[Biomod-commits] Projection.raster ERROR
PEP Serra Diaz
Josep.Serra at uab.cat
Wed Mar 9 22:22:23 CET 2011
Hi there,
Wilfried, you were right, just a typo in the script I could not see it. Sorry again for the inconveniences. It just kind of scared me the error message "Models() failure".
Thanks.
Pep
Pep Serra Díaz
Despatx C1/211
Unitat de Botànica.
Departament de Biologia Animal, Biologia Vegetal i Ecologia.
Facultat de Biociències. Edifici C. Campus de Bellaterra
Universitat Autònoma de Barcelona
08193 Cerdanyola del Vallès
Spain
----- Missatge original -----
De: Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
Data: Dimarts, Març 8, 2011 11:31 pm
Assumpte: Re: [Biomod-commits] Projection.raster ERROR
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Dear Pep,
Are sure to be in the right working directory? Sounds like the function does not find the models. I guess that if you run the Projection function, let's say on the original data (Sp.Env[,c("BIO1","BIO12","BIO14","BIO5","BIO6")]), this is not going to work either. Right?
For instance, there is something wrong. In the WARNING message, it looks for repetition 4 whereas you only set up 3 evaluation (NbRunEval = 3). This is why I suspect a mix of data/workspace.
Have you tried to plot the rasters?
plot(Proj_CurrentRaster_QUWI_BinTSS_PA1_ANN.raster)
I'll suggest to create a new working directory, set the working directory with R (setwd()) and then re-run everything. Let me know if this is working better.
Cheers,
Wilfried
Le 9 mars 2011 à 02:31, PEP Serra Diaz a écrit :
>
> Dear BIOMODers,
>
> It may be a stupid question. First time I am seriously running Projection.raster function. I get this error :
>
> WARNING: Could not find data for model ANN evaluation repetition 1 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 2 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 3 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 4 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 1 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 2 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 3 . Probable cause : failure when running Models()
> WARNING: Could not find data for model ANN evaluation repetition 4 . Probable cause : failure when running Models()
> .....
> and so on for all models
> ...
>
> RESULT: It creates projections full of NAs
>
>
> I run the Models function as I normally do. I checked evaluation results and different models and their outputs after running Models(). Everything seems to work ok but projection. Here it is the whole R history:
>
>
> Initial.State(Response=Sp.Env[,i], Explanatory=Sp.Env[,c("BIO1","BIO12","BIO14","BIO5","BIO6")], IndependentResponse=NULL, IndependentExplanatory=NULL, sp.name=naam[sp])
>
> Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = T, No.trees = 3000, GAM = T, CTA = T, CV.tree = 50, ANN = T, CV.ann = 2, SRE = F, FDA = T, MARS = T, RF = T, NbRunEval = 3, DataSplit = 70, Yweights=NULL, Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent = F, VarImport=T, NbRepPA=3, strategy="random", nb.absences=5000)
>
>
> Projection.raster(RasterProj = CurrentStack, Proj.name='CurrentRaster', GLM = T, GBM = T, GAM = T, CTA = T, ANN = T, SRE = F, FDA=T, MARS = T, RF = T, BinRoc = F, BinKappa = F, BinTSS = T, FiltRoc = F, FiltKappa = F, FiltTSS = F, repetition.models=T, stack.out=F)
>
>
>> ls()
> [1] "Biomod.material" "Biomod.PA.data"
> [3] "Biomod.PA.sample" "CurrentBio1"
> [5] "CurrentBio12" "CurrentBio14"
> [7] "CurrentBio5" "CurrentBio6"
> [9] "CurrentStack" "DataBIOMOD"
> [11] "Evaluation.results.Kappa" "Evaluation.results.Roc"
> [13] "Evaluation.results.TSS" "GBM.list"
> [15] "GBM.perf" "isnullYweights"
> [17] "naam" "path"
> [19] "Proj_CurrentRaster_QUWI_BinTSS_PA1_ANN.raster" "root"
> [21] "Sp.Env" "sp.name"
> [23] "VarImportance"
>
>
>
>
>
>
>
>
> Pep Serra Díaz
>
> Despatx C1/211
> Unitat de Botànica.
> Departament de Biologia Animal, Biologia Vegetal i Ecologia.
> Facultat de Biociències. Edifici C. Campus de Bellaterra
> Universitat Autònoma de Barcelona
> 08193 Cerdanyola del Vallès
> Spain
>
>
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
--------------------------
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
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu
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