[Biomod-commits] Need help with some basic questions
Wilfried Thuiller
wilfried.thuiller at ujf-grenoble.fr
Wed Feb 22 18:36:59 CET 2012
Dear Ashley,
The weights, thresholds etc are the same because they are estimated from the models, not from the projections. The Ensemble.Forecasting function does not re-run the models, it just pick up the results from every model run in Models, and then estimate the weights and threshold. These weights are then used to make the ensemble forecast. Obviously, the weighting scheme is not going to change in function of the climate change scenario you use because it only relates to the models themselves that are independent of the climate change scenarios.
Concerning your second question, of course it could be done easily. BIOMOD does not do the for you but this is rather easy to compute.
Averaging needs to be done with the probability values (not the binary ones).
For instance, if you want to average your two projections for Cflorida:
load the Total_consensus projections for each GCMs. They should be named along these lines
load("MYPATH/Total_consensus_cccm80a2a")
Let's say your second GCM is called hadcm3
load("MYPATH/Total_consensus_hadcm3a2a")
then let's say you want to average the prob.mean.weighted projections.
Each Total_consensus file is a 3-D array. In the second dimension, you should just have one column (one species). The third dimension corresponds to the different ensemble forecast strategies.
We are going to use the mean function between the two datasets, using the apply function.
MyAverage = apply(cbind(Total_consensus_cccm80a2a[,1,"prob.mean.weighted"], Total_consensus_hadcm3a2a[,1,"prob.mean.weighted"]), 1, mean)
For the threshold, just do the same and take the average.
Does it help?
Wilfried
Le 22 févr. 2012 à 18:18, Ashley Brooks a écrit :
> Hi All!
>
> I have a few questions that I'm a little confused about and need some clarification:
>
> 1) I have run a few projections and then ensemble forecasts using different sets of future climate data. However the weights, thresholds, etc for the different runs have the same exact output. Is this normal or have I messed something up somewhere? See below:
>
> > Initial.State(Response=my.data[1], Explanatory=my.data[,4:13], IndependentResponse=my.data[1], IndependentExplanatory=my.data[,4:13])
>
> > Models(GLM=T, TypeGLM="poly", Test="AIC", GBM=T, No.trees=2000, GAM=T, Spline=3, CTA=T, CV.tree=50, ANN=T, CV.ann=2, SRE=T,quant=0.05, FDA=T, MARS=T, RF=T, NbRunEval=3, DataSplit=70, Yweights=NULL, Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent=T, VarImport=5, NbRepPA=2, strategy="circles", coor=Coor, distance=2, nb.absences=1000)
>
> > Projection(Proj=cccm80a2a[,3:12], Proj.name='cccm80a2a', GLM=T, GBM=T, GAM=T, CTA=T, ANN=T, SRE=T, quant=0.05, FDA=F, MARS=T, RF=T, BinRoc=T, BinKappa=F, BinTSS=F, FiltRoc=T, FiltKappa=F, FiltTSS=F, repetition.models=T)
>
> > Ensemble.Forecasting(Proj.name="cccm80a2a", weight.method='Roc', PCA.media=F, binary=T, bin.method='Roc', Test=T, decay=1.6, repetition.models=T)
> Cflorida
>
> consensus_cccm80a2a_results
> $Cflorida
> $Cflorida$weights
> ANN CTA GAM GBM GLM MARS FDA RF SRE
> PA1 0.0371 0.0232 0.1522 0.2434 0.0951 0.0594 0 0.3895 0
> PA1_rep1 0.0371 0.0232 0.1522 0.0594 0.0951 0.3895 0 0.2434 0
> PA1_rep2 0.0594 0.0232 0.1522 0.3895 0.0951 0.0371 0 0.2434 0
> PA1_rep3 0.0232 0.0483 0.0951 0.2434 0.0483 0.1522 0 0.3895 0
> PA2 0.0371 0.0232 0.0951 0.1522 0.0594 0.3165 0 0.3165 0
> PA2_rep1 0.1022 0.0232 0.1022 0.2434 0.0371 0.3895 0 0.1022 0
> PA2_rep2 0.0371 0.0232 0.0951 0.1522 0.0594 0.2434 0 0.3895 0
> PA2_rep3 0.0302 0.0302 0.0951 0.1522 0.0594 0.3165 0 0.3165 0
>
> $Cflorida$PCA.median
> model.selected
> PA1 NA
> PA1_rep1 NA
> PA1_rep2 NA
> PA1_rep3 NA
> PA2 NA
> PA2_rep1 NA
> PA2_rep2 NA
> PA2_rep3 NA
>
> $Cflorida$thresholds
> PA1 PA1_rep1 PA1_rep2 PA1_rep3 PA2 PA2_rep1 PA2_rep2 PA2_rep3
> prob.mean 552.4331 476.5176 476.5653 459.1243 485.8907 485.8569 428.8626 292.2260
