<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>The main problem with Maxent (Maximum Entropy) is that this is a technique (like a GLM or Bayesian framework) and not the name of a model.</div><div><br></div><div>The Maxent you are refering to (in FD) is not made to a model species distributions but to retrieve abundance distribution within communities based on functional traits. </div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 36px; text-indent: -36px; font: normal normal normal 12px/normal Helvetica; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 36px; text-indent: -36px; font: normal normal normal 12px/normal Helvetica; ">Shipley, B., D. Vile, et al. (2006). From plant traits to plant communities: a statistical mechanistic approach to biodiversity. <i>Science</i> <b>314</b>, 812-814.</div></div><div><br></div><div>Cheers,</div><div>Wilfried</div><div><br></div><br><div><div>Le 25 avr. 2011 à 23:39, Charles Novaes de Santana a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Thank you very much for your answer, Wilfried!! That are really good<br>news!! It is good to know that you are working on it!<br><br>Just a comment more: Do you know that there is a package in R (FD)<br>that already have an implementation of MaxEnt? Would it be useful to<br>implement MaxEnt for BIOMOD?<br><br>- <a href="http://cran.r-project.org/web/packages/FD/">http://cran.r-project.org/web/packages/FD/</a><br>- <a href="http://cran.r-project.org/web/packages/FD/FD.pdf">http://cran.r-project.org/web/packages/FD/FD.pdf</a><br><br>Anyway, good luck with your great work!! I hope I can help you with<br>this someday in the future (I am still starting to know the world of<br>niche modeling... :) )<br><br>Charles<br><br>On Sat, Apr 23, 2011 at 10:38 AM, Wilfried Thuiller<br><<a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a>> wrote:<br><blockquote type="cite">Dear Charles,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">First of all, I must say that it is a great pleasure to read all the<br></blockquote><blockquote type="cite">interesting discussions we have in this list, we learn a lot with<br></blockquote><blockquote type="cite">every message! Thanks, and congratulations!!<br></blockquote><blockquote type="cite">Well, sorry if the question I will point here has been done before,<br></blockquote><blockquote type="cite">but I really didn't find anything about it in previous messages I<br></blockquote><blockquote type="cite">have:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is it posible to include MaxEnt among the models simulated by BIOMOD?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In my opinion, the great strength of BIOMOD, beyond many other<br></blockquote><blockquote type="cite">benefits, is to allow the ensemble of many models in an easy way, and<br></blockquote><blockquote type="cite">so to give us more confidence results of our simulations. But I see<br></blockquote><blockquote type="cite">that MaxEnt is often used to simulate distribution of species and<br></blockquote><blockquote type="cite">sometimes I ask myself why it is not included in BIOMOD (yet). Is it a<br></blockquote><blockquote type="cite">"stupid" question? (I really believe that there are NO "stupid"<br></blockquote><blockquote type="cite">questions, but... :-))<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This is indeed a very interesting question.<br></blockquote><blockquote type="cite">The answer is no and yes.<br></blockquote><blockquote type="cite">No because Maxent is coded in Java, much more efficient than in R. We'll<br></blockquote><blockquote type="cite">have to recode the entire program in C or C++ to fully integrate it in R and<br></blockquote><blockquote type="cite">latter in BIOMOD.<br></blockquote><blockquote type="cite">However, this is easy to run Maxent using a batch command from R. I have<br></blockquote><blockquote type="cite">thought about putting Maxent within BIOMOD that way since a while. I am just<br></blockquote><blockquote type="cite">to busy to do it but hope to start looking at that this year.<br></blockquote><blockquote type="cite">For curious, find below a short code for running Maxent from R.<br></blockquote><blockquote type="cite">You need the ascii data for running it and modify all paths and data for<br></blockquote><blockquote type="cite">your own data.<br></blockquote><blockquote type="cite">My species is Sp290.csv (Sp290 from SpEnv data in BIOMOD exported in csv<br></blockquote><blockquote type="cite">format for Maxent).<br></blockquote><blockquote type="cite">The environmental variables are the same than SpEnv, as many ascii files as<br></blockquote><blockquote type="cite">variables.<br></blockquote><blockquote type="cite">You need maxent.jar in your working directory.