<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Wilfried</div><div><br></div><div>Thanks for the suggestions to drop low performing techniques (CTA, ANN and SRE) and redundant evaluation methods (KAPPA), and to choose another pseudo absence strategy (random). I look forward to reading the paper, and that's all great practical guidance. </div><div><br></div><div>I ran all the models mostly for exploratory purposes, with the assumption that i could identify the worst performers with evaluation scores and drop them from Ensemble.Forecasting ( ) with flags such as weight.method='proportional', decay = 1.6, <a href="http://qual.th">qual.th</a> = 0.5. With that said, it makes since to drop weak approaches up front, so thanks again for the advice.</div><div><br></div><div>In case there are other methods producing curious errors besides CTA, a different species fell over yesterday on FDA, with the following error:</div><div><div>Model=Flexible Discriminant Analysis </div><div><font class="Apple-style-span" color="#b6212a">Error in family$linkfun(mustart) : </font></div><div><font class="Apple-style-span" color="#b6212a"> Argument mu must be a nonempty numeric vector</font></div></div><div><font class="Apple-style-span" color="#000001"><br></font></div><div><font class="Apple-style-span" color="#000001">Cheers, </font></div><div><font class="Apple-style-span" color="#000001">Jason</font></div><div><font class="Apple-style-span" color="#b6212a"><br></font></div><div><br></div><br><div><div>On Feb 10, 2012, at 6:11 PM, Wilfried Thuiller wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Jason,</div><div><br></div><div>The problem is related to the classification tree. It seems the tree has no branches and BIOMOD does not manage to get the optimal number of leaves. </div><div>My take on that is that your species is very difficult to model for CTA and it does not manage to find any good combination of variables explaining the distribution. </div><div>Perhaps we need to make an error trap around this call as this is not the first time we got this error, which is not a BIOMOD bug, but rather the failure of CTA to find an optimal number of leaves. </div><div>I will suggest removing the model for this species.</div><div><br></div><div>Looking at the code you sent with this message and the other one, I would also suggest:</div><div><br></div><div>Removing some techniques. Some generally performed quite poorly compared to the other ones. CTA and ANN are the weakest ones. SRE is more like a null model, the most liberal. I would drop the three. </div><div>Same for evaluation, you do not need to use both TSS and KAPPA, they are quite redundant. Just keep TSS, less influenced by prevalence and ROC. </div><div><br></div><div>I would recommend using "random" for pseudo absence instead of SRE or circle which tends to over fit a bit the data.</div><div>I take the liberty to send you this paper in press with Methods in Ecology and Evolution that discuss the different strategies for selecting pseudo-absence:</div><div><a href="http://www.will.chez-alice.fr/pdf/BarbetMEE2012.pdf">PDF</a></div><div><br></div><div>Hope it helps,</div><div><br></div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><br><div><div>Le 7 févr. 2012 à 05:06, jason b mackenzie a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="Arial">Dear all,</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">I recently had a BIOMOD run crash mid-stream after 20+ species appear to have run successfully. The error message is pasted below. Any ideas or workarounds? </font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><div><span class="Apple-style-span" style="font-family: Arial; "><i>...</i></span></div><div><font class="Apple-style-span" face="Arial"><i>#####<span class="Apple-tab-span" style="white-space: pre; "> </span> ERFA2 <span class="Apple-tab-span" style="white-space: pre; "> </span>#####</i></font></div><div><font class="Apple-style-span" face="Arial"><i>#####<span class="Apple-tab-span" style="white-space: pre; "> </span> pseudo-absence run 1 <span class="Apple-tab-span" style="white-space: pre; "> </span>#####</i></font></div><div><font class="Apple-style-span" face="Arial"><i>Model=Artificial Neural Network </i></font></div><div><font class="Apple-style-span" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span> 3 Fold Cross Validation + 3 Repetitions </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Calibration and evaluation phase: Nb of cross-validations: 3 </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Evaluating Predictor Contributions in ANN ... </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Model=Classification tree </i></font></div><div><font class="Apple-style-span" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span> 50 Fold Cross-Validation </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Error in newx$cptable[max(keep), 1L] <- cp : subscript out of bounds</i></font></div></div><div><font class="Apple-style-span" face="Arial"><i><div>> warnings()</div><div>Warning messages:</div><div>1: In predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type == ... :</div><div> prediction from a rank-deficient fit may be misleading</div></i></font><span class="Apple-style-span" style="font-family: Arial; "><i><div style="display: inline !important; ">2: In cor(g.pred[, ], as.integer(.Rescaler4(as.numeric(predict(model.sp, ... :</div></i></span><font class="Apple-style-span" face="Arial"><i><div> the standard deviation is zero</div><div>...