<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Emilie,</div><div><br></div><div>Thank you for your email. </div><div><br></div><div>First of all, you have 73 variables which is way too much for most of the models included in BIOMOD. Either you make a pre-selection by removing highlightly correlated ones (for instance you can combine your temperature variable by calculating seasonal mean instead of monthly variables which are correlated in time. Same of precip and sdmav. If you can go down to 10-12 variables, it would be enough. OR you only use the techniques that can handle such a high number of variables (random forest, GBM). </div><div><br></div><div>Could you please send me your data (off-list) to see what is going on with your data (the first 100 rows will be sufficient). </div><div>Just a suggestion. Could you switch off ANN to see if the other models work? </div><div><br></div><div>Best</div><div>Wilfried</div><div><br></div><br><div><div>Le 16 févr. 2012 à 23:20, Emilie Roy-Dufresne a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><span style="">confirm 18ee744ad3977b59039ac17e53e4bc</span><span style="">7c154780d9</span> <br><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Hi!</div><div>I having some issues while trying to run the BioMod script in R. I keep getting this error message while I run the different models provided my BioMod with my data. What does it mean?</div><div><br></div>
<div><pre><span><span lang="EN-US" style="font-family:"Lucida Console";color:blue">> </span></span><span><span lang="EN-US" style="font-family:"Lucida Console";color:blue">Models(GLM=T,TypeGLM="poly",Test="AIC",GBM=T,No.trees=2000,GAM=T,Spline=3,CTA=T,CV.tree=50,ANN=T,CV.ann=2,SRE=T,quant=0.025,FDA=T,MARS=T,RF=T,NbRunEval=3,DataSplit=70,Yweights=NULL,Roc=T,Optimized.Threshold.Roc=T,Kappa=T,TSS=T,KeepPredIndependent=T,VarImport=5,NbRepPA=2,strategy="sre",coor=My.Data[,2:3],distance=2,nb.absences=100)</span></span><span lang="EN-US" style="font-family:'Lucida Console'"></span></pre><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">-----------------------------------
</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">Modelling
summary </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">-----------------------------------
</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">Number of
species modelled : 1</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">peromyscus</span></p><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">numerical
variables : photo01,
photo02, photo03, photo04, photo05, photo09, photo10, photo11, photo12,
allqcland, recancover, tminavg01, tminavg02, tminavg03, tminavg04, tminavg05,
tminavg06, tminavg07, tminavg08, tminavg09, tminavg10, tminavg11, tminavg12,
tmaxavg01, tmaxavg02, tmaxavg03, tmaxavg04, tmaxavg05, tmaxavg06, tmaxavg07,
tmaxavg08, tmaxavg09, tmaxavg10, tmaxavg11, tmaxavg12, trngavg, precavg01,
precavg02, precavg03, precavg04, precavg05, precavg06, precavg07, precavg08,
precavg09, precavg10, precavg11, precavg12, sdmavg01, sdmavg02, sdmavg03,
sdmavg04, sdmavg05, sdmavg06, sdmavg07, sdmavg08, sdmavg09, sdmavg10, sdmavg11,
sdmavg12, wlenavg, wpravg, wtmnavg, wtmxavg</span></p><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">number of
evaluation repetitions : 3</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">number of
pseudo-absences runs : 2</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">models
selected : ANN, CTA,
GAM, GBM, GLM, MARS, FDA, RF, SRE</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">total number
of model runs : 72</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">-----------------------------------
</span></p><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><div style="margin-bottom: 0.0001pt; "><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">##### peromyscus #####</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">#####
pseudo-absence run 1 #####</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">Model=Artificial
Neural Network </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> 2
Fold Cross Validation + 3 Repetitions </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">Calibration
and evaluation phase: Nb of cross-validations:
3 </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">Error in
parse(text = paste("Target[Samp$calibration]",
paste(.scopeExpSyst(Input[1:10, : </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> <text>:2:0: unexpected end of input</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'">1: 12 +
tmaxavg01 + tmaxavg02 + tmaxavg03 + tmaxavg04 + tmaxavg05 + tmaxavg06 +
tmaxavg07 + tmaxavg08 + tmaxavg09 + tmaxavg10 + tmaxavg11 + tmaxavg12 + trngavg
+ precavg01 + precavg02 + precavg03</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-US" style="font-size:10pt;font-family:'Lucida Console'"> ^</span></p></div><div><br></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><font face="'Lucida Console'">Thank you,</font></p>
<span style="font-family:Tahoma;font-size:13px"><div><font face="Tahoma"><u>____________________________________</u></font></div><span class="HOEnZb"><font color="#888888"><div><font face="Tahoma">Emilie Roy-Dufresne</font></div>
<div><font face="tahoma">M. Sc. Candidate Geography Department - McGill - Biogeography studies</font></div>
<div><font face="tahoma">Guide en tourisme d'aventure</font></div></font></span></span><br>
</blockquote></div><br><br>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); 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; color: rgb(0, 0, 0); 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; 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; "><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></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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