[Biomod-commits] Error in newx$cptable[max(keep), 1L] <- cp : subscript out of bounds

[Wilfried Thuiller]

Dear Jason,

The problem is related to the classification tree. It seems the tree has no branches and BIOMOD does not manage to get the optimal number of leaves. 
My take on that is that your species is very difficult to model for CTA and it does not manage to find any good combination of variables explaining the distribution. 
Perhaps we need to make an error trap around this call as this is not the first time we got this error, which is not a BIOMOD bug, but rather the failure of CTA to find an optimal number of leaves. 
I will suggest removing the model for this species.

Looking at the code you sent with this message and the other one, I would also suggest:

Removing some techniques. Some generally performed quite poorly compared to the other ones. CTA and ANN are the weakest ones. SRE is more like a null model, the most liberal. I would drop the three. 
Same for evaluation, you do not need to use both TSS and KAPPA, they are quite redundant. Just keep TSS, less influenced by prevalence and ROC. 

I would recommend using "random" for pseudo absence instead of SRE or circle which tends to over fit a bit the data.
I take the liberty to send you this paper in press with Methods in Ecology and Evolution that discuss the different strategies for selecting pseudo-absence:
PDF

Hope it helps,

Wilfried




Le 7 févr. 2012 à 05:06, jason b mackenzie a écrit :

> Dear all,
> 
> I recently had a BIOMOD run crash mid-stream after 20+ species appear to have run successfully. The error message is pasted below. Any ideas or workarounds? 
> 
> ...
> #####			 ERFA2 			#####
> #####		   pseudo-absence run 1        		#####
> Model=Artificial Neural Network 
> 	 3 Fold Cross Validation + 3 Repetitions 
> Calibration and evaluation phase: Nb of cross-validations:  3 
> Evaluating Predictor Contributions in  ANN ... 
> Model=Classification tree 
> 	 50 Fold Cross-Validation 
> Error in newx$cptable[max(keep), 1L] <- cp : subscript out of bounds
> > warnings()
> Warning messages:
> 1: In predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type ==  ... :
>   prediction from a rank-deficient fit may be misleading
> 2: In cor(g.pred[, ], as.integer(.Rescaler4(as.numeric(predict(model.sp,  ... :
>   the standard deviation is zero
> ...
> 
> 
> FYI, not sure if this matters, but my starting conditions were set as follows:
> 
> Initial.State(Response=SP.ENV[,12:75], Explanatory=SP.ENV[,4:11], IndependentResponse=NULL, 
> 		IndependentExplanatory=NULL)
> 
> Models(GLM = FALSE, GAM = TRUE, Spline=4, GBM = TRUE, No.trees = 3000, CTA = TRUE, CV.tree = 50, ANN = TRUE, CV.ann = 3, 
> 		SRE = TRUE, quant = 0.025, FDA = TRUE, MARS = TRUE, RF = TRUE, NbRunEval = 3, DataSplit = 70, 
> 		Yweights = NULL, Roc = TRUE, Optimized.Threshold.Roc = TRUE, Kappa = TRUE, TSS = TRUE, 
> 		KeepPredIndependent = FALSE, VarImport = 5, NbRepPA = 2, strategy = "sre", nb.absences = 1000)
> 
> 
> Thanks in advance for any help!
> 
> Cheers, 
> Jason
> 
> 
> --
> 
> jason b mackenzie
> 80 banambila street
> aranda, act 2614
> 
> 0447 002 629  [mobile]
> jasonbmackenzie    [skype]
> 
> 
> 
> 
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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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