[Biomod-commits] biomod2/ Maxent run

semra yalcin semra.yalcin at gmail.com
Fri Jul 27 14:58:21 CEST 2012

Dear Damien and BIOMOD-users,

I would like to ask a question about MaxEnt results on biomod2. I followed
each step and run the models of Myocastor from vignette/biomod2.

When I compare the results of biomod2-maxent (on R) with the results in the
folder of MaxEnt model ("Myocastor\models\Myocastor_PA1_RUN1_MAXENT"), I
saw that the order of importance of the variance and AUC values of the
model are different.

For example;

getModelsVarImport(myBiomodModelOut) returns as

, , RUN1, PA1

       SRE    RF MAXENT
Var1 0.048 0.343  0.531
Var2 0.048 0.270  0.140
Var3 0.140 0.187  0.134
Var4 0.162 0.328  0.568
Var5 0.074 0.115  0.126

while " Myocastor_PA1_RUN1.html" shows the order of the variables as

VariablePercent contribution Permutation importancebio_3(Var1)4741.1
bio_11(Var4)24.439.7bio_4(Var2)19.4 3bio_12(Var5)6.511bio_7(Var3)2.85.2

As you see, the order of the variance by "getModelsVarImport" is Var4/
Var1/ Var2/ Var3/ Var5 whereas the order of the variance in the MaxEnt
results is Var1/ Var4/ Var2/ Var5/Var3. So what could be the reason for
this differences?

Moreover, there is a difference between ROC(AUC) values between
biomod2-maxent and MaxEnt documents. Is this because that biomod2
calculates ROC of testing data ("myBiomodModelEval["ROC",,"MAXENT",,]"?

By the way I run models with my own data and I have same differences in the
order of importance of the variance in the maxent results.

Thank you in advance.

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