[Biomod-commits] Ensemble.Forecasting error

[Wilfried Thuiller]

Hi there,
You should not have to edit the function if you updated the BIOMOD package. We have made quite a few changes in Ensemble.Forecasting the last weeks. The last version has been update a week ago.
As far as I can tell, the FDA = TRUE is indeed in the function. 
Best
WIlfried



Le 15 avr. 2010 à 19:19, Alisa Wade a écrit :

> I solved my own problem. The Ensemble.Forecasting function needs to be edited to change MDA to FDA.  Then it runs. 
> 
> On Thu, Apr 15, 2010 at 10:59 AM, Alisa Wade <alisaww at gmail.com> wrote:
> I am receiving an Ensemble.Forecasting error that I can not solve. Has anyone else seen this?
> 
> Here are my calls:
> 
> #Notes: 
> #MDA=T must be changed to FDA = T; incorrect in the manual, correct in the online help pages
> #Need this to make ANN to work (says invalid weight vector in nnet)
> caseweights =matrix(ncol = ncol(spp.Mat), nrow = nrow(spp.Mat)); caseweights[,] =1 
> 
> Models(GLM = T, TypeGLM = "quad", Test = "AIC", GBM = T, No.trees = 3000, GAM = T, 
> CTA = T, CV.tree = 50, ANN = T, CV.ann = 3, SRE = T, Perc025=T, Perc05=F, FDA = T, 
> MARS = T, RF = T, NbRunEval = 4, DataSplit = 80,Yweights=caseweights, 
> Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent = F, VarImport=5, 
> NbRepPA=0)
> 
> ##all outputs look correct/exist; Evaluation.results.xxx all exist (except for SRE under Roc is NA)
> 
> 
> Projection (Proj = env.Dat.Fut[,c(1, 3:20)], Proj.name = "NCAR_fut", GLM = T, 
> GBM = T, GAM = T, CTA = T, ANN = T, SRE = T, Perc025 = T, Perc05 = F, 
> FDA = T, MARS = T, RF = T, BinRoc = T, BinKappa = T, BinTSS = T, 
> FiltRoc = T, FiltKappa = T, FiltTSS = T, repetition.models=TRUE)
> 
> ##all outputs look correct/exist
> 
> 
> And here is my ensemble call attempts and resulting errors:
> 
> ##If I use FDA instead of MDA, it gives me an FDA error, no matter what  weight.method or bin.method I use or no matter if FDA turned on or off
> 
> Ensemble.Forecasting(ANN = T, CTA=T, GAM = T, GBM = T, FDA=T, GLM = T, MARS = T, RF = T, SRE = F, Proj.name= "NCAR_fut", weight.method='Kappa', PCA.median=T, binary=T, bin.method='Kappa', Test=T, decay=2, repetition.models=F)
> 
> Error in Ensemble.Forecasting(ANN = T, CTA = T, GAM = T, GBM = T, FDA = T,  : 
>   unused argument(s) (FDA = T)
> 
> ##If I use MDA, then I get a parse error, no matter the bin method
> 
> Ensemble.Forecasting(ANN = T, CTA=T, GAM = T, GBM = T, MDA=T, GLM = T, MARS = T, RF = T, SRE = F, Proj.name= "NCAR_fut", weight.method='Roc', PCA.median=T, binary=T, bin.method='Roc', Test=T, decay=2, repetition.models=F)
> Error in !eval(parse(text = j)) : invalid argument type
> 
> Is this just a problem with ensemble.forecasting using the old MDA terminology when all the other functions have been changed to FDA?
> Or am I doing something wrong?
> 
> Thanks for any ideas,
> Alisa
> -- 
> *****************************************************
> Alisa A. Wade
> Postdoctoral Center Associate
> National Center for Ecological Analysis and Synthesis
> wade at nceas.ucsb.edu
> (406) 529-9722
> home email: alisaww at gmail.com
> 
> 
> 
> -- 
> *****************************************************
> Alisa A. Wade
> Postdoctoral Center Associate
> National Center for Ecological Analysis and Synthesis
> wade at nceas.ucsb.edu
> (406) 529-9722
> home email: alisaww at gmail.com
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--------------------------
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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