<br></blockquote><blockquote type="cite">dir.create(path=paste(getwd(), "/MaxEnt.res", sep=""))<br></blockquote><blockquote type="cite">MaxEnt.layers <- paste(getwd(), "/europe/ascii/current", sep="")<br></blockquote><blockquote type="cite">MaxEnt.out <- paste(getwd(), "/MaxEnt.res", sep="")<br></blockquote><blockquote type="cite">MaxEnt.samples <- paste(getwd(), "/europe/point", sep="")<br></blockquote><blockquote type="cite">layers <- list.files(MaxEnt.layers)<br></blockquote><blockquote type="cite"># run MaxEnt:<br></blockquote><blockquote type="cite">system(command=paste("java -jar maxent.jar environmentallayers=",<br></blockquote><blockquote type="cite">MaxEnt.layers, " samplesfile=", MaxEnt.samples, "/Sp290.csv", "<br></blockquote><blockquote type="cite">outputdirectory=", MaxEnt.out, " maximumiterations=100 redoifexists autorun<br></blockquote><blockquote type="cite">nowarnings notooltips", sep=""))<br></blockquote><blockquote type="cite"># NOT RUN<br></blockquote><blockquote type="cite">system(command=paste("java -mx4000m -jar maxent.jar environmentallayers=",<br></blockquote><blockquote type="cite">MaxEnt.layers, " samplesfile=", MaxEnt.samples, "/Sp290.csv", "<br></blockquote><blockquote type="cite">outputdirectory=", MaxEnt.out, " 'applythresholdrule=equal training<br></blockquote><blockquote type="cite">sensitivity and specificity' maximumiterations=100 redoifexists autorun<br></blockquote><blockquote type="cite">nowarnings notooltips", sep=""))<br></blockquote><blockquote type="cite">list.files(MaxEnt.out)<br></blockquote><blockquote type="cite">#Import the predictions on the presence points<br></blockquote><blockquote type="cite">Pred.Maxent.Sp290.sample <- read.csv(paste(getwd(),<br></blockquote><blockquote type="cite">"/MaxEnt.res/Sp290_samplePredictions.csv", sep=""))<br></blockquote><blockquote type="cite">#Plot the results from Maxent<br></blockquote><blockquote type="cite">library(BIOMOD)<br></blockquote><blockquote type="cite">par(mfrow=c(1,2))<br></blockquote><blockquote type="cite">level.plot(Sp.Env$Sp290, XY=Sp.Env[,2:3], color.gradient = "grey",<br></blockquote><blockquote type="cite">cex=0.3,show.scale=F, title="Original data")<br></blockquote><blockquote type="cite">level.plot(Pred.Maxent.Sp290.sample$Logistic.prediction,<br></blockquote><blockquote type="cite">XY=Pred.Maxent.Sp290.sample[,1:2], color.gradient = "grey",<br></blockquote><blockquote type="cite">cex=0.3,show.scale=F, title="Maxent")<br></blockquote><blockquote type="cite">points(Sp.Env[Sp.Env$Sp290<1,2], Sp.Env[Sp.Env$Sp290<1,3], cex=0.3,<br></blockquote><blockquote type="cite">pch=2,col="grey93")<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You see, this is not that difficult. I just need to see how to fully<br></blockquote><blockquote type="cite">implement this in the existing structure of BIOMOD, the most difficult part<br></blockquote><blockquote type="cite">obviously.<br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite">Wilfried<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks for the attention,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best regards,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Charles<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Um axé! :)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Charles Novaes de Santana<br></blockquote><blockquote type="cite">PhD student - Global Change<br></blockquote><blockquote type="cite">Laboratorio Internacional de Cambio Global<br></blockquote><blockquote type="cite">Department of Global Change Research<br></blockquote><blockquote type="cite">Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)<br></blockquote><blockquote type="cite">Calle Miquel Marques 21, 07006<br></blockquote><blockquote type="cite">Esporles - Islas Baleares - España<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Biomod-commits mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Biomod-commits@lists.r-forge.r-project.org">Biomod-commits@lists.r-forge.r-project.org</a><br></blockquote><blockquote type="cite"><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--------------------------<br></blockquote><blockquote type="cite">Dr. Wilfried Thuiller<br></blockquote><blockquote type="cite">Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br></blockquote><blockquote type="cite">Université Joseph Fourier<br></blockquote><blockquote type="cite">BP53, 38041 Grenoble cedex 9, France<br></blockquote><blockquote type="cite">tel: +33 (0)4 76 51 44 97<br></blockquote><blockquote type="cite">fax: +33 (0)4 76 51 42 79<br></blockquote><blockquote type="cite">Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br></blockquote><blockquote type="cite">Personal website: <a href="http://www.will.chez-alice.fr">http://www.will.chez-alice.fr</a><br></blockquote><blockquote type="cite">Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">FP6 European MACIS project: <a href="http://www.macis-project.net">http://www.macis-project.net</a><br></blockquote><blockquote type="cite">FP6 European EcoChange project: <a href="http://www.ecochange-project.eu">http://www.ecochange-project.eu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br><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">
</div>
<br></body></html>