Running the analysis

Fit the models - Step 10/14

It is possible to specify if we want to use all the models (em.by="all") or just some of these, which metrics we want to use to evaluate performance (“eval.metric” argument) and to set a threshold (“eval.metric.quality.threshold” argument) to filter the single models according to their performance (see also Swets, 1988 and Allouche et al., 2006). Furthermore, we specified which metrics must be used to evaluate the ensemble model (“models.eval.meth” argument):

> myEM<-BIOMOD_EnsembleModeling(modeling.output=mymodel,
+             em.by="all",
+             eval.metric=c('ROC','TSS'),
+             eval.metric.quality.threshold=c(0.7,0.4),
+             models.eval.meth = c('ROC', 'TSS'),
+             prob.mean=F,
            + prob.mean.weight=T)

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Build Ensemble Models -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

> Evaluation & Weighting methods summary :
ROC over 0.7
TSS over 0.4


> TotalConsensus ensemble modeling
! Models projections for whole zonation required...
> Projecting krameri.1_PA1_RUN1_GLM ...
> Projecting krameri.1_PA1_RUN1_GAM ...
> Projecting krameri.1_PA1_RUN1_GBM ...
> Projecting krameri.1_PA1_RUN1_MAXENT ...
> Projecting krameri.1_PA1_RUN2_GLM ...
> Projecting krameri.1_PA1_RUN2_GAM ...
> Projecting krameri.1_PA1_RUN2_GBM ...
> Projecting krameri.1_PA1_RUN2_MAXENT ...
> Projecting krameri.1_PA1_RUN3_GLM ...
> Projecting krameri.1_PA1_RUN3_GAM ...
> Projecting krameri.1_PA1_RUN3_GBM ...
> Projecting krameri.1_PA1_RUN3_MAXENT ...

> Prababilities wegthing mean...
original models scores = 0.73 0.724 0.715 0.702 0.762 0.727 0.75 0.751 0.708 0.722 0.711 0.708
final models weights = 0.084 0.083 0.082 0.081 0.087 0.083 0.086 0.086 0.081 0.083 0.082 0.081
Evaluating Model stuff...
> Prababilities wegthing mean...
original models scores = 0.427 0.401 0.448 0.471 0.434
final models weights = 0.196 0.184 0.205 0.216 0.199
Evaluating Model stuff...
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

From the output we understand that all the 12 models of the first replicate passed the threshold and will be used to obtain the ensemble model. It is likely that in other replicates only a part of the models will be included in the ensemble model.