[seek-dev] Re: implementing garp in ptolemy

Deana Pennington dpennington at lternet.edu
Mon Nov 10 07:53:56 PST 2003


Chad,

These questions were discussed meticulously in the breakout group at 
Santa Barbara (see...you should have picked the other group :-)

The conclusion was that there are pieces within GARP that it would be 
nice to reuse, specifically, the sampling piece that splits the input 
samples into two groups (testing and training), which is currently shown 
on the pipeline as a separate piece..  However, Dave thinks it might be 
alot of work to change the code to make that work (but suggested Ricardo 
might think differently).  If the GARP code can be relatively easily 
rewritten to break out the steps that are in the pipeline, then we 
should do that, otherwise we should lump it all together as one step 
(which would make a much simpler pipeline).

Shawn has a revised species distribution pipeline that you should make 
sure you have.

Deana


Ricardo Scachetti Pereira wrote:

>Hi, Chad and all,
>
>I can provide all the details about GARP that you 
>need. 
>I'm in a middle of a household move, but a phone 
>call on Wednesday afternoon or Thursday would be 
>good for me.
>I'll be in Brazil which is now 6 hours ahead of 
>California Time.
>Let me know whether that works for you.
>
>Regards,
>
>Ricardo
>
>  
>
>>Hi All,
>>
>>I've been looking at trying to get GARP working 
>>    
>>
>in ptolemy a bit, and I 
>  
>
>>have a few questions.  First of all, is the 
>>    
>>
>modularity that is described 
>  
>
>>in the PPT files the modularity that you would 
>>    
>>
>want in a ptolemy model? 
>  
>
>>  for example, is the "data calculation" step in 
>>    
>>
>the "GARP Native 
>  
>
>>Species Pipeline" something that you would want 
>>    
>>
>to reuse in other 
>  
>
>>pipelines?  When I talked to Dave when we were 
>>    
>>
>here in SB, I got the 
>  
>
>>impression that he thought GARP should just be 
>>    
>>
>one atomic actor (is that 
>  
>
>>really what you think Dave?)  If these components 
>>    
>>
>are never going to be 
>  
>
>>reused for any other pipeline, then they should 
>>    
>>
>probably just be folded 
>  
>
>>into one generic GARP actor.
>>
>>I'd like get together, either physically or 
>>    
>>
>virtually, with someone that 
>  
>
>>can explain to me the exact steps that it takes 
>>    
>>
>to go from the training 
>  
>
>>data and layers to output.  The specifications of 
>>    
>>
>the modules within the 
>  
>
>>PPT documents are a bit vague.  For instance, I 
>>    
>>
>have no idea what data 
>  
>
>>calculation does.  A mid-level pseudo-code 
>>    
>>
>implementation of GARP might 
>  
>
>>be a good idea, as it would help me get my head 
>>    
>>
>around this thing a bit 
>  
>
>>more.
>>
>>Could any of you have a phone call next week?  
>>    
>>
>maybe wednesday since 
>  
>
>>tuesday is a holiday?
>>
>>chad
>>-- 
>>-----------------------
>>Chad Berkley
>>National Center for
>>Ecological Analysis
>>and Synthesis (NCEAS)
>>berkley at nceas.ucsb.edu
>>-----------------------
>>
>>
>>    
>>
>
>  
>

-- 
********

Deana D. Pennington, PhD
Long-term Ecological Research Network Office

UNM Biology Department
MSC03  2020
1 University of New Mexico
Albuquerque, NM  87131-0001

505-272-7288 (office)
505 272-7080 (fax)





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