[Biomod-commits] (no subject)

[Javier Nori]

Dear Deamien:
Thank you very much for  your answer!
myExpl are rasters --- myExpl<-stack("D:/prueba/ACA/bio1","D:/ .....---I
don't understand how to use the function 'getprediction' with these rasters.

after some adjustments in the script, I do not get any errors (console or
warning). However, although I can create the raster for all the individual
projections, I'm unable to generate the total consensus files. My list of
files:

> list.files("Bammody/proj_current/")
[1] "Bammody.current.projection.out"
[2] "proj_current_Bammody.img"
[3] "proj_current_Bammody.img.aux.xml"
[4] "proj_current_Bammody_TSSbin.img"
[5] "proj_current_Bammody_TSSbin.img.aux.xml"
[6] "proj_current_ClampingMask.img"
[7] "proj_current_ClampingMask.img.aux.xml"

I'm probably forgetting some lines in my script. I would like to send you
the files and maybe you can help me find the 'mistake'. Would that be
possible?

Thanks in advance
Javier.


2013/9/2 Damien Georges <damien.georges2 at gmail.com>

>  Dear Javier,
>
> Your scripts seem to be ok.
> Do you get a console error message when you make ensemble and/or
> projections?
>
> Is 'myExpl' a rater or a dataframe? If it is a raster you can access
> projected raster with get_prediction() function else you will get a
> data.frame that you will have to rasterize manually.
>
> Hope that helps,
> Damien.
>
> PS : If you don't work with the last version of the package, I recommend
> you to update it (* install.packages("biomod2", repos=
> "http://R-Forge.R-project.org" <http://R-Forge.R-project.org>)*) That
> will probably solve your evaluation issue.
>
>
> On 23/08/2013 19:23, Javier Nori wrote:
>
> Dear all!
>
> I am new with Biomod. I'm trying to perform an ensemble between results of
> five algorithms ('MARS','GAM','GBM', 'MAXENT', 'GLM', 'FDA'), using
> Pres-PAbs data. I have not problems to generate and project the results of
> the individual models. However probably i'am making a mistake in the
> emsemble of them or in the projection' script because I cannot generate the
> rasters of the ensemble. In addition, I cannot obtain the values of the
> evaluation index of the ensemble (*Error: Error in (function (classes,
> fdef, mtable)  :   unable to find an inherited method for function
> ‘getModelsEvaluations’ for signature ‘"BIOMOD.EnsembleModeling.out"’*)
>
> Could anyone help me please?
>
> Thanks in advance!!
>
> below I attached the scripts for projection and ensemble
> **
> Ensemble
> myBiomodEM <- BIOMOD_EnsembleModeling(
> modeling.output = myBiomodModelOut,
> chosen.models = 'all',em.by='all',
> eval.metric = c('ROC'),
> eval.metric.quality.threshold = c(0.8),
> 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' )
>
> Projection
> myBiomodProj <- BIOMOD_Projection(
> modeling.output = myBiomodModelOut,
> new.env = myExpl,proj.name = 'current',
> selected.models = 'all',
> binary.meth = 'TSS',
> filtered.meth ='TSS',
> cmpress = 'gzip',
> clamping.mask = T,
> output.format = '.img')
>
>
>
>
>


-- 
***************************************************************************
Javier Nori

Centro de Zoología Aplicada - F.C.E.F.y.N.
Universidad Nacional de Córdoba