<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Ashley,</div><div><br></div><div>Yes you need to update R and then BIOMOD. </div><div>I think we have addressed this problem which was in the Kappa/TSS calculation. </div><div>Please update and then let me know if the bug is still there. </div><div><br></div><div>Best</div><div>Wilfried</div><div><br></div><div><br></div><br><div><div>Le 14 sept. 2010 à 14:55, Ashley Brooks a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>I am using BioMod version 1.1-3 and R version 2.9.2. I suppose I should update these versions?<br>The following is what I typed into R to run the models and the error message I recieved. Also I have listed the summary of my data. Occurance is just the name of the column with my 0/1 info on species data. <br>
<br><br>> Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = T, No.trees = 2000, GAM = T, Spline = 3, CTA = T, CV.tree = 50, ANN = T, CV.ann = 3, SRE = T, Perc025=F, Perc05 = T, MDA = 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 = "circles", coor = Coors, distance = 2, nb.absences = 1000)<br>
<br><br>----------------------------------- <br>Modelling summary <br>----------------------------------- <br>Number of species modelled : 1<br>Occurance<br><br>numerical variables : curbio1cli, curbio2cli, curbio7cli, curbio12cl, curbio15cl, curbio17cl<br>
<br><br>number of evaluation repetitions : 3<br>number of pseudo-absences runs : 2<br>models selected : ANN, CTA, GAM, GBM, GLM, MARS, MDA, RF, SRE<br>total number of model runs : 72<br>
----------------------------------- <br><br><br>##### Occurance #####<br>##### pseudo-absence run 1 #####<br>Model=Artificial Neural Network <br> 3 Fold Cross Validation + 3 Repetitions <br>
Calibration and evaluation phase: Nb of cross-validations: 3 <br>Evaluating Predictor Contributions in ANN ... <br>Error in if (a != "NA") if (a > 0) { : <br> missing value where TRUE/FALSE needed<br>In addition: Warning message:<br>
In n1. * n.1 : NAs produced by integer overflow<br><br><br>summary(My.Data)<br> X Y curbio1cli curbio2cli curbio7cli curbio12cl curbio15cl <br> Min. :-106.65 Min. : 0.00 Min. : -4.0 Min. : 69.0 Min. :155.0 Min. : 170 Min. : 6.00 <br>
1st Qu.: -93.98 1st Qu.:33.35 1st Qu.: 89.0 1st Qu.:119.0 1st Qu.:337.0 1st Qu.: 798 1st Qu.:17.00 <br> Median : -87.65 Median :37.44 Median :130.0 Median :126.0 Median :368.0 Median :1015 Median :23.00 <br>
Mean : -78.52 Mean :34.31 Mean :127.9 Mean :127.4 Mean :370.6 Mean :1001 Mean :29.97 <br> 3rd Qu.: -78.94 3rd Qu.:41.65 3rd Qu.:169.0 3rd Qu.:134.0 3rd Qu.:403.0 3rd Qu.:1214 3rd Qu.:44.00 <br>
Max. : 0.00 Max. :49.35 Max. :247.0 Max. :186.0 Max. :505.0 Max. :2043 Max. :91.00 <br> curbio17cl Occurance <br> Min. : 6.0 Min. :0.000000 <br> 1st Qu.: 88.0 1st Qu.:0.000000 <br>
Median :184.0 Median :0.000000 <br> Mean :171.2 Mean :0.005968 <br> 3rd Qu.:246.0 3rd Qu.:0.000000 <br> Max. :480.0 Max. :1.000000 <br><br>Again, I am not sure where to start with troubleshooting. Any help would be most appreciated!<br>
<br>Ashley<br>
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<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; "><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>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></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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