()
and a priori excluded Var2, then Var3 became most important for GAMs.
Actually this indicates collinearity, which is 0.77 for Var2 and Var3
(pearson correlation coefficient). This doesn’t occur with GBMs, because
they are more robust against multi-collinearity? Any suggestions? Many
thanks, cheers Jonathan 
PS: The settings in Models():
Models(GAM = T, GBM = T, NbRepPA=1, strategy="random",
      NbRunEval = 5, DataSplit = 70, Yweights=NULL, Roc=TRUE,
      Kappa=F, TSS=F, KeepPredIndependent = FALSE, VarImport=5)
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