<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>hi there all,</div><div><br></div><div>Good point Brenna.</div><div><br></div><div>Funny enough, I wrote the function BestModel more than 10 years ago where the basic thing of comparing different techniques was new. </div><div>I made that for this paper:</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; ">Thuiller, W. (2003) Biomod: Optimising predictions of species distributions and projecting potential future shifts under global change. <i>Global Change Biology</i>, <b>9</b>, 1353-1362</div></div><div><br></div><div>However, as recommended by Brenna, this is not something really recommended anymore as ensemble forecasts are much more robust than the best model. </div><div>Thanks for the paper.</div><div><br></div><div>There is also that one:</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; ">Araújo, M.B., Pearson, R.G., Thuiller, W. & Erhard, M. (2005) Validation of species-climate impact models under climate change. <i>Global Change Biology</i>, <b>11</b>, 1504-1513</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; ">Araújo, M.B., Whittaker, R.J., Ladle, R. & Erhard, M. (2005) Reducing uncertainty in projections of extinction risk from climate change. <i>Global Ecology and Biogeography</i>, <b>14</b>, 529-538</div></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; ">Marmion, M., Parviainen, M., Luoto, M., Heikkinen, R.K. & Thuiller, W. (2009) Evaluation of consensus methods in predictive species distribution modelling. <i>Diversity and Distributions</i>, <b>15</b>, 59-69</div></div><div>Thuiller, W. (2004) Patterns and uncertainties of species' range shifts under climate change. Global Change Biology, 10, 2020-2027<br><br></div><div><br></div><div>We let the function BestModel for people who wants to quickly extract which is the best model for a given data but this is something which should be applied when extrapolating the models into new areas or time.</div><div><br></div><div>Cheers</div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><br><div><div>Le 20 févr. 2012 à 14:47, Brenna Forester a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello Damien and Andreas --<br><br>I just wanted to comment on Andreas' question #2, "Is the best model for my dataset also the best for a new dataset?"<br><br>This is not necessarily the case, and (in my opinion) is one of the main arguments for using an ensemble approach to forecasting species distributions onto new time period or locations. A recent reference on this topic is:<br><br>Heikkinen RK, Marmion M, Luoto M (2011) Does the interpolation accuracy of species distribution models come at the expense of transferability? Ecography:1–13. DOI: 10.1111/j.1600-0587.2011.06999.x<br><br>Cheers,<br>Brenna<br><br>~~~~~~<br>Brenna Forester<br>PhD Student<br>Landscape Ecology Lab<br>Duke University<br>Durham, NC, US<br><br><br>________________________________________<br>From: <a href="mailto:biomod-commits-bounces@r-forge.wu-wien.ac.at">biomod-commits-bounces@r-forge.wu-wien.ac.at</a> [<a href="mailto:biomod-commits-bounces@r-forge.wu-wien.ac.at">biomod-commits-bounces@r-forge.wu-wien.ac.at</a>] on behalf of Damien Georges [<a href="mailto:damien.georges2@gmail.com">damien.georges2@gmail.com</a>]<br>Sent: Monday, February 20, 2012 5:16 AM<br>To: <a href="mailto:biomod-commits@r-forge.wu-wien.ac.at">biomod-commits@r-forge.wu-wien.ac.at</a><br>Subject: Re: [Biomod-commits] Biomod-commits Digest, Vol 34, Issue 15<br><br>Hi Andreas,<br><br>Here some comments and partial answer to your questions..<br><br><br>1) How can I obtain info about the predictive performance of a model on my already known localities? There are three functions, Models(), CurrentPred() and PredictionBestModel(), whose differences I find hard to understand.<br><br>The main function of BIOMOD is Models(), you have to run its function which all other functions needs to be computed.<br>Models run all selected models('GLM', 'GAM', 'RF'....) with data given to InitialState() function. It also does evaluation of each model predictive performance according to an accurancy metric (Roc, TSS or Kappa). This evaluations are stored in objects in your workspace called "Evaluation.results.Roc", "Evaluation.results.TSS" or "Evaluation.results.Kappa".<br><br>CurrentPred() returns the predictions of all selected models using InitialState() input data (considered as current data). It creates objects in the pred/ folder. Objects are a 4 dimensions arrays by species (may be several obects if you have decide to do binary or filtering transformation). All models, all PA selection, and all repetition are stored in this object (dim2, dim3 and dim4 respectively)<br><br>PredictionBestModel() does the same but keep only the best model for each Evaluation run and PA selection (so it's a 3D array). The best model is selected according to TSS, Roc or Kappa score. Noting is returne but objects are created in the pred/ folder.<br><br><br><br><br>2) Under what criterion can someone chose the best model for new datasets (e.g. other regions or climate change scenarios)? Is the best model for my dataset also the best for a new dataset?<br><br>That effectively the assumption we made.<br><br><br><br><br>3) What is the difference between Projections() and Ensemble.Forecasting()? Which of these two functions is suitable for predicting the species' presence in another region??<br><br>Projections give predictions of all models run on new environmental dataset.. (future or new zone for instance). It produce a 4D array like describe upper. object are stored in a new folder create when you compute this function.