[Biomod-commits] Ensemble Modelling error

[Damien Georges]

Dear Jesus,

What version of biomod2 are you working with?

The error you have is due to a bug during DataFormating (see your odd 
models names e.g 'P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GAM' containing a 
$..). The strange thing is that seems to be a machine dependent bug.. 
Could you please send me the console output of your 
BIOMOD_FormatingData() function?
If you are agree, you can send me off-line your script and your 
dataset.. I will try to reproduce and correct the bug you have.

All the best,
Damien

On 24/06/2013 10:20, Jesus wrote:
> Dear Damien,
>
> I continuously get the following error message when computing the Ensemble
> models:
>
> "Error in `[.data.frame`(prediction.kept, , models.kept) :
>    undefined columns selected"
>
> The code I use is:
>   myBiomodEM <- BIOMOD_EnsembleModeling(
> + modeling.output = myBiomodModelOut,
> + chosen.models = "all",
> +   em.by='all',
> + eval.metric = c('TSS'),
> + eval.metric.quality.threshold = NULL,
> + prob.mean = T,
> + prob.cv = T,
> + prob.ci = T,
> + prob.ci.alpha = 0.05,
> + prob.median = T,
> + committee.averaging = T,
> + prob.mean.weight = T,
> + prob.mean.weight.decay = 'proportional')
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Build Ensemble Models
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
>     ! all models available will be included in ensemble.modeling
>     ! No eval.metric.quality.threshold -> All models will be kept for
> Ensemble Modeling
>
>    > TotalConsensus ensemble modeling
>     > TSS
>     > models kept :  P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GAM,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN1_RF,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GLM,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GBM,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GAM,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN2_RF,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GLM,
> P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GBM,
> P.ayacahuite_pa.data.tmp$pa.tab_Full_GAM,
> P.ayacahuite_pa.data.tmp$pa.tab_Full_RF,
> P.ayacahuite_pa.data.tmp$pa.tab_Full_GLM,
> P.ayacahuite_pa.data.tmp$pa.tab_Full_GBM
>     ! Models projections for whole zonation required...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GAM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN1_RF ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GLM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN1_GBM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GAM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN2_RF ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GLM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_RUN2_GBM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_Full_GAM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_Full_RF ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_Full_GLM ...
>> Projecting P.ayacahuite_pa.data.tmp$pa.tab_Full_GBM ...
> Error in `[.data.frame`(prediction.kept, , models.kept) :
>    undefined columns selected
>
>
> ***I have been trying to figure out exactly what is going on but have not
> been successful. The single models seem to be OK.
>
> Could you please give me an insight about it?
>
> Cheers,
>
> Jesus
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