<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Charles,</div><div><br></div><div><blockquote type="cite"><div>First of all, I must say that it is a great pleasure to read all the<br>interesting discussions we have in this list, we learn a lot with<br>every message! Thanks, and congratulations!!<br>Well, sorry if the question I will point here has been done before,<br>but I really didn't find anything about it in previous messages I<br>have:<br><br>Is it posible to include MaxEnt among the models simulated by BIOMOD?<br><br>In my opinion, the great strength of BIOMOD, beyond many other<br>benefits, is to allow the ensemble of many models in an easy way, and<br>so to give us more confidence results of our simulations. But I see<br>that MaxEnt is often used to simulate distribution of species and<br>sometimes I ask myself why it is not included in BIOMOD (yet). Is it a<br>"stupid" question? (I really believe that there are NO "stupid"<br>questions, but... :-))<br></div></blockquote><div><br></div><div>This is indeed a very interesting question. </div><div>The answer is no and yes. </div><div>No because Maxent is coded in Java, much more efficient than in R. We'll have to recode the entire program in C or C++ to fully integrate it in R and latter in BIOMOD. </div><div><br></div><div>However, this is easy to run Maxent using a batch command from R. I have thought about putting Maxent within BIOMOD that way since a while. I am just to busy to do it but hope to start looking at that this year. </div><div><br></div><div>For curious, find below a short code for running Maxent from R.</div><div>You need the ascii data for running it and modify all paths and data for your own data.</div><div>My species is Sp290.csv (Sp290 from SpEnv data in BIOMOD exported in csv format for Maxent).</div><div>The environmental variables are the same than SpEnv, as many ascii files as variables. </div><div>You need maxent.jar in your working directory. </div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">dir.create<span style="color: #042299">(</span>path<span style="color: #042299">=</span>paste<span style="color: #042299">(</span>getwd<span style="color: #042299">(), </span><span style="color: #b0140c">"/MaxEnt.res"</span><span style="color: #042299">, </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">""</span><span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">MaxEnt.layers<span style="color: #042299"> <- </span>paste<span style="color: #042299">(</span>getwd<span style="color: #042299">(), </span><span style="color: #b0140c">"/europe/ascii/current"</span><span style="color: #042299">, </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">""</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">MaxEnt.out<span style="color: #042299"> <- </span>paste<span style="color: #042299">(</span>getwd<span style="color: #042299">(), </span><span style="color: #b0140c">"/MaxEnt.res"</span><span style="color: #042299">, </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">""</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">MaxEnt.samples<span style="color: #042299"> <- </span>paste<span style="color: #042299">(</span>getwd<span style="color: #042299">(), </span><span style="color: #b0140c">"/europe/point"</span><span style="color: #042299">, </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">""</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">layers<span style="color: #042299"> <- </span>list.files<span style="color: #042299">(</span>MaxEnt.layers<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(169, 65, 203); "># run MaxEnt:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #007128">system</span><span style="color: #042299">(</span><span style="color: #007128">command</span><span style="color: #042299">=</span><span style="color: #007128">paste</span><span style="color: #042299">(</span>"java -jar maxent.jar environmentallayers="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.layers</span><span style="color: #042299">, </span>" samplesfile="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.samples</span><span style="color: #042299">, </span>"/Sp290.csv"<span style="color: #042299">, </span>" outputdirectory="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.out</span><span style="color: #042299">, </span>" maximumiterations=100 redoifexists autorun nowarnings notooltips"<span style="color: #042299">, </span><span style="color: #007128">sep</span><span style="color: #042299">=</span>""<span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(169, 65, 203); "># NOT RUN</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #007128">system</span><span style="color: #042299">(</span><span style="color: #007128">command</span><span style="color: #042299">=</span><span style="color: #007128">paste</span><span style="color: #042299">(</span>"java -mx4000m -jar maxent.jar environmentallayers="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.layers</span><span style="color: #042299">, </span>" samplesfile="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.samples</span><span style="color: #042299">, </span>"/Sp290.csv"<span style="color: #042299">, </span>" outputdirectory="<span style="color: #042299">, </span><span style="color: #007128">MaxEnt.out</span><span style="color: #042299">, </span>" 'applythresholdrule=equal training sensitivity and specificity' maximumiterations=100 redoifexists autorun nowarnings notooltips"<span style="color: #042299">, </span><span style="color: #007128">sep</span><span style="color: #042299">=</span>""<span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">list.files<span style="color: #042299">(</span>MaxEnt.out<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(169, 65, 203); ">#Import the predictions on the presence points</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Pred.Maxent.Sp290.sample<span style="color: #042299"> <- </span>read.csv<span style="color: #042299">(</span>paste<span style="color: #042299">(</span>getwd<span style="color: #042299">(), </span><span style="color: #b0140c">"/MaxEnt.res/Sp290_samplePredictions.csv"</span><span style="color: #042299">, </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">""</span><span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(169, 65, 203); ">#Plot the results from Maxent</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">library<span style="color: #042299">(</span>BIOMOD<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">par<span style="color: #042299">(</span>mfrow<span style="color: #042299">=</span>c<span style="color: #042299">(</span><span style="color: #2b6fb8">1</span><span style="color: #042299">,</span><span style="color: #2b6fb8">2</span><span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">level.plot<span style="color: #042299">(</span>Sp.Env<span style="color: #042299">$</span>Sp290<span style="color: #042299">, </span>XY<span style="color: #042299">=</span>Sp.Env<span style="color: #042299">[,</span><span style="color: #2b6fb8">2</span><span style="color: #042299">:</span><span style="color: #2b6fb8">3</span><span style="color: #042299">], </span>color.gradient<span style="color: #042299"> = </span><span style="color: #b0140c">"grey"</span><span style="color: #042299">, </span>cex<span style="color: #042299">=</span><span style="color: #2b6fb8">0.3</span><span style="color: #042299">,</span>show.scale<span style="color: #042299">=</span>F<span style="color: #042299">, </span>title<span style="color: #042299">=</span><span style="color: #b0140c">"Original data"</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">level.plot<span style="color: #042299">(</span>Pred.Maxent.Sp290.sample<span style="color: #042299">$</span>Logistic.prediction<span style="color: #042299">, </span>XY<span style="color: #042299">=</span>Pred.Maxent.Sp290.sample<span style="color: #042299">[,</span><span style="color: #2b6fb8">1</span><span style="color: #042299">:</span><span style="color: #2b6fb8">2</span><span style="color: #042299">], </span>color.gradient<span style="color: #042299"> = </span><span style="color: #b0140c">"grey"</span><span style="color: #042299">, </span>cex<span style="color: #042299">=</span><span style="color: #2b6fb8">0.3</span><span style="color: #042299">,</span>show.scale<span style="color: #042299">=</span>F<span style="color: #042299">, </span>title<span style="color: #042299">=</span><span style="color: #b0140c">"Maxent"</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">points<span style="color: #042299">(</span>Sp.Env<span style="color: #042299">[</span>Sp.Env<span style="color: #042299">$</span>Sp290<span style="color: #042299"><</span><span style="color: #2b6fb8">1</span><span style="color: #042299">,</span><span style="color: #2b6fb8">2</span><span style="color: #042299">], </span>Sp.Env<span style="color: #042299">[</span>Sp.Env<span style="color: #042299">$</span>Sp290<span style="color: #042299"><</span><span style="color: #2b6fb8">1</span><span style="color: #042299">,</span><span style="color: #2b6fb8">3</span><span style="color: #042299">], </span>cex<span style="color: #042299">=</span><span style="color: #2b6fb8">0.3</span><span style="color: #042299">, </span>pch<span style="color: #042299">=</span><span style="color: #2b6fb8">2</span><span style="color: #042299">,</span>col<span style="color: #042299">=</span><span style="color: #b0140c">"grey93"</span><span style="color: #042299">)</span></div><div><span style="color: #042299"><br></span></div></div><div><br></div><div>You see, this is not that difficult. I just need to see how to fully implement this in the existing structure of BIOMOD, the most difficult part obviously. </div><div><br></div><div>Cheers,</div><div><br></div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><br><blockquote type="cite"><div><br>Thanks for the attention,<br><br>Best regards,<br><br>Charles<br><br>-- <br>Um axé! :)<br><br>--<br>Charles Novaes de Santana<br>PhD student - Global Change<br>Laboratorio Internacional de Cambio Global<br>Department of Global Change Research<br>Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)<br>Calle Miquel Marques 21, 07006<br>Esporles - Islas Baleares - España<br>_______________________________________________<br>Biomod-commits mailing list<br><a href="mailto:Biomod-commits@lists.r-forge.r-project.org">Biomod-commits@lists.r-forge.r-project.org</a><br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits<br></div></blockquote></div><br><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: 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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: 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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-style-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: +33 (0)4 76 51 44 97</div><div>fax: +33 (0)4 76 51 42 79</div><div><br></div><div>Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br>Personal website: <a href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br><br>FP6 European MACIS project: <a href="http://www.macis-project.net/">http://www.macis-project.net</a><br>FP6 European EcoChange project: <a href="http://www.ecochange-project.eu/">http://www.ecochange-project.eu</a></div><div><br></div></span></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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