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<div class="moz-cite-prefix">Dear Semra,<br>
<br>
In fact the results of variables importances obtained with biomod2
(the first table) and directly with MAXENT (the second one)
differs because they are not based on the same metrics.<br>
<br>
What is calculated in biomod2 correspond more to Permutation
importance (2nd column) than to Percent of contribution (1st
column).<br>
<br>
In both case the prediction of the model with calibrating+testing
data is compared to the one obtained with one variable randomly
shuffled.<br>
<br>
In MAXENT, the AUC decreasing is used to quantify the variable
importances whereas we used the correlation between 'normal'
predictions and 'shuffled' ones in biomod2. (one of reasons not to
take AUC decreasing for variables importance calculation is that
it's uncomputable for SRE models) <br>
<br>
That's mainly why the results differs.<br>
<br>
Moreover, the shuffling process is repeated 'VarImport' times in
biomod2 (the mean is returned) whereas (if I remember well) it's
only done one time in MAXENT.<br>
<br>
If we decide to recalculate our own variables importance and
evaluation for MAXENT models in biomod2 it's because we want to be
able to compare all models with each other.<br>
<br>
That being said, keep in mind that variable importances
calculation is an heuristic metric that can vary a lot between
different runs. <span style="color: rgb(34, 34, 34); font-family:
Arial, Helvetica, sans-serif; font-size: 13px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-align: -webkit-auto; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none; "><span class="Apple-converted-space"></span></span>This
metric is also realy dependent of variables correlations. That's
why, you might be really careful when you want to make conclusion
using it.<br>
<br>
Hope that's understandable and helpful,<br>
<br>
Best,<br>
<br>
Damien<br>
<br>
<br>
<br>
On 27/07/2012 14:58, semra yalcin wrote:<br>
</div>
<blockquote
cite="mid:CABX-FmoL6DndQs9DtZu+Onhs0mTDHAPHdPYhynh3VVL56b+7Jg@mail.gmail.com"
type="cite">Dear <span
style="color:rgb(34,34,34);font-size:13px;font-family:Helvetica">Damien </span>and <span
style="color:rgb(34,34,34);font-size:13px;font-family:Helvetica">BIOMOD-users,</span>
<div><br>
</div>
<div>I would like to ask a question about MaxEnt results on
biomod2. I followed each step and run the models of Myocastor
from <span
style="color:rgb(34,34,34);font-size:13px;font-family:Helvetica">vignette/biomod2. </span></div>
<div><br>
</div>
<div>When I compare the results of biomod2-maxent (on R) with the
results in the folder of MaxEnt model
("Myocastor\models\Myocastor_PA1_RUN1_MAXENT"), I saw that the
order of importance of the variance and AUC values of the model
are different. </div>
<div><br>
</div>
<div>For example;</div>
<div><br>
</div>
<div>getModelsVarImport(myBiomodModelOut) returns as </div>
<div><br>
</div>
<div>....</div>
<div>
<div>, , RUN1, PA1</div>
<div><br>
</div>
<div> SRE RF MAXENT</div>
<div>Var1 0.048 0.343 0.531</div>
<div>Var2 0.048 0.270 0.140</div>
<div>Var3 0.140 0.187 0.134</div>
<div>Var4 0.162 0.328 0.568</div>
<div>Var5 0.074 0.115 0.126</div>
</div>
<div>
</div>
<div>....</div>
<div><br>
</div>
<div>while " Myocastor_PA1_RUN1.html" shows the order of the
variables as </div>
<div><br>
</div>
<div>
<table border="" cols="3">
<tbody>
<tr>
<th>Variable</th>
<th>Percent contribution</th>
<th>Permutation importance</th>
</tr>
<tr align="right">
<td>bio_3(Var1)</td>
<td>47</td>
<td>41.1</td>
</tr>
<tr align="right">
<td>bio_11(Var4)</td>
<td>24.4</td>
<td>39.7</td>
</tr>
<tr align="right">
<td>bio_4(Var2)</td>
<td>19.4</td>
<td>3</td>
</tr>
<tr align="right">
<td>bio_12(Var5)</td>
<td>6.5</td>
<td>11</td>
</tr>
<tr align="right">
<td>bio_7(Var3)</td>
<td>2.8</td>
<td>5.2</td>
</tr>
</tbody>
</table>
</div>
<div><br>
</div>
<div><br>
</div>
<div>As you see, the order of the variance by "getModelsVarImport"
is Var4/ Var1/ Var2/ Var3/ Var5 whereas the order of
the variance in the MaxEnt results is Var1/ Var4/ Var2/
Var5/Var3. So what could be the reason for this differences? </div>
<div><br>
</div>
<div>Moreover, there is a difference between ROC(AUC) values
between biomod2-maxent and MaxEnt documents. Is this because
that biomod2 calculates ROC of testing data
("myBiomodModelEval["ROC",,"MAXENT",,]"? </div>
<div><br>
</div>
<div>By the way I run models with my own data and I have same
differences in the order of importance of the variance in the
maxent results. </div>
<div><br>
</div>
<div>Thank you in advance.</div>
<div><br>
</div>
<div>Semra.</div>
<div><br>
</div>
<div><br>
</div>
<div><span
style="color:rgb(34,34,34);font-family:Helvetica;font-size:13px"><br>
</span></div>
<div><br>
</div>
<div>
<br>
</div>
<br>
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<br>
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