[Biomod-commits] How to plot individual projections?

Antonio Canepa ajcanepa at gmail.com
Wed May 22 11:16:42 CEST 2013

Hi Damien,
Thanks for the advice. the command plot(subset(proj_val,1)) works fine.


On 22 May 2013 10:22, Damien Georges <damien.georges2 at gmail.com> wrote:

>  Dear Antonio,
> The simplest way to process if you want to produce non -default plots is
> to extract the 'formal' projection information and to plot it with
> non-biomod plotting function.
> You can access "formal" projection values with getProjection(...) function
> (e.g. proj_val <- getProjection(myBiomodProj) ). Then, depending on if you
> made your projections with environmental raster or data.frame, the plotting
> function you will use will change.
> for RasterStack environment :
> plot(subset(proj_val,1)) will plot the first layer (i.e your first model
> projection)
> for data.frame, you have to get the XY data.fame that correspond to your
> projection points. Then you can make your plots with level.plot function
> (see ?level.plot for examples)
> the last thing you can do is to use the biomod2 plotting function you
> mentioned and increase the str.grep arg to precise the selection(e.g
> plot(myBiomodProj, str.grep = 'PA1_RUN1_GAM')
> Hope that helps,
> Damien.
> On 21/05/2013 23:20, Antonio Canepa wrote:
> Dear all,
> I have a silly question but I can't find the solution.
> I have my myBiomodProj, using the BIOMOD_Projection() function.
> Now I have like 36 projected models (4 models, 3PA, 3RUN), but I would like
> to plot them, individually). In the help file the most closer solution is:
> plot(myBiomodProj, str.grep = 'GAM'), but all the 3 Runs and 3 PA (9 plots)
> appears.
> Also I would like to change the color of the probabilities but I can't
> modify it through the color() command.
> I appreciate so much if you can give a hand on it!,
> Thank you, so much.
> Cheers,
> Antonio

Antonio Canepa Oneto
PhD student
Dept. Biologia Marina i Oceanografia
Institut de Ciencies Del Mar CMIMA, CSIC
Ps. Marítim de la Barceloneta,37-49, c.p. 08003
BARCELONA, Catalunya,Spain
Phone: +34 932 30 9500  (ext. 6067)
Mobile: +34 628 320 778
e-mail: canepa at icm.csic.es
           ajcanepa at gmail.com

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