[Biomod-commits] error message FDA - RF

Ahmed El-Gabbas ahmed_elgabass at hotmail.com
Tue Mar 6 18:20:53 CET 2012

Hello Biomoders,
I am new to BIOMOD, and I have a couple of problems while running FDA and RF .I am using the latest version of R (2.14.2) and BIOMOD V1.1-7.00 downloaded from: http://www.will.chez-alice.fr/Software.html - I am using Windows 7 (32 bit) (3GB of ram - core i3)
While running RF, I am always got this error message:        Error: cannot allocate vector of size 596.2 Mb

For FDA, it was working fine on the tutorial data but when I am trying to work on my own data, I am receiving this error:        Error in if (min(Fit) < 0) Fit[Fit < 0] <- 0 :         missing value where TRUE/FALSE needed
I am pretty sure that there are no na values in my data using this command        sum(is.na(currentclim))        sum(is.na(species)) in both cases I got 0 na values.
That is the code used to calibrate the models:Initial.State (Response = species[,1:2], Explanatory = currentclim, IndependentResponse = species[,1:2], IndependentExplanatory = currentclim)        Models(        GLM = T, TypeGLM = "poly", Test = "AIC",        GBM = T, No.trees = 2000,        GAM = T, Spline = 3,        CTA = F, CV.tree = 50,        ANN = T, CV.ann = 2,        SRE = T, quant=0.025,   # requires opening R with administrative previllages.        FDA = T,        MARS = T,        # RF = T,                       NbRunEval = 3, DataSplit = 75, Yweights=NULL,         Roc = T, Optimized.Threshold.Roc = T, Kappa = T, TSS=T,        KeepPredIndependent = T, VarImport=5,        NbRepPA=0, strategy="circles", coor=latlong,        distance=0.125, nb.absences=1000)

This is the results:----------------------------------- Modelling summary ----------------------------------- Number of species modelled :            2sp1, sp2numerical variables :                   bio3, bio5, bio6, bio7, bio8, bio9, bio10, bio11, bio15, bio16, bio19number of evaluation repetitions :      3number of pseudo-absences runs :        0models selected :                       ANN, GAM, GBM, GLM, MARS, FDA, SREtotal number of model runs :            56----------------------------------- #####                    sp1                    #####Model=Artificial Neural Network          2 Fold Cross Validation + 3 Repetitions Calibration and evaluation phase: Nb of cross-validations:  3 Evaluating Predictor Contributions in  ANN ... Model=GAM spline          3  Degrees of smoothing Evaluating Predictor Contributions in  GAM ... Model=Generalised Boosting Regression          2000 maximum different trees and lambda Fold Cross-Validation Evaluating Predictor Contributions in  GBM ... Model=GLM polynomial + quadratic         Stepwise procedure using AIC criteria Evaluating Predictor Contributions in  GLM ... Model=Multiple Adaptive Regression Splines Evaluating Predictor Contributions in  MARS ... Model=Flexible Discriminant Analysis Error in if (min(Fit) < 0) Fit[Fit < 0] <- 0 :   missing value where TRUE/FALSE needed

Thanks in advance,Ahmed 		 	   		  
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