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Mon Feb 21 17:26:18 CET 2011

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,
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Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit=E9 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<mailto:wilfried.thuiller at ujf-greno=>
Personal website:<http://www.will.chez-alice.=
Team website:

FP6 European MACIS project:<http://www.macis-p=>
FP6 European EcoChange project:<http://www.=>


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Thanks Bruno &amp; Wilfried,<br>
So to clarify: I run pseudo.abs - in my case as so:<br>
<font size=3D"2"><span style=3D"font-family: Courier New;">PA1 &lt;- pseudo=
.abs(coor=3DSp.Env[,2:3], status=3DSp.Env[,1], strategy=3D&quot;random&quot=
</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp=
;&nbsp; <span style=3D"font-family: Courier New;">env=3DSp.Env[,4:10], nb.p=
</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp=
;&nbsp; <span style=3D"font-family: Courier New;">add.pres=3DF,</span><span=
 style=3D"font-family: Courier New;"> create.dataset=3DT, plot=3DT, pcol=3D=
&quot;red&quot;, acol=3D&quot;grey80&quot;)</span></font><br>
This creates two objects, &quot;<span style=3D"font-family: Courier New;">P=
A1</span>&quot; (a vector of cell numbers chosen as absences) and &quot;<sp=
an style=3D"font-family: Courier New;">Dataset.Rhodiola.random.partial</spa=
n>&quot;, a dataframe of coordinates and &quot;status&quot; (zero).<br>
I would then create a new dataset that has just my presence records (304) a=
nd these 2736 absences.&nbsp; I would run that dataset (<span style=3D"font=
-family: Courier New;">Sp.Env.PA1</span>) in the
<span style=3D"font-family: Courier New;">Intial.State()</span> and <span s=
tyle=3D"font-family: Courier New;">
Models() </span>functions, for example, as so:<br>
<span style=3D"font-family: Courier New;">Initial.State(Response=3DSp.Env.P=
A1[,c(1)], Explanatory=3DSp.Env.PA1[,4:10],<br>
; <span style=3D"font-family: Courier New;">IndependentResponse=3DNULL,</sp=
an><span style=3D"font-family: Courier New;"> IndependentExplanatory=3DNULL=
;&nbsp; <span style=3D"font-family: Courier New;">;Rhodiola&=
<span style=3D"font-family: Courier New;">Models(GLM =3D T, TypeGLM =3D &qu=
ot;simple&quot;, Test =3D &quot;AIC&quot;, GBM =3D T, No.trees =3D 5000,<br=
</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; <spa=
n style=3D"font-family: Courier New;">GAM =3D T, CTA =3D T, </span>
<span style=3D"font-family: Courier New;">CV.tree =3D 100, ANN =3D T,
n =3D 5, SRE =3D F, FDA =3D T,
</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; <spa=
n style=3D"font-family: Courier New;">MARS =3D T, RF =3D T,</span><span sty=
le=3D"font-family: Courier New;"> NbRunEval =3D 10, DataSplit =3D 70, Yweig=
hts=3DNULL,</span><span style=3D"font-family: Courier New;"><br>
</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
 <span style=3D"font-family: Courier New;">NbRepPA=3D0, </span><span style=
=3D"font-family: Courier New;">Roc=3DT, Optimized.Threshold.Roc=3DT, Kappa=
=3DT, TSS=3DT,<br>
&nbsp;</span>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span=
 style=3D"font-family: Courier New;">KeepPredIndependent =3D F,</span><span=
 style=3D"font-family: Courier New;"> VarImport=3D5)</span><br>
I keep <span style=3D"font-family: Courier New;">NbRepPA =3D 0 </span>so it=
 uses the entire dataset to evaluate the model, maintaining my prevalence a=
t 0.1 (304 presence records/3040 total records in the dataset).<br>
I think I am correct on everything to this point?<br>
So my question is: I want to do 5 PA pulls (as I would if I ran it in the <=
span style=3D"font-family: Courier New;">
Models() </span>function, <span style=3D"font-family: Courier New;">NbRepPA=
 =3D 5</span>), maintaining my 0.1 prevalence.&nbsp; But I would then have =
<span style=3D"font-family: Courier New;">Models() </span>five times on 5 d=
atasets (each with different PA pulls).&nbsp; How does BIOMOD create a fina=
l model when using PA pulls (e.g.
<span style=3D"font-family: Courier New;">NbRepPA =3D 5)</span> within the =
<span style=3D"font-family: Courier New;">
Models()</span><span style=3D"font-family: Courier New;"><span style=3D"fon=
t-family: Helvetica;"> function, and can I replicate that
</span></span>when I run my PA pulls manually as above?<br>
I hope this isn't too confusing! <br>
Thank you!<br>
<div style=3D"font-family: Times New Roman; color: rgb(0, 0, 0); font-size:=
<hr tabindex=3D"-1">
<div style=3D"direction: ltr;" id=3D"divRpF114927"><font color=3D"#000000" =
face=3D"Tahoma" size=3D"2"><b>From:</b> Bruno Lafourcade [brunolafourcade at a=]<br>
<b>Sent:</b> Thursday, April 21, 2011 11:37 PM<br>
<b>To:</b> wilfried.thuiller at; Brenna Forester<br>
<b>Cc:</b> biomod-commits at<br>
<b>Subject:</b> Re : [Biomod-commits] prevalence and pseudoabsences<br>
<div><font color=3D"black" face=3D"arial" size=3D"2"><font color=3D"black" =
face=3D"arial" size=3D"2">
<div><font face=3D"Arial, Helvetica, sans-serif">Hi Brenna, <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>
To make sure that the prevalence doesn't change, you have to build your own=
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
standard input data.<br>
Use the pseudo.abs() function to this matter. Don't hesitate to ask for det=
ails on how to use it.<br>
Bruno <br>
<div style=3D"clear: both;">-------<br>
Bruno Lafourcade<br>
Statistical tools engineer<br>
Laboratoire d'Ecologie Alpine, bureau 308<br>
CNRS - UMR 5553, 2233 rue de la piscine<br>
38400 Saint Martin d'H=E8res<br>
<div style=3D"font-family: arial,helvetica; font-size: 10pt; color: black;"=
>-----E-mail d'origine-----<br>
De : Wilfried Thuiller &lt;wilfried.thuiller at;<br>
A : Brenna Forester &lt;forestb at;<br>
Cc : biomod-commits at &lt;biomod-commits at r-forge.=;<br>
Envoy=E9 le : Vendredi, 22 Avril 2011 7:09<br>
Sujet : Re: [Biomod-commits] prevalence and pseudoabsences<br>
<div id=3D"AOLMsgPart_2_edb92e8f-d92e-4871-b43e-ec9efd37ba90">
<div>Dear Brenna,</div>
<div>Yes and no...&nbsp;</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 =
<div>Does it help?</div>
<div>Le 22 avr. 2011 =E0 00:53, Brenna Forester a =E9crit :</div>
<br class=3D"Apple-interchange-newline">
<blockquote type=3D"cite"><span class=3D"Apple-style-span" style=3D"border-=
collapse: separate; font-family: Helvetica; font-style: normal; font-varian=
t: normal; font-weight: normal; letter-spacing: normal; line-height: normal=
; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; font-size: medium;">
<div style=3D"direction: ltr; font-family: Helvetica; color: rgb(0, 0, 0); =
font-size: 10pt;">
I see in the &quot;Presentation Manual for BIOMOD&quot; (page 18) the follo=
wing statement: &quot;In all procedures, BIOMOD ensures that the prevalence=
 of the original data is conserved in the calibration and evaluation datase=
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>

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