[Biomod-commits] Psuedo-absence: PA.nb.rep = 0, and Raster as Factor

Wilfried Thuiller wilfried.thuiller at ujf-grenoble.fr
Tue Feb 12 15:02:57 CET 2013

Dear Leon,

> I have a question regarding pseudo-absence selection: Firstly, my data-set consists species presence for 238 bee species in the Netherlands. I have this data in a single table arranged as requested by biomod2.
> Am I correct in understanding that if I set PA.nb.rep = 0, biomod2 will then take as pseudo absences only the locations where my focus species is not present but other bee species have been collected?

Yes, as soon as they are coded in 1 and 0. 

> Also, I have my explanatory variables in Raster format, one of which is a categorical variable (Levels: 10,20,21,30,40,50,60,70,80,98,99):

I will let Damien answers to that one coz I am usually not playing with categorical rasters.
However, if I may give my two cents on your analysis, I was wondering how many variables to you have? Having a factor variable with 11 levels is equivalent to have 10 variables. If you have other variables, you may go into troubles for some models. GAM for instance is not made for running over lots of variables. 


> If I define it as.factor, will biomod then recognize it as such?
> ##Define raster as factor
> soilF<-as.factor(raster("soil.img"))
> Thanks for your help,
> Leon
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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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