[Biomod-commits] Re : prevalence and pseudoabsences

Bruno Lafourcade brunolafourcade at aol.com
Fri Apr 22 08:37:51 CEST 2011


 Hi Brenna, 

The pseudo-absence procedure within the Models function is automated and generates a
weighting to give a prevalence of 0.5 for each run.

To make sure that the prevalence doesn't change, you have to build your own pseudo-absence
data outside of the Models function (even prior to Initial.State). In that way, the Models function
will not recognize your data as being pseudo.abs and will not weight them, just like for any 
standard input data.

Use the pseudo.abs() function to this matter. Don't hesitate to ask for details on how to use it.


Bruno Lafourcade
Statistical tools engineer

Laboratoire d'Ecologie Alpine, bureau 308
CNRS - UMR 5553, 2233 rue de la piscine
38400 Saint Martin d'Hères


-----E-mail d'origine-----
De : Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
A : Brenna Forester <forestb at students.wwu.edu>
Cc : biomod-commits at lists.r-forge.r-project.org <biomod-commits at r-forge.wu-wien.ac.at>
Envoyé le : Vendredi, 22 Avril 2011 7:09
Sujet : Re: [Biomod-commits] prevalence and pseudoabsences

Dear Brenna,

Yes and no... 

If you do not ask for pseudo-absence (NbPA=0), there is no weigthing and all your pseudo-absence will be used at once. Prevalence = 0.1
If you add NbPA = 3040 (or more), yes, there is. The prevalence = 0.5

Does it help?

Le 22 avr. 2011 à 00:53, Brenna Forester a écrit :


I see in the "Presentation Manual for BIOMOD" (page 18) the following statement: "In all procedures, BIOMOD ensures that the prevalence of the original data is conserved in the calibration and evaluation datasets."

I have 304 presence records and am running my pseudoabsence pulls with 3040 absences (a prevalence of 0.1).  The number of pixels in my study area is 6808.

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