[Biomod-commits] Noisy binary prediction

[Wilfried Thuiller]

Dear Alexandre,
You did not correctly specifiy the XY coordinates in the level.plot function. You used the same variables that for running the models (back[,1:3]). I gathered these are the explanatory variables right? If you do have a CoorYX file, use it with level.plot

> level.plot(consensus_melinis_melinis_full_bin[,2], CoorYX)

Hope it helps,
Wilfried


Le 20 avr. 2010 à 04:41, alexandre sampaio a écrit :

> Hi,
> 
> I've produced an ensemble forecast prediction that have a noisy
> pattern of dispersion of binary presence points. There are some
> continuous areas of predicted presence but most of the prediction
> comes on scattered present points dispersed on systematic patterns
> like waves (see attached pic). Is this normal? Is this related to the
> method to create pseudo-absences? If not what may be causing it?
> 
> Thanks for the help!
> 
> Alexandre Sampaio
> 
> Code:
>  Initial.State(Response = back[,7], Explanatory = back[,1:3],
>  IndependentResponse = NULL, IndependentExplanatory = NULL,
>  sp.name="melinis")
> 
>  Models(GLM = T, TypeGLM = "poly", Test = "AIC", GBM = T, No.trees =
>  2000, GAM = T,
>  Spline = 3, CTA = T, CV.tree = 50, ANN = T, CV.ann = 2, SRE = T,
>  Perc025=T, Perc05=F, MDA = T,
>  MARS = T, RF = T, NbRunEval = 3, DataSplit = 80, Yweights=NULL, Roc =
>  T, Optimized.Threshold.Roc = T,
>  Kappa = T, TSS=T, KeepPredIndependent = F, VarImport=F, NbRepPA=1,
>  strategy="circles",
>  coor=CoorXY, distance=2, nb.absences=1000)
> 
>  Projection(Proj = back[,1:3], Proj.name='melinis', GLM = T, GBM = T, GAM = T,
>  CTA = F, ANN = T, SRE = T, MDA =T, MARS = T, RF = T,
>  BinRoc = T, BinKappa = T, BinTSS = T, FiltRoc = F, FiltKappa = F, FiltTSS = F,
>  repetition.models=T)
> 
>  Ensemble.Forecasting(Proj.name= "melinis", weight.method='Roc', PCA.median=T,
>  binary=T, bin.method='Roc', Test=F, decay=1.6, repetition.models=T)
> 
>  level.plot(consensus_melinis_melinis_full_bin[,2], back[,1:3])
> 
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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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