[seek-beam] GARP pipeline diagrams
Deana Pennington
dpennington at lternet.edu
Tue Apr 15 10:40:08 PDT 2003
>
>but from another area (continent usually), where the
> species is supposed to invade.
Aha! This one statement makes it all fall into place! I kept trying to
make sense of it in one area.
The diagrams were not all that ambiguous, they were actually pretty
good...I was able to figure out most of what you expanded on below.
Thanks! Deana
>
>
> Deana Pennington wrote:
>
>> Ricardo,
>>
>> I am trying to understand conceptually the differences between the 3
>> diagrams...
>>
>> 1. The native species diagram is clear.
>> 2. Climate change diagram. Looks to me like the difference is that
>> you run the analyses twice..once with a set of layers representing
>> current climatic differences, then with a different set of layers
>> representing environmental conditions after climate change, then
>> compare the results.
>> 3. Invasive species diagram. This is the one I'm having trouble
>> with. It's the same as the climate change diagram, except that you
>> take the original point data for the invading species and check it
>> against the output invaded range map. Please summarize conceptually
>> what it is you are doing in this diagram. What is the difference
>> between the native range and invaded range environmental layers in
>> this diagram?
>>
>> Thanks,
>> Deana Pennington
>>
>>
>> Ricardo Scachetti Pereira wrote:
>>
>>> Hi again Bill,
>>>
>>> I believe that now the diagrams are readable.
>>> I changed the letter references on the diagrams so they reflect
>>> unique data types.
>>> Also added a brief description of each analytical step and data type
>>> involved on file "GarpDiagramKeys.txt".
>>> Enjoy.
>>> Cheers,
>>>
>>> Ricardo
>>>
>>> Ricardo Scachetti Pereira wrote:
>>>
>>> > Hi, Bill.
>>> >
>>> > You might want to wait a little bit more so I can put more
>>> > information on the diagrams, before starting to process them.
>>> > I was just trying to get some feedback regarding the format of the
>>> > diagrams, and whether they will be useful in that format for BEAM.
>>> > I will now describe better each box and data type on every model,
>>> > so it is more readable and understandable.
>>> > I will keep you and the other group members posted.
>>> > All the best,
>>> >
>>> > Ricardo
>>> >
>>> > Bill Michener wrote:
>>> >
>>> >> Hi Ricardo,
>>> >>
>>> >> I will need some time to fully process the diagrams. But, I
>>> think they
>>> >> represent an incredibly valuable first step in the process. For the
>>> >> present, it does make the most sense to denote data types with
>>> letters.
>>> >>
>>> >> These diagrams will be quite valuable for presentation at the NCEAS
>>> >> working
>>> >> group meeting.
>>> >>
>>> >> Thanks for taking the initiative on this.
>>> >>
>>> >> More comments later,
>>> >>
>>> >> Bill
>>> >>
>>> >> William K. Michener
>>> >> LTER Network Office
>>> >> Department of Biology
>>> >> MSC03 2020
>>> >> University of New Mexico
>>> >> Albuquerque, NM 87131-0001
>>> >>
>>> >> Ph. 505.272.7831
>>> >> FAX 505.272.7080
>>> >>
>>> >> -----Original Message-----
>>> >> From: seek-beam-admin at ecoinformatics.org
>>> >> [mailto:seek-beam-admin at ecoinformatics.org]On Behalf Of Ricardo
>>> >> Scachetti
>>> >> Pereira
>>> >> Sent: Wednesday, March 19, 2003 5:43 AM
>>> >> To: seek-beam at ecoinformatics.org
>>> >> Subject: [seek-beam] GARP pipeline diagrams
>>> >>
>>> >> Dear, SEEK BEAM WG members,
>>> >>
>>> >> I believe that this is the first message posted to the SEEK BEAM
>>> >> mailing list, so welcome you all!!
>>> >>
>>> >> As I promised during our last meeting in New Mexico, I produced 3
>>> >> pipeline diagrams showing the data flow and the analytical steps
>>> >> involved in GARP Analyses.
>>> >> The diagrams are available at SEEK CVS repository, at
>>> >>
>>> >>
>>> http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/#dirlist
>>> >>
>>> >> From there, follow the links through /beam/niche modeling/garp
>>> >> directories to get to the diagrams.
>>> >>
>>> >> These are first drafts and I would like you guys to take a
>>> look and
>>> >> make suggestions and comments.
>>> >> There is a diagram for a native prediction, one for invasive
>>> species
>>> >> analysis and the last one is for climate change analysis.
>>> >> The numbers in parenthesis on each process box identify unique
>>> >> processes (repeated number refer to the same analytical step, but
>>> with
>>> >> different input data). Each data flow is also marked with one
>>> letter.
>>> >> Same letter refers to same data flowing (not only type but identical
>>> >> data). Should those letters refer to data flow types rather than
>>> unique
>>> >> data sets flowing? I think so, because that (data type) is what
>>> will be
>>> >> the target of SMS & KR WGs.
>>> >> The diagrams are a little bit oversimplified, regarding two
>>> >> procedures that are frequently used in GARP analysis. They are: i)
>>> >> jackknife of env layers to define which ones are more appropriate
>>> for
>>> >> analysis (between analytical step 1, 2 and 3), and the best subset
>>> >> procedure, in which we generate many GARP models and then sum
>>> them up to
>>> >> create a probability map instead of a boolean presence/absence
>>> >> prediction map. Those procedures might make the pipeline more
>>> >> complicated as they might require for loops and other complex
>>> >> constructions. So let's leave them out for now. I can add those
>>> >> complexities later on the diagrams for information purposes, if
>>> >> required.
>>> >> If the pipelines look good, I can add more detailed specs on each
>>> >> process and each data flow.
>>> >> Feel free to send comments and ask questions.
>>> >>
>>> >> That is about it for now.
>>> >> All the best,
>>> >>
>>> >> Ricardo
>>> >>
>>> >> PS. I'm (B)CC'ing this message to all Kansas KDI developers,
>>> also. We
>>> >> had some discussions about SEEK after the NM meeting, and they
>>> might be
>>> >> interested in following up. I would also like to invite the
>>> Kansas croud
>>> >> to join the mailing list, as I will use that as the primary
>>> >> communication means regarding BEAM activities.
>>> >>
>>> >>
>>> >> --
>>> >> Ricardo Scachetti Pereira
>>> >> Research Manager
>>> >> Centro de Referência em Informação Ambiental - CRIA
>>> >> http://www.cria.org.br/
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> This message has been scanned for viruses and
>>> >> dangerous content and is believed to be clean.
>>> >>
>>> >> _______________________________________________
>>> >> seek-beam mailing list
>>> >> seek-beam at ecoinformatics.org
>>> >> http://www.ecoinformatics.org/mailman/listinfo/seek-beam
>>> >>
>>> >>
>>> >> --
>>> >> This message has been scanned for viruses and
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>>> >>
>>> >>
>>> >>
>>> >
>>>
>>
>>
>
--
********
Dr. Deana D. Pennington
Long-term Ecological Research Network Office
UNM Biology Department
MSC03 2020
1 University of New Mexico
Albuquerque, NM 87131-0001
505-272-7460
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