[Biomod-commits] Weight in ensemble forecasting

[Wilfried Thuiller]

Dear Kumar,

> Ensemble.Forecasting. How the software computes ensemble probabilities is not clear in the manual. But somewhere I came across the information that the weights are based on cross validated evaluation score. Since I do not have such score, the function should not work.

No, it works. This is mostly because so few people have independent dataset that by default we wrote that the weights are based on the cross-validation results. Indeed, when you have independent dataset, the weight are calculate based on the scores on the independent evaluation. 
This is something we need to modify in the manual, sorry for the confusion it gave you. 

> Instead, it gives me weight:
> 
> $weights
>     ANN CTA    GAM    GBM   GLM MARS FDA     RF SRE
> PA1   0   0 0.1729 0.2766 0.108    0   0 0.4425   0
> 
> Where are these weights coming from? These numbers do not match with any column in Evaluation.results (after rescaling to make the total =1). 
> https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168 

It depends on the weighting scheme you use (i.e. decay). Please look at the "decay" explanation in the help of Ensemble.Forecasting. 
If you set decay= 'proportional', you should retrieve easily the weights with the evaluation scores (as they are proportional). 

Hope it helps,

Wilfried



> 
> Thanks in advance,
> Kumar
> -- 
> Section of Integrative Biology
> University of Texas at Austin
> Austin, Texas 78712, USA
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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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