[Biomod-commits] (no subject)

Damien Georges damien.georges2 at gmail.com
Mon Sep 2 14:25:11 CEST 2013

Hi Jenny,

On 14/08/2013 16:26, Jenny Williams wrote:
> I am still trying to get my head around biomod2. I have run through the tutorial a few times, which works really well in a linear format.
> But, I want to see the models and assess them at every part of the process. So, I need to:
> 1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed and all the file links are lost.
> e.g myBiomodModelOut
You just have to load the 'formated.input.data' object within 
/.BIOMOD_DATA/ directory. Then object loaded (i.e
myBiomodModelOut) is loaded as 'data' in your workspace. So typing smth 
like myBiomodModelOut <- data should let you re-run your previous script 
quite easily.

> 2: call the summary parameters for the models e.g GLM, I can see the files but not sure how to access them.
> e.g
>> myGLMs <- BIOMOD_LoadModels(myBiomodModelOut, models='GLM')
> #just produces a list
>> summary(myGLMs[1])
>     Length     Class      Mode
>     1 character character
> #summary(GLM) doesn't work, but is the output that I am looking to find.
Here objects are also loaded with standard names in your workspace. The 
names of objects are stored within  myGLMs (just type myGLMs in your 
console to get it)

> 3. find the split datasets used for each of the iterations BIOMOD_Modeling options; NbRunEval for DataSplit
This info are stored within calib.lines object of /.BIOMOD_DATA/ directory
> Any help or pointers in the right direction would be greatly appreciated.
> FYI the vignette does not seem to work:
I guess that it is due to package installation issue. reinstall the 
package should solve it.

Hope that helps,
> ******************
> Jenny Williams
> Spatial Information Scientist, GIS Unit
> Herbarium, Library, Art & Archives Directorate
> Royal Botanic Gardens, Kew
> Richmond, TW9 3AB, UK
> Tel: +44 (0)208 332 5277
> email: jenny.williams at kew.org<mailto:jenny.williams at kew.org>
> ******************
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