> prob.mean.weighted 567.7707 305.4160 432.0515 423.9614 447.9690 351.9328 297.7658 237.1679
> median 599.1970 529.4070 492.7660 582.6600 594.6120 520.6430 497.5000 301.3960
> Roc.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
> Kappa.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
> TSS.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
>
> $Cflorida$test.results
> PA1 PA1_rep1 PA1_rep2 PA1_rep3 PA2 PA2_rep1 PA2_rep2
> prob.mean 0.9986525 0.9958785 0.9951836 0.9978842 0.9985311 0.9991299 0.9975960
> prob.mean.weighted 0.9995932 0.9970734 0.9957514 0.9991808 0.9993503 0.9987062 0.9987006
> median 0.9982740 0.9945085 0.9942486 0.9974350 0.9977938 0.9975819 0.9970339
> Roc.mean 0.9979492 0.9911780 0.9908023 0.9960763 0.9982514 0.9969859 0.9920226
> Kappa.mean 0.9991215 0.9951836 0.9917288 0.9977910 0.9988672 0.9991667 0.9926667
> TSS.mean 0.9987797 0.9946638 0.9928955 0.9974322 0.9986610 0.9993701 0.9954548
> PA2_rep3
> prob.mean 0.9971582
> prob.mean.weighted 0.9979944
> median 0.9972599
> Roc.mean 0.9948672
> Kappa.mean 0.9934689
> TSS.mean 0.9931836
>
> And then I get the same exact results for other runs as well:
>
> > Projection(Proj=cccm80b2b[,3:12], Proj.name='cccm80b2b', GLM=T, GBM=T, GAM=T, CTA=T, ANN=T, SRE=T, quant=0.05, FDA=F, MARS=T, RF=T, BinRoc=T, BinKappa=F, BinTSS=F, FiltRoc=T, FiltKappa=F, FiltTSS=F, repetition.models=T)
>
> > Ensemble.Forecasting(Proj.name="cccm80b2b", weight.method='Roc', PCA.media=F, binary=T, bin.method='Roc', Test=T, decay=1.6, repetition.models=T)
> Cflorida
>
> consensus_cccm80b2b_results
> $Cflorida
> $Cflorida$weights
> ANN CTA GAM GBM GLM MARS FDA RF SRE
> PA1 0.0371 0.0232 0.1522 0.2434 0.0951 0.0594 0 0.3895 0
> PA1_rep1 0.0371 0.0232 0.1522 0.0594 0.0951 0.3895 0 0.2434 0
> PA1_rep2 0.0594 0.0232 0.1522 0.3895 0.0951 0.0371 0 0.2434 0
> PA1_rep3 0.0232 0.0483 0.0951 0.2434 0.0483 0.1522 0 0.3895 0
> PA2 0.0371 0.0232 0.0951 0.1522 0.0594 0.3165 0 0.3165 0
> PA2_rep1 0.1022 0.0232 0.1022 0.2434 0.0371 0.3895 0 0.1022 0
> PA2_rep2 0.0371 0.0232 0.0951 0.1522 0.0594 0.2434 0 0.3895 0
> PA2_rep3 0.0302 0.0302 0.0951 0.1522 0.0594 0.3165 0 0.3165 0
>
> $Cflorida$PCA.median
> model.selected
> PA1 NA
> PA1_rep1 NA
> PA1_rep2 NA
> PA1_rep3 NA
> PA2 NA
> PA2_rep1 NA
> PA2_rep2 NA
> PA2_rep3 NA
>
> $Cflorida$thresholds
> PA1 PA1_rep1 PA1_rep2 PA1_rep3 PA2 PA2_rep1 PA2_rep2 PA2_rep3
> prob.mean 552.4331 476.5176 476.5653 459.1243 485.8907 485.8569 428.8626 292.2260
> prob.mean.weighted 567.7707 305.4160 432.0515 423.9614 447.9690 351.9328 297.7658 237.1679
> median 599.1970 529.4070 492.7660 582.6600 594.6120 520.6430 497.5000 301.3960
> Roc.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
> Kappa.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
> TSS.mean 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000 500.0000
>
> $Cflorida$test.results
> PA1 PA1_rep1 PA1_rep2 PA1_rep3 PA2 PA2_rep1 PA2_rep2 PA2_rep3
> prob.mean 0.9986525 0.9958785 0.9951836 0.9978842 0.9985311 0.9991299 0.9975960 0.9971582
> prob.mean.weighted 0.9995932 0.9970734 0.9957514 0.9991808 0.9993503 0.9987062 0.9987006 0.9979944
> median 0.9982740 0.9945085 0.9942486 0.9974350 0.9977938 0.9975819 0.9970339 0.9972599
> Roc.mean 0.9979492 0.9911780 0.9908023 0.9960763 0.9982514 0.9969859 0.9920226 0.9948672
> Kappa.mean 0.9991215 0.9951836 0.9917288 0.9977910 0.9988672 0.9991667 0.9926667 0.9934689
> TSS.mean 0.9987797 0.9946638 0.9928955 0.9974322 0.9986610 0.9993701 0.9954548 0.9931836
>
>
>
> 2) Also I am using two GCM (cccma and had) with two strylines each (A2A and B2B) and would like to average the two GCM's to have just two predictions (one for the A2A storyline and one for the B2B storyline). My question is how do I average the two GCM's? Can I do this in Biomod or do I do it in another program? What commands would I use?
>
> Any advice or help would be most appreciated!
> Thanks,
> Ashley
>
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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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