[Biomod-commits] Error in BIOMOD v1.1-5 on R-2.11.1 running on Windows (i386)

[Wilfried Thuiller]

Dear Brenna,
Sorry we modified some functions recently notably 'Biomod.Models' called by the Models function. There was a mistake in the neural nets when providing independent weights. it seems another bug percolated from that.
Anyway, we uploaded a new version 3 hours ago which works perfectly fine. I just run the example. R-Forge should compile the package as binary in the next 24h.
You can also load the package as source and compile it yourself it is urgent:

install.packages("BIOMOD", repos="http://R-Forge.R-project.org", type="source")

Sorry for the inconvenience,

Best
Wilfried




Le 7 oct. 2010 à 19:39, Brenna Forester a écrit :

> Hello, I'm trying to run BIOMOD on a fresh install of R and the example code in ?Models is not executing. I'm running BIOMOD version 1.1-5 installed via install.packages("BIOMOD", repos="http://R-Forge.R-project.org")
> 
> and all packages are up-to-date using update.packages()
> 
> When running the example from Models I get:
> 
> > data(Sp.Env)
> > data(CoorXY)
> > #use fix(Sp.Env) to visualise the dataset
> >
> > #This command is necessary for the run of BIOMOD as a new dataframe is produced for the Models function
> > Initial.State(Response=Sp.Env[,12:14], Explanatory=Sp.Env[,4:10],
> + IndependentResponse=NULL, IndependentExplanatory=NULL)
> >
> > #Here are done 2 PA runs and 2 repetitions for each run. Here we will have 36 runs per species. This will hence take several minutes.
> > Models(GLM = TRUE, TypeGLM = "quad", Test = "AIC", GBM = TRUE, No.trees = 3000, GAM = TRUE, CTA = TRUE, CV.tree = 50,
> +    ANN = TRUE, CV.ann = 2, SRE = TRUE, quant=0.05, FDA = TRUE, MARS = TRUE, RF = TRUE, NbRunEval = 2, DataSplit = 80,
> +    Yweights=NULL, Roc=TRUE, Optimized.Threshold.Roc=TRUE, Kappa=TRUE, TSS=TRUE, KeepPredIndependent = FALSE, VarImport=5,
> +    NbRepPA=2, strategy="circles", coor=CoorXY, distance=2, nb.absences=1000)
> 
> -----------------------------------
> Modelling summary
> -----------------------------------
> Number of species modelled :            3
> Sp290, Sp277, Sp164
> 
> numerical variables :                   Var1, Var2, Var3, Var4, Var5, Var6, Var7
> 
> 
> number of evaluation repetitions :      2
> number of pseudo-absences runs :        2
> models selected :                       ANN, CTA, GAM, GBM, GLM, MARS, FDA, RF, SRE
> total number of model runs :            162
> -----------------------------------
> 
> 
> #####                    Sp290                  #####
> #####              pseudo-absence run 1                 #####
> Model=Artificial Neural Network
>          2 Fold Cross Validation + 3 Repetitions
> Calibration and evaluation phase: Nb of cross-validations:  2
> Error in Rescaler4(as.numeric(TempArray), ref = DataBIOMOD[PA.samp, NbVar +  :
>   object 'TempArray' not found
> >
> 
> 
> My version information is:
> 
> > version
>                _
> platform       i386-pc-mingw32
> arch           i386
> os             mingw32
> system         i386, mingw32
> status
> major          2
> minor          11.1
> year           2010
> month          05
> day            31
> svn rev        52157
> language       R
> version.string R version 2.11.1 (2010-05-31)
> 
> Thank you!
> Brenna
> _______________________________________
> 
> Brenna Forester
> 
> M.Sc. Candidate
> Huxley College of the Environment
> Western Washington University
> Bellingham, WA
> 
> forestb at students.wwu.edu
> 360-738-0711
> _______________________________________________
> 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
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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