<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Ahmed,</div><div><br></div><div><blockquote type="cite"><div class="hmmessage"><div dir="ltr"><div>I am new to BIOMOD, and I have a couple of problems while running FDA and RF .</div><div><span style="font-size: 10pt; ">I am using the latest version of R (2.14.2) and BIOMOD V1.1-7.00 downloaded from: </span><a href="http://www.will.chez-alice.fr/Software.html" style="font-size: 10pt; ">http://www.will.chez-alice.fr/Software.html</a><span style="font-size: 10pt; "> - I am using Windows 7 (32 bit) (3GB of ram - core i3)</span></div><div><br></div><div>While running RF, I am always got this error message:</div><div><i> Error: cannot allocate vector of size 596.2 Mb</i>
</div></div></div></blockquote><div><br></div><div>You do not enough RAM unfortunately. </div><div>Would be better to work on 64 bit machine. </div><div><br></div><div>However, you may give a try with this trick, not sure if this is gonna work, but let's give it a try:</div><div><br></div><div>Make a shortcut of the R.exe program.</div><div>Copy and paste this shortcut into your working directory.</div><div>Right click on the short cut and add the following command in the target window</div><div><br></div><div>
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<!--StartFragment--><p class="MsoNormal"><span lang="EN-US">--max-mem-size=5000000000<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">So in the target window, you'll have something like</span></p><div><br></div><div>"C:\Program Files\R\Rgui.exe" --max-mem-size=5000000000</div>
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<!--EndFragment--><p class="MsoNormal"><span lang="EN-US">Then double click on the shortcut and try again random forest.</span></p><div><br></div><div>If you are using Tinn-R, they is also a similar procedure that gives the same results. I do not know if it is working on Win7 (I am a Mac user) but it used to work on Win XP. </div>
<!--EndFragment--></div><div><br></div><blockquote type="cite"><div class="hmmessage"><div dir="ltr"><div>For FDA, it was working fine on the tutorial data but when I am trying to work on my own data, I am receiving this error:</div><div><div><i style="font-size: 10pt; "> </i><i>Error in if (min(Fit) < 0) Fit[Fit < 0] <- 0 : </i></div><div><i style="font-size: 10pt; "> m</i><i>issing value where TRUE/FALSE needed</i></div></div></div></div></blockquote><div><br></div><div>Sounds like the FDA does not work for your species. Better switch it off for now and see whether it works for your second species.</div><div><br></div><div>HIH,</div><div><br></div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><div><br></div><br><blockquote type="cite"><div class="hmmessage"><div dir="ltr"><div><br></div><div>I am pretty sure that there are no na values in my data using this command</div><div><i style="font-size: 10pt; "> </i><i>sum(is.na(currentclim))</i></div><div><i style="font-size: 10pt; "> </i><i>sum(is.na(species))</i> </div><div>in both cases I got 0 na values.</div><div><br></div><div>That is the code used to calibrate the models:</div><div><i>Initial.State (Response = species[,1:2], Explanatory = currentclim, IndependentResponse = species[,1:2], IndependentExplanator
y = currentclim)</i></div><div><i style="font-size: 10pt; "> </i><i>Models(</i></div><div><i style="font-size: 10pt; "> </i><i>GLM = T, TypeGLM = "poly", Test = "AIC",</i></div><div><i style="font-size: 10pt; "> </i><i>GBM = T, No.trees = 2000,</i></div><div><i style="font-size: 10pt; "> </i><i>GAM = T, Spline = 3,</i></div><div><i style="font-size: 10pt; "> </i><i>CTA = F, CV.tree = 50,</i></div><div><i style="font-size: 10pt; "> </i><i>ANN = T, CV.ann = 2,</i></div><div><i style="font-size: 10pt; "> </i><i>SRE = T, quant=0.025, # requires opening R with administrative previllages.</i></div><div><i style="font-size: 10pt; "> </i><i>FDA = T,</i></div><div><i style="font-size: 10pt; ">
</i><i>MARS = T,</i></div><div><i style="font-size: 10pt; "> </i><i># RF = T, </i></div><div><i style="font-size: 10pt; "> </i><i>NbRunEval = 3, DataSplit = 75, Yweights=NULL, </i></div><div><i style="font-size: 10pt; "> </i><i>Roc = T, Optimized.Threshold.Roc = T, Kappa = T, TSS=T,</i></div><div><i style="font-size: 10pt; "> </i><i>KeepPredIndependent = T, VarImport=5,</i></div><div><i style="font-size: 10pt; "> </i><i>NbRepPA=0, strategy="circles", coor=latlong,</i></div><div><i style="font-size: 10pt; "> </i><i>distance=0.125, nb.absences=1000)</i></div><div><br></div><div><br></div><div>This is the results:</div><div><i style="font-size: 10pt; ">----------------------------------- </i></div><div><div><i>Modelling summar
y </i></div><div><i>----------------------------------- </i></div><div><i>Number of species modelled : 2</i></div><div><i>sp1, sp2</i></div><div><i style="font-size: 10pt; ">numerical variables : bio3, bio5, bio6, bio7, bio8, bio9, bio10, bio11, bio15, bio16, bio19</i></div><div><i style="font-size: 10pt; ">number of evaluation repetitions : 3</i></div><div><i>number of pseudo-absences runs : 0</i></div><div><i>models selected : ANN, GAM, GBM, GLM, MARS, FDA, SRE</i></div><div><i>total number of model runs : 56</i></div><div><i>----------------------------------- </i></div><div><i style="font-size: 10pt; ">##### sp1
; #####</i></div><div><i>Model=Artificial Neural Network </i></div><div><i> 2 Fold Cross Validation + 3 Repetitions </i></div><div><i>Calibration and evaluation phase: Nb of cross-validations: 3 </i></div><div><i>Evaluating Predictor Contributions in ANN ... </i></div><div><i>Model=GAM spline </i></div><div><i> 3 Degrees of smoothing </i></div><div><i>Evaluating Predictor Contributions in GAM ... </i></div><div><i>Model=Generalised Boosting Regression </i></div><div><i> 2000 maximum different trees and lambda Fold Cross-Validation </i></div><div><i>Evaluating Predictor Contributions in GBM ... </i></div><div><i>Model=GLM polynomial + quadratic Stepwise procedure using AIC criteria </i></div><div><i>Evaluating Pre
dictor Contributions in GLM ... </i></div><div><i>Model=Multiple Adaptive Regression Splines </i></div><div><i>Evaluating Predictor Contributions in MARS ... </i></div><div><i>Model=Flexible Discriminant Analysis </i></div><div><i>Error in if (min(Fit) < 0) Fit[Fit < 0] <- 0 : </i></div><div><i> missing value where TRUE/FALSE needed</i></div></div><div><i><br></i></div><div><i><br></i></div><div>Thanks in advance,</div><div><span style="font-size: 10pt; ">Ahmed</span></div> </div></div>
_______________________________________________<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</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; "><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>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></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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