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

[Brenna Forester]

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
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