[Biomod-commits] Error while running Models

[Wilfried Thuiller]

Dear Ana,

There is nothing to do with BIOMOD. The internal procedure of neural networks fails for this species. Remove ANN and let the other models run. Then look at the accuracy of the models. Perhaps your species is difficult to model give the environmental data at hands. 

Wilfried


Le 13 févr. 2012 à 16:56, Ana a écrit :

> Hi!
> 
> I am having this error message when running Models: Error in rep(0, net$nunits + 1L) : invalid 'times' argument
> 
> Models(GLM = T, TypeGLM = "simple", Test = "AIC", GBM = T, No.trees = 2000, GAM = T,
> Spline = 3, CTA = T, CV.tree = 50, ANN = T, CV.ann = 2, SRE = T, 
> MARS = T, RF = T, NbRunEval = 3, DataSplit = 80, Yweights=NULL, Roc = T, Optimized.Threshold.Roc = T,
> Kappa = T, TSS=T, KeepPredIndependent = T, VarImport=5, NbRepPA=2, strategy="circles",
> coor=dataset[,8:9], distance=2, nb.absences=100)
> 
> 
> 
> ------------------------------
> ----- 
> Modelling summary 
> ----------------------------------- 
> Number of species modelled :            1
> Species 01
> 
> numerical variables :                   var1, var2, var3, var4, var5, var6
> 
> 
> number of evaluation repetitions :      3
> number of pseudo-absences runs :        2
> models selected :                       ANN, CTA, GAM, GBM, GLM, MARS, RF, SRE
> total number of model runs :            64
> ----------------------------------- 
> 
> 
> #####                    Species 01                     #####
> #####              pseudo-absence run 1                 #####
> Model=Artificial Neural Network 
>          2 Fold Cross Validation + 3 Repetitions 
> Calibration and evaluation phase: Nb of cross-validations:  3 
> Error in rep(0, net$nunits + 1L) : invalid 'times' argument
> 
> 
> I had this problem before, I solved it but I didn't keep a track of the change I made to solve it.
> 
> My data is in data.frame format, the species columns has only presence absence ( 1 or 0) and there are no NA values.
> My variables have decimal numbers.
> 
> By initial state is the following:
> Initial.State(Response = dataset[,7],
>         Explanatory = dataset[,1:6],
>         IndependentResponse = NULL,
>         IndependentExplanatory = NULL,
>         sp.name="Species 01")
> 
> 
> Thanks in advance
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--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Université Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu







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