[Biomod-commits] testing points for model evaluation

[Wilfried Thuiller]

Hi there all,

You are right Robin. This is not retrievable. In the first version of BIOMOD, we did extract the training and testing data and associated predictions. However, given the number of outputs BIOMOD can now create (especially if you make projections) we then decided to remove this information for memory and space limitations. 

We now only use the testing data for the estimating Kappa/TSS/AUC and then remove the data. 

Cheers,
Wilfried




Le 23 sept. 2011 à 00:32, Robin Engler a écrit :

> Hi Brenna,
> 
> As of the current version of BIOMOD and as far as I know (Wilfried,
> correct me if I'm wrong), you cannot retrieve this information from
> the BIOMOD outputs.
> Best,
> Robin
> 
> 
> On Thu, Sep 22, 2011 at 7:24 PM, Brenna Forester
> <brenna.forester at duke.edu> wrote:
>> Hello everyone,
>> 
>> Here is my model call:
>> 
>> Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = T, No.trees = 5000,
>> GAM = T, CTA = T, CV.tree = 50, ANN = T, CV.ann = 5, SRE = F, FDA = T, MARS
>> = T, RF = T, NbRunEval = 10, DataSplit = 70, Yweights=NULL, NbRepPA=1,
>> strategy="random", nb.absences=6504, Roc=T, Optimized.Threshold.Roc=T,
>> Kappa=T, TSS=T, KeepPredIndependent = F, VarImport=5)
>> 
>> I would like to know (1) which presence points are withheld for testing in
>> each of the 10 reps, and (2) what the predictions are for those testing
>> points for each rep and each model.
>> 
>> Where can I find this information in the BIOMOD output?
>> 
>> Thanks!
>> Brenna
>> 
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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

FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu






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