[Biomod-commits] Question about: Error in if (a != "NA") if (a > 0)

[Wilfried Thuiller]

Hi Ashley,

Yes you need to update R and then BIOMOD. 
I think we have addressed this problem which was in the Kappa/TSS calculation. 
Please update and then let me know if the bug is still there. 

Best
Wilfried



Le 14 sept. 2010 à 14:55, Ashley Brooks a écrit :

> Hi,
> 
> I am using BioMod version 1.1-3 and R version 2.9.2.  I suppose I should update these versions?
> 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. 
> 
> 
> > 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)
> 
> 
> ----------------------------------- 
> Modelling summary 
> ----------------------------------- 
> Number of species modelled :            1
> Occurance
> 
> numerical variables :                   curbio1cli, curbio2cli, curbio7cli, curbio12cl, curbio15cl, curbio17cl
> 
> 
> number of evaluation repetitions :      3
> number of pseudo-absences runs :        2
> models selected :                       ANN, CTA, GAM, GBM, GLM, MARS, MDA, RF, SRE
> total number of model runs :            72
> ----------------------------------- 
> 
> 
> #####                    Occurance                      #####
> #####              pseudo-absence run 1                 #####
> Model=Artificial Neural Network 
>          3 Fold Cross Validation + 3 Repetitions 
> Calibration and evaluation phase: Nb of cross-validations:  3 
> Evaluating Predictor Contributions in  ANN ... 
> Error in if (a != "NA") if (a > 0) { : 
>   missing value where TRUE/FALSE needed
> In addition: Warning message:
> In n1. * n.1 : NAs produced by integer overflow
> 
> 
> summary(My.Data)
>        X                 Y           curbio1cli      curbio2cli      curbio7cli      curbio12cl     curbio15cl   
>  Min.   :-106.65   Min.   : 0.00   Min.   : -4.0   Min.   : 69.0   Min.   :155.0   Min.   : 170   Min.   : 6.00  
>  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  
>  Median : -87.65   Median :37.44   Median :130.0   Median :126.0   Median :368.0   Median :1015   Median :23.00  
>  Mean   : -78.52   Mean   :34.31   Mean   :127.9   Mean   :127.4   Mean   :370.6   Mean   :1001   Mean   :29.97  
>  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  
>  Max.   :   0.00   Max.   :49.35   Max.   :247.0   Max.   :186.0   Max.   :505.0   Max.   :2043   Max.   :91.00  
>    curbio17cl      Occurance       
>  Min.   :  6.0   Min.   :0.000000  
>  1st Qu.: 88.0   1st Qu.:0.000000  
>  Median :184.0   Median :0.000000  
>  Mean   :171.2   Mean   :0.005968  
>  3rd Qu.:246.0   3rd Qu.:0.000000  
>  Max.   :480.0   Max.   :1.000000  
> 
> Again, I am not sure where to start with troubleshooting.  Any help would be most appreciated!
> 
> Ashley
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--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Université Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Home page: http://www.will.chez-alice.fr
Website: http://www-leca.ujf-grenoble.fr/equipes/tde.htm

FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu





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