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