[Biomod-commits] memory error- again...

PEP Serra Diaz Josep.Serra at uab.cat
Mon Jul 5 16:47:22 CEST 2010

Dear BIOMODers,

I have a hughe dataset (more or less 70000 rows) and the error is, of course: cannot allocate vector size of 459.1 MB. (I already increased memory.limt ()  )

In that huge DF many species are recorded, so I though creating a litle loop so I could go species by species and therefore would not load a huge dataset (Question 1- Is that making any sense?). In each species model, presences and absences are equaled, so we keep prevalence constant, and the strategy of PseudoA selection is SRE. (see script below)

For the first species (only 4500 presences) R retrieves this memory error when computing RF, which I cannot understand for a DF of 9000 rows (P+A), and I even the number of repetitions is set to 1.

Secondly, I checked that BIOMOD creates an object: Biomod.PA.data with 40000 records aprox. I assume that these are the presences and the ALL absences selected outside the SurfaceRange (strategy selected), and later on BIOMOD will select the number of absences indicated (=Number of Presences in this case). Question 2- Is this correct or is it loading ALL absences outside the range? (maybe that's why it retrieves an error.) 

Question 3- Any suggestion?

# i corresponds to the column where the species Presence or Absence is located

for (i in "spColumID") {

Initial.State (Response=Sp.Env[,i], Explanatory=Sp.Env[,c(250,248,251,199,164,181)],IndependentResponse=NULL, IndependentExplanatory=NULL,sp.name=names[i])

Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = T, No.trees = 3000, GAM = T, Spline=2, CTA = T, CV.tree = 50, ANN = T, CV.ann = 2, SRE = F, FDA = T, MARS = T, RF = T, NbRunEval = 1, DataSplit = 70, Yweights=NULL, Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent = F, VarImport=5, NbRepPA=1, strategy="sre", coor=Coor, distance=2, nb.absences=sum(Sp.Env[,i]))


Thank you very much in advance for reading such a long post with 3 Questions!


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