Running the analysis
Fit the models - Step 4/14
Now we are ready to compute the models. By using the BIOMOD_Modeling() function we tell to biomod2 which models we want to use, the percentage of the dataset used to train the model and the evaluation metrics used for the single models. Here we will use 70% of the occurrence data (DataSplit=70) to train the models while the remaining 30% will be use for validation. This process was repeated 3 times (NbRunEval=3). The ROC and TSS were the metrics used to evaluate model performances:
> mymodel<-BIOMOD_Modeling(data=mydata,
+ models=c('GLM','GAM','GBM','MAXENT'),
+ models.options=myBiomodOption,
+ NbRunEval=3,
+ DataSplit=70,
+ VarImport=2,
+ models.eval.meth=c('ROC', 'TSS'),
+ do.full.models=F)
Loading required library...
Checking Models arguments...
Creating suitable Workdir...
! Weights where automaticly defined for krameri.1_PA1 to rise a 0.5 prevalence !
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= krameri.1 Modeling Summary -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
7 environmental variables ( bio1 bio2 bio7 bio12 bio15 bio17 bio19 )
Number of evaluation repetitions : 3
Models selected : GLM GAM GBM MAXENT
Total number of model runs : 12
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-=-=-=- Run : krameri.1_PA1
-=-=-=--=-=-=- krameri.1_PA1_RUN1
Model=GLM polynomial with no interaction
Stepwise procedure using AIC criteria
selected formula : krameri.1 ~ bio1 + I(bio2^3) + bio7 + I(bio1^3) + bio15 + I(bio15^3) +
I(bio15^2) + I(bio12^2)
Evaluating Model stuff...
Evaluating Predictor Contributions...
Model=GAM
GAM_mgcv algorithm chosen
Automatic formula generation...
> GAM (mgcv) modelling...
Evaluating Model stuff...
Evaluating Predictor Contributions...
Model=Generalised Boosting Regression
1000 maximum different trees and 3 Fold Cross-Validation
Evaluating Model stuff...
Evaluating Predictor Contributions...
Model=MAXENT
Creating Maxent Temp Proj Data..
Running Maxent...
Getting predictions...
Removing Maxent Temp Data..
Evaluating Model stuff...
Evaluating Predictor Contributions...
…
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-