[Biomod-commits] Need help with some basic questions

[Wilfried Thuiller]

> > Ensemble.Forecasting(Proj.name="cccm80a2a", weight.method='Roc', PCA.media=F, binary=T, bin.method='Roc', Test=T, decay="proportional", repetition.models=T, final.model.out=TRUE)
> > Ensemble.Forecasting(Proj.name="had80a2a", weight.method='Roc', PCA.media=F, binary=T, bin.method='Roc', Test=T, decay="proportional", repetition.models=T, final.model.out=TRUE)
> 
> > load("proj.cccm80a2a/Total_consensus_cccm80a2a_Bin")
> > load("proj.had80a2a/Total_consensus_had80a2a_Bin")

You should not work with the Bin but rather with the probability values first and then transform them

> load("proj.cccm80a2a/Total_consensus_cccm80a2a")
> load("proj.had80a2a/Total_consensus_had80a2a")

> 
> > MyAverageA2A=apply(cbind(Total_consensus_cccm80a2a_Bin[,1,"prob.mean.weighted"], Total_consensus_had80a2a_Bin[,1,"prob.mean.weighted"]),1,mean)

OK.

Alternative

MyAverageA2A = rowMeans(cbind(Total_consensus_cccm80a2a[,1,"prob.mean.weighted"], Total_consensus_had80a2a[,1,"prob.mean.weighted"]))


> > MyThresA2A=apply(cbind(consensus_cccm80a2a_results[[1]][[3]][3,2], consensus_had80a2a_results[[1]][[3]][3,2]),1,mean)

For the threshold, you need to remove the threshold for the models calibrated on 100% of the data
As I already explained, the thresholds are the same whatever the projections or GCM. You can use the consensus outputs from either cccm or had80, does not make any difference. 

MyThresA2A = mean(consensus_cccm80a2a_results$Cflorida$thresholds["prob.mean.weighted", c(2:4, 6:8)]


> > MyAverageBinA2A=BinaryTransformation(MyAverageA2A, MyThresA2A)
> 

That should work now. 

level.plot(MyAverageA2A, Coor) 
level.plot(MyAverageBinA2A, Coor) 

Both should return a visual by now.


Cheers

--------------------------
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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