<font><font face="tahoma,sans-serif">Hello Wilfried,</font></font><div><font><font face="tahoma,sans-serif"><br></font></font></div><div><font><font face="tahoma,sans-serif">Thank you for the explanation. In my case where there are no repetitions, every model is a final model. Wouldn't you need a way to validate the model before assigning a weight? That necessitates either cross validation score or validation score with independent data.</font></font></div>
<div><font><font face="tahoma,sans-serif"><br></font></font></div><div><font><font face="tahoma,sans-serif">A separate question: I have run BIOMOD in regular R (v 2.14.1) and also in Revolution R Enterprise. In regular R, it uses just 1/n of the processing capacity, "n" being the number of processors. It does use different processors but at different time. Is there a way to use all of the processing capacity? I encountered the situation even when I had set up the code for multiple runs. To use all the processing capacity of my machine, I had to run "n" number of separate R programs.</font></font></div>
<div><font><font face="tahoma,sans-serif"><br></font></font></div><div><font><font face="tahoma,sans-serif">Many thanks,</font></font></div><div><font><font face="tahoma,sans-serif">Kumar<br></font></font><br><div class="gmail_quote">
On Fri, May 11, 2012 at 3:03 AM, Wilfried Thuiller <span dir="ltr"><<a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div>Our mistake, actually not.</div><div><br></div><div>The weights are calculated on the final model (100%) if you do not have any repetition (like in your case). </div><div><br></div>
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We are changing that. </div><div>Priority will be given to "Independent data". Then, cross-validation, then final model. </div><div><br></div><div>At the moment, we do not check whether or not independent dataset have been used. </div>
<div><br></div><div>We'll keep you updated on the package building but everything should work back during the day.</div><div><br></div><div>Cheers,</div><div>Wilfried</div><div><br></div><div><br></div><br><div><div>
Le 11 mai 2012 à 08:46, Wilfried Thuiller a écrit :</div>
<div><div class="h5"><br><blockquote type="cite"><div style="word-wrap:break-word"><div>Dear Kumar,</div><div><br></div><div><blockquote type="cite"><div><font face="tahoma, sans-serif">Ensemble.Forecasting. </font><span style="font-family:tahoma,sans-serif">How the software computes ensemble probabilities is not clear in the manual.</span><span style="font-family:tahoma,sans-serif"> </span><span style="font-family:tahoma,sans-serif">But somewhere I came across the information that the weights are based on cross validated evaluation score. Since I do not have such score, the function should not work. </span></div>
</blockquote><div><br></div><div>No, it works. This is mostly because so few people have independent dataset that by default we wrote that the weights are based on the cross-validation results. Indeed, when you have independent dataset, the weight are calculate based on the scores on the independent evaluation. </div>
<div>This is something we need to modify in the manual, sorry for the confusion it gave you. </div><br><blockquote type="cite"><div><span style="font-family:tahoma,sans-serif">Instead, it gives me weight:</span></div>
<div><span style="font-family:tahoma,sans-serif"><div><br></div><div>$weights</div><div> ANN CTA GAM GBM GLM MARS FDA RF SRE</div><div>PA1 0 0 0.1729 0.2766 0.108 0 0 0.4425 0</div><div><br></div>
</span></div><div><span style="font-family:tahoma,sans-serif">Where are these weights coming from? These numbers do not match with any column in Evaluation.results (after rescaling to make the total =1). </span></div><div>
<a href="https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168" target="_blank">https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168</a> </div>
</blockquote><div><br></div><div>It depends on the weighting scheme you use (i.e. decay). Please look at the "decay" explanation in the help of Ensemble.Forecasting. </div><div>If you set decay= 'proportional', you should retrieve easily the weights with the evaluation scores (as they are proportional). </div>
<div><br></div><div>Hope it helps,</div><div><br></div><div>Wilfried</div><div><br></div><div><br></div><br><blockquote type="cite">
<div><div><div><br></div><div>Thanks in advance,</div><div>Kumar</div>-- <br><font color="#666666" face="tahoma, sans-serif">Section of Integrative Biology<br>University of Texas at Austin<br>Austin, Texas 78712, USA</font><br>
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<div><span style="font-size:12px"><div>--------------------------</div><div>Dr. Wilfried Thuiller</div><div>Laboratoire d'Ecologie Alpine, UMR CNRS 5553</div><div>Université Joseph Fourier</div><div>BP53, 38041 Grenoble cedex 9, France</div>
<div>tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a></div><div>fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a></div>
<div><br></div><div>Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>Personal website: <a href="http://www.will.chez-alice.fr/" target="_blank">http://www.will.chez-alice.fr</a><br>
Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br><br>ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
FP6 European EcoChange project: <a href="http://www.ecochange-project.eu/" target="_blank">http://www.ecochange-project.eu</a></div><div><br></div></span></div></div></span><br></div></span><br></div></span><br></div></span><br>
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<div><span style="font-size:12px"><div>--------------------------</div><div>Dr. Wilfried Thuiller</div><div>Laboratoire d'Ecologie Alpine, UMR CNRS 5553</div><div>Université Joseph Fourier</div><div>BP53, 38041 Grenoble cedex 9, France</div>
<div>tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a></div><div>fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a></div>
<div><br></div><div>Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>Personal website: <a href="http://www.will.chez-alice.fr/" target="_blank">http://www.will.chez-alice.fr</a><br>
Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br><br>ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
FP6 European EcoChange project: <a href="http://www.ecochange-project.eu/" target="_blank">http://www.ecochange-project.eu</a></div><div><br></div></span></div></div></span><br></div></span><br></div></span><br></div></span><br>
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<br></div></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#666666" face="tahoma, sans-serif">Section of Integrative Biology<br>University of Texas at Austin<br>Austin, Texas 78712, USA</font><br>
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