[seek-beam] GARP pipeline diagrams
Ricardo Scachetti Pereira
ricardo at cria.org.br
Tue Apr 15 10:28:55 PDT 2003
Hi, Deana,
Your questions are pertinent. Let me try to clarify some points.
On the climate change diagram, the model (rule set) is obtained only
once (but the notation does not make that clear). This very same rule
set is then projected into the current geography and the geography
changed by some climate change model. So the analysis is run only once.
The result is then projected onto 2 different set of environmental layers.
That is because we assume that the basic environmental conditions
required for the species to maintain populations (which is expressed by
the rule set) does not change from one scenario (native distribution) to
the climate change scenario.
Actually, looking at the climate change diagram again, it looks
ambiguous. The rule set flowing out of step 3 (rule set development)
into both projections (step 4) is the same rule set. There should be
just one arrow, that would be split in two arrows instead of two arrows.
I think that this is a limitation of Data Flow Diagrams. Sorry about that.
So if you check CVS again, you will notice that I tried to removed
that ambiguity on notation. Arrows representing the same instance of
data flow are now linked together.
Also, to summarize conceptually, the three kinds of environmental
layers we use in this method are:
1) Native layers: environmental layers from the native range of the
species, from the same period in time when the species was collected. It
is the only dataset used to produce GARP models;
2) Climate changed layers: climate layers on the native range of the
species changed following a climate change model (global circulation
models). They are usually a prediction of how temperature, rainfall,
etc, will be in the future if a climate change scenario takes place (or
in the past);
3) Invaded range: same kind of environmental layers used for native
range predictions, but from another area (continent usually), where the
species is supposed to invade.
Conceptually, a model (GARP rule set, obtained from a GARP run)
describes the the set of environmental conditions that allow the species
to survive. Once we have a rule set, we can project that rule set into a
set of layers modified due to climate changes, or we can project it into
a continent where the species has never been before, to have an idea
where in that landscape the species would be able to survive.
To project, in this context, means to apply the rule set to a set of
environmental layers, i.e., to identify or highlight in the landscape,
what would be the cells or points that match the conditions for the
species to survive.
In summary, that is about it. For more details on the procedure, I
suggest you to refer to the literature. There is a preliminary list on
DesktopGarp web site at:
http://www.lifemapper.org/desktopgarp
Follow the link to the user's manual, then to bibliography, or