<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Hakim,</div><div>I have no clue. It seems the GAM has failed to run for whatever reason independent of BIOMOD. </div><div>It happens sometimes when you do not have enough data to calibrate the full model or when the GAM does not manage to converge. </div><div>Try to run it off BIOMOD but I am pretty sure the results will be the same. The easiest solution is to turn GAM as wrong for that particular species. </div><div><br></div><div>Cheers,</div><div>Wilfried</div><div><br></div><br><div><div>Le 23 oct. 2009 à 21:42, Hakim Abdi a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear All:</div><div><br></div><div>I'm getting the following error when loading the GAM model:</div><div><br></div><div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> load("models/SPECIES1_GAM_full")</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> SPECIES1_GAM_full</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Family: binomial </span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Link function: logit </span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Formula:</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">SPECIES1 ~ s(BAND5, 3) + s(BAND7, 3)</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Estimated degrees of freedom:</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Error in x$smooth[[i]]$first.para : </span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"> $ operator is invalid for atomic vectors</span></div><div><br></div><div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> summary(SPECIES1_GAM_full)</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">NULL</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Formula:</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">NULL</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Error in if (x$m > 0) { : argument is of length zero</span></div>
</div></div><div><br></div><div>While the GLM model returns the following:</div><div><br></div><div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> load("models/SPECIES1_GLM_full")</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> SPECIES1_GLM_full</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Call: glm(formula = SPECIES1 ~ I(BAND7^3) + BAND4 + I(BAND5^2), family = binomial, data = DataBIOMOD[calib.lines, ], weights = Yweights[calib.lines, i]) </span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br></span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Coefficients:</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">(Intercept) I(BAND7^3) BAND4 I(BAND5^2) </span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"> -6.566e-01 -3.090e-06 -1.373e-02 1.527e-04 </span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);"><br>
</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Degrees of Freedom: 342 Total (i.e. Null); 339 Residual</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Null Deviance: 467.3 </span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Residual Deviance: 428.4 AIC: 436.4 </span></div></div><div><br></div><div>My model setup parameters are as follows:<br></div><div><br>
</div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">> Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = F, No.trees = 3000, GAM = T, CTA = F, CV.tree = 50, ANN = F, CV.ann = 2, SRE = F, Perc025=T, Perc05=F, MDA = F, MARS = F, RF = F, NbRunEval = 2, DataSplit = 80, Yweights=NULL, Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent = F, VarImport=5, NbRepPA=0, strategy="circles", coor=CoorXY, distance=2, nb.absences=1000)</span><br>
</div><div><br></div><div>Am I missing something?</div><div><br></div><div>Thanks in advance for the assistance.</div><div><br></div><br>-- <br>Mit freundlichen Grüßen/Regards<br>__________________________________<br>Hakim Abdi<br>
Erasmus Mundus Master's Programme<br><br>Institut für Geoinformatik<br>Universität Münster<br>32U 5755408.16mN, 404463.35mE<br><a href="http://ifgi.uni-muenster.de/">ifgi.uni-muenster.de</a><br><br>Instituto Superior de Estatística e Gestão de Informação<br>
Universidade Nova de Lisboa<br>29S 4287095.5mN, 486099.7mE<br><a href="http://www.isegi.unl.pt/">www.isegi.unl.pt</a><br><br><a href="http://www.geospatialtechnologist.com/">www.geospatialtechnologist.com</a><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></blockquote></div><br><div>
<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-align: auto; 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><span class="Apple-style-span" style="font-size: 12px; "><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 63 54 53</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>Home page: <a href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>Website: <a href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm">http://www-leca.ujf-grenoble.fr/equipes/tde.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></span><br class="Apple-interchange-newline">
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