[seek-beam] GARP pipeline diagrams

[Bill Michener]

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/



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