[Biomod-commits] How to plot individual projections?

[Damien Georges]

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
>