No subject

lance of 0.1.  Is that correct?  I just want to be sure that there is no we=
ighting of absence records (e.g. weighting to simulate a prevalence of 0.5)=
.

Thank you,
Brenna

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--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit=C3=A9 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

FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu












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----------MB_8CDCECEEFEC5500_1068_26DDF_webmail-m137.sysops.aol.com
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html; charset="utf-8"

<font color=3D'black' size=3D'2' face=3D'arial'><font color=3D"black" face=
=3D"arial" size=3D"2">

<div> <br>

</div>



<div> <font face=3D"Arial, Helvetica, sans-serif">Hi Brenna, <br>
<br>
The pseudo-absence procedure within the Models function is automated and ge=
nerates a<br>
weighting to give a prevalence of 0.5 for each run.<br>
<br>
To make sure that the prevalence doesn't change, you have to build your own=
 pseudo-absence<br>
data outside of the Models function (even prior to Initial.State). In that =
way, the Models function<br>
will not recognize your data as being pseudo.abs and will not weight them, =
just like for any <br>
standard input data.<br>
<br>
Use the pseudo.abs() function to this matter. Don't hesitate to ask for det=
ails on how to use it.<br>
<br>
Best,<br>
Bruno <br>
<br>
<br>
</font>
</div>



<div style=3D"clear: both;">-------<br>

Bruno Lafourcade<br>

Statistical tools engineer<br>

<br>

Laboratoire d'Ecologie Alpine, bureau 308<br>

CNRS - UMR 5553, 2233 rue de la piscine<br>

38400 Saint Martin d'H=C3=A8res<br>

-------</div>



<div> <br>

</div>



<div> <br>

</div>



<div style=3D"font-family: arial,helvetica; font-size: 10pt; color: black;"=
>-----E-mail d'origine-----<br>

De : Wilfried Thuiller &lt;wilfried.thuiller at ujf-grenoble.fr&gt;<br>

A : Brenna Forester &lt;forestb at students.wwu.edu&gt;<br>

Cc : biomod-commits at lists.r-forge.r-project.org &lt;biomod-commits at r-forge.=
wu-wien.ac.at&gt;<br>

Envoy=C3=A9 le : Vendredi, 22 Avril 2011 7:09<br>

Sujet : Re: [Biomod-commits] prevalence and pseudoabsences<br>

<br>








<div id=3D"AOLMsgPart_2_edb92e8f-d92e-4871-b43e-ec9efd37ba90">

<base>

<div>Dear Brenna,</div>



<div><br>

</div>



<div>Yes and no...&nbsp;</div>



<div><br>

</div>



<div>If you do not ask for pseudo-absence (NbPA=3D0), there is no weigthing=
 and all your pseudo-absence will be used at once. Prevalence =3D 0.1</div>



<div>If you add NbPA =3D 3040 (or more), yes, there is. The prevalence =3D =
0.5</div>



<div><br>

</div>



<div>Does it help?</div>



<div>Wilfried</div>



<div><br>

</div>



<div><br>

</div>



<div><br>

</div>



<div>

<div>Le 22 avr. 2011 =C3=A0 00:53, Brenna Forester a =C3=A9crit :</div>

<br class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><span cla=
ss=3D"Apple-style-span" style=3D"border-collapse: separate; font-family: He=
lvetica; font-style: normal; font-variant: normal; font-weight: normal; let=
ter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; tex=
t-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-=
size: medium;">

<div>

<div style=3D"direction: ltr; font-family: Helvetica; color: rgb(0, 0, 0); =
font-size: 10pt;">Hello,<br>

<br>

I see in the "Presentation Manual for BIOMOD" (page 18) the following state=
ment: "In all procedures, BIOMOD ensures that the prevalence of the origina=
l data is conserved in the calibration and evaluation datasets."<br>

<br>

I have 304 presence records and am running my pseudoabsence pulls with 3040=
 absences (a prevalence of 0.1).&nbsp; The number of pixels in my study are=
a is 6808.<br>

<br>