[R-sig-eco] Error in run GAM (Biomod 2)

[Drew Tyre]

I don't think the number of presences is the problem. 
"A term has fewer unique covariate combinations than specified maximum degrees of freedom"
One of your covariates has a small number of unique values. 
lapply(your_data_frame, function(x)length(unique(x)))
will print out the number of unique values in each variable. Values < 30 could be problematic -- the docs are a bit ambiguous on the default values of k, the maximum degrees of freedom for a smooth term. Another approach to diagnose the problem is to set k to a low value, like 5, and see if that makes the problem go away. I'm not familiar with biomod2, but I think doing something like
MO <- BIOMOD_ModelingOptions(GAM  = list(k = 5))
BIOMOD_Modeling( ..., models.options = MO, ...) 

should do it. Note that setting k to a low value causes other problems, I would use mcgv::gam.check() to ensure k is large enough, but I don't know how to do that with biomod2. 

hth

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Drew Tyre
 
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On 3/18/19, 6:28 AM, "R-sig-ecology on behalf of Lara Silva" <r-sig-ecology-bounces using r-project.org on behalf of lara.sfp.silva using gmail.com> wrote:

    Hello
    
    I am trying to run several algorithms in biomod 2 (GLM, GAM, ANN, SRE) but
    I received the following menssage.
    
    Model=GAM
             GAM_mgcv algorithm chosen
            Automatic formula generation...
            > GAM (mgcv) modelling...Error in
    smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
      A term has fewer unique covariate combinations than specified maximum
    degrees of freedom
    Error in predict(model.bm, Data[, expl_var_names, drop = FALSE], on_0_1000
    = TRUE) :
      object 'model.bm' not found
    
    *** inherits(g.pred,'try-error')
       ! Note :  Lactuca.global_AllData_RUN1_GAM failed!
    
    I have 19 presences and 1019 pseudo-absences ...
    It is because the low number of presences?
    
    Thanks
    
    Lara
    
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