[Biomod-commits] you have to load the projections yourself?

[Damien Georges]

Dear Josep,

I guess the issue you have comes from a specific combination of 
parameters you used (keep.in.memory=F , do.stack=F ) that are not well 
supported yet within biomod2.

If the projecting step is not too much time consuming, please re-run it 
with do.stack=T then try to build ensemble-models

myBiomodProj.Present <- BIOMOD_Projection ( modeling.output =
myBiomodModelOut,
new.env = expl.var ,
proj.name = paste(gcm,'_strategy_',strategy,sep=''),
selected.models = 'all',
binary.meth = 'TSS',
compress = 'xz',
clamping.mask = T,
keep.in.memory=F  ,
do.stack=T
)

Is it working better?

If not, please try this code:

rasterOptions(todisk=T)

myBiomodProj.Present <- BIOMOD_Projection ( modeling.output =
myBiomodModelOut,
new.env = expl.var ,
proj.name = paste(gcm,'_strategy_',strategy,sep=''),
selected.models = 'all',
binary.meth = 'TSS',
compress = 'xz',
clamping.mask = T,
keep.in.memory=T  ,
do.stack=T
)


Hope that helps,
Best,
Damien.



On 09/05/2013 12:27, Josep M Serra diaz wrote:
> Dear List!
>
> am sure it is a silly error but I am getting stack...
>
> I did my modeling and my projection to present (hurra!)
>
> but when I want to apply my ensemble modeling rules to the projections...it
> says:
>
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Do
> Ensemble Models Projections
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
>
>          > Projecting Pinuspinaster_GLM_AllRun_EMbyTSS ...
>                  > em.mean
> !! You have to load your projections by yourself !!Error en
> raster:::mean(raster:::subset(getProjection(projection.output),  :
>    error in evaluating the argument 'x' in selecting a method for function
> 'mean': Error en subset.default(getProjection(projection.output),
> getEMkeptModels(EM.output,  :
>    'subset' must be logical
>
> #################################################################
>
> .... SO THEN I TRIED DOING FIRST
>
> myPresenetProj <- getProjection(myBiomodProj.Present)
>
> but...error:
>
> !! You have to load your projections by yourself !!
>
>
> ##################################################################
>
> HERE YOU HAVE THE CODE I USED
>
>
>
> ##### PROJECTION OUTPUT
>
> myBiomodProj.Present <- BIOMOD_Projection ( modeling.output =
> myBiomodModelOut,
> new.env = expl.var ,
> proj.name = paste(gcm,'_strategy_',strategy,sep=''),
> selected.models = 'all',
> binary.meth = 'TSS',
> compress = 'xz',
> clamping.mask = T,
> keep.in.memory=F  ,
> do.stack=F
> ) #end BIOMOD_PROJECTION
> # NOW THE ENSEMBLE FORECASTING FOR PROJECTIONS IN CRU FOR EACH ALGORITHM
>
> myPresentProj <- getProjection(myBiomodProj.Present)
>
> myBiomodProj.EF.algo.Present <- BIOMOD_EnsembleForecasting (
>   projection.output= myBiomodProj.Present  , # name of the projection
>                                                                EM.output =
> myBiomodEM.algo , # modeling rules
>
> binary.method= "TSS"
>                                                              ) #end
> BIOMOD_PROJECTION
>
>
> ######################################################################
> HERE YOU HAVE SESSION INFO
>
>> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
>   LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] splines   grid      stats     graphics  grDevices utils     datasets
>   methods   base
>
> other attached packages:
>   [1] mgcv_1.7-22         foreign_0.8-52      biomod2_2.1.20      pROC_1.5.4
>           plyr_1.8            rpart_4.1-0         randomForest_4.6-7
>   mda_0.4-2
>   [9] class_7.3-5         gbm_2.0-8           survival_2.37-2     nnet_7.3-5
>           rasterVis_0.20-05   hexbin_1.26.1       latticeExtra_0.6-24
> RColorBrewer_1.0-5
> [17] lattice_0.20-13     abind_1.4-0         raster_2.1-16       sp_1.0-8
>
>
> loaded via a namespace (and not attached):
> [1] Matrix_1.0-11 nlme_3.1-108  tools_2.15.3  zoo_1.7-9
>
>
> #################################################################
>
> ANY HELP IS GREATLY APPRECIATED THANKS A LOT
>
>
> Pep
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