</div></i></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">FYI, not sure if this matters, but my starting conditions were set as follows:</font></div><div><div style="color: rgb(12, 32, 153); font-size: 12px; "><font class="Apple-style-span" face="Arial"><br></font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#000001" face="Arial"><i>Initial.State(<span class="Apple-style-span" style="font-size: 12px; ">Response</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">SP.ENV</span><span class="Apple-style-span" style="font-size: 12px; ">[,</span><span class="Apple-style-span" style="font-size: 12px; ">12</span><span class="Apple-style-span" style="font-size: 12px; ">:</span><span class="Apple-style-span" style="font-size: 12px; ">75</span><span class="Apple-style-span" style="font-size: 12px; ">],</span><span class="Apple-style-span" style="font-size: 12px; "> Explanatory</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">SP.ENV</span><span class="Apple-style-span" style="font-size: 12px; ">[,</span><span class="Apple-style-span" style="font-size: 12px; ">4</span><span class="Apple-style-span" style="font-size: 12px; ">:</span><span class="Apple-style-span" style="font-size: 12px; ">11</span><span class="Apple-style-span" style="font-size: 12px; ">],</span><span class="Apple-style-span" style="font-size: 12px; "> IndependentResponse</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">NULL</span><span class="Apple-style-span" style="font-size: 12px; ">,</span><span class="Apple-style-span" style="font-size: 12px; "> </span></i></font></div><div style="font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>IndependentExplanatory=NULL)</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><br></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i>Models(GLM = FALSE, GAM = TRUE, Spline=4, GBM = TRUE, No.trees = 3000, CTA = TRUE, CV.tree = 50, ANN = TRUE, CV.ann = 3, </i></font></div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>SRE = TRUE, quant = 0.025, FDA = TRUE, MARS = TRUE, RF = TRUE, NbRunEval = 3, DataSplit = 70, </i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>Yweights = NULL, Roc = TRUE, Optimized.Threshold.Roc = TRUE, Kappa = TRUE, TSS = TRUE, </i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>KeepPredIndependent = FALSE, VarImport = 5, NbRepPA = 2, strategy = "sre", nb.absences = 1000)</i></font></div><div style="color: rgb(12, 32, 153); margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><span style="color: rgb(12, 32, 153); "><font class="Apple-style-span" face="Arial"><br></font></span></div></div></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Thanks in advance for any help!</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Cheers, </font></div><div><font class="Apple-style-span" face="Arial">Jason</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial"><br></font></span></div><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial"><br></font></span></div><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial">--</font></span></div></div><div><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; "><font class="Apple-style-span" face="Arial"><span class="Apple-style-span" style="border-collapse: separate; font-size: medium; font-variant: 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; "><span class="Apple-style-span" style="border-collapse: separate; font-size: medium; font-variant: 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 style="color: rgb(0, 0, 0); "><br></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">jason b mackenzie</font></div><div><font class="Apple-style-span" color="#5c5c5c">80 banambila street</font></div><div><font class="Apple-style-span" color="#5c5c5c">aranda, act 2614</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C"><br></font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">0447 002 629 [mobile]</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">jasonbmackenzie [skype]</font></div><div style="color: rgb(0, 0, 0); "><br></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></font></div></div></div><font class="Apple-style-span" face="Arial">
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<br></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><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></blockquote></div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; 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; font-size: medium; "><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; 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; 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; 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></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; "><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; font-family: 'Helvetica Neue'; 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; font-family: 'Helvetica Neue'; 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; font-family: 'Helvetica Neue'; 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; "><span class="Apple-style-span" style="border-collapse: separate; font-family: 'Helvetica Neue'; 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 style="color: rgb(0, 0, 0); "><br class="Apple-interchange-newline"><font class="Apple-style-span" color="#5C5C5C">--</font></div><div style="color: rgb(0, 0, 0); "><br></div><div style="color: rgb(0, 0, 0); "><b><font class="Apple-style-span" color="#5C5C5C">jason b mackenzie</font></b></div><div><font class="Apple-style-span" color="#5c5c5c">80 banambila street</font></div><div><font class="Apple-style-span" color="#5c5c5c">aranda, act 2614</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C"><br></font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">0447 002 629 [mobile]</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">jasonbmackenzie [skype]</font></div><div style="color: rgb(0, 0, 0); "><br></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span></div></span></div></span></span>
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