<br><br>Ensemble.Forcasting try to give you a consensus modeling projection, that means that every selected model will be contribute (more or less depending on arguments given) to a consensus and supposed better projection. So you get a 3D array containing the "consensus projections" for all evaluation run and all PA selections<br><br><br><br>4) I have information about my species' presence but not for their absence. Does this still mean that I have to create a presence-absence table and then use pseudo-absences?<br><br>Yes because models needs presences and absences to compute..<br><br><br>Hope that helps you,<br><br>Cheers.<br><br>Damien<br><br>On 19/02/2012 12:00, <a href="mailto:biomod-commits-request@r-forge.wu-wien.ac.at">biomod-commits-request@r-forge.wu-wien.ac.at</a> wrote:<br><blockquote type="cite">Send Biomod-commits mailing list submissions to<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"><br></blockquote><blockquote type="cite">To subscribe or unsubscribe via the World Wide Web, visit<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">or, via email, send a message with subject or body 'help' to<br></blockquote><blockquote type="cite"> <a href="mailto:biomod-commits-request@lists.r-forge.r-project.org">biomod-commits-request@lists.r-forge.r-project.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You can reach the person managing the list at<br></blockquote><blockquote type="cite"> <a href="mailto:biomod-commits-owner@lists.r-forge.r-project.org">biomod-commits-owner@lists.r-forge.r-project.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When replying, please edit your Subject line so it is more specific<br></blockquote><blockquote type="cite">than "Re: Contents of Biomod-commits digest..."<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Today's Topics:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> 1. New with BIOMOD; how can I predict my species distributions<br></blockquote><blockquote type="cite"> in another region? (Andreas Soteriades)<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">Message: 1<br></blockquote><blockquote type="cite">Date: Sat, 18 Feb 2012 10:50:06 -0800 (PST)<br></blockquote><blockquote type="cite">From: Andreas Soteriades<<a href="mailto:andreassot10@yahoo.com">andreassot10@yahoo.com</a>><br></blockquote><blockquote type="cite">To: "<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="mailto:biomod-commits@lists.r-forge.r-project.org">biomod-commits@lists.r-forge.r-project.org</a>><br></blockquote><blockquote type="cite">Subject: [Biomod-commits] New with BIOMOD; how can I predict my<br></blockquote><blockquote type="cite"> species distributions in another region?<br></blockquote><blockquote type="cite">Message-ID:<br></blockquote><blockquote type="cite"> <<a href="mailto:1329591006.42296.YahooMailNeo@web121305.mail.ne1.yahoo.com">1329591006.42296.YahooMailNeo@web121305.mail.ne1.yahoo.com</a>><br></blockquote><blockquote type="cite">Content-Type: text/plain; charset="iso-8859-1"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am trying to learn BIOMOD by using the sample Sp.Data and by following the instructions in BIOMOD Tutorial, 2012.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">What interests me is to predict species distributions in other regions or under climate change scenarios. Unfortunately, I have not really understood what is the procedure to follow; I am afraid that the tutorial can be very confusing for non experts in SDM...?Here are my questions:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">1) How can I obtain info about the predictive performance of a model on my already known localities? There are three functions, Models(), CurrentPred() and PredictionBestModel(), whose differences I find hard to understand.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">2) Under what criterion can someone chose the best model for new datasets (e.g. other regions or climate change scenarios)? Is the best model for my dataset also the best for a new dataset?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">3) What is the difference between Projections() and Ensemble.Forecasting()? Which of these two functions is suitable for predicting the species' presence in another region??<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">4) I have information about my species' presence but not for their absence. Does this still mean that I have to create a presence-absence table and then use pseudo-absences?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Andreas<br></blockquote><blockquote type="cite">-------------- next part --------------<br></blockquote><blockquote type="cite">An HTML attachment was scrubbed...<br></blockquote><blockquote type="cite">URL:<<a href="http://lists.r-forge.r-project.org/pipermail/biomod-commits/attachments/20120218/71c7bb87/attachment-0001.html">http://lists.r-forge.r-project.org/pipermail/biomod-commits/attachments/20120218/71c7bb87/attachment-0001.html</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">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">End of Biomod-commits Digest, Vol 34, Issue 15<br></blockquote><blockquote type="cite">**********************************************<br></blockquote><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>_______________________________________________<br>Biomod-commits mailing list<br>Biomod-commits@lists.r-forge.r-project.org<br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits<br></div></blockquote></div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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>ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html">http://www.will.chez-alice.fr/Research.html</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><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
</div>
<br></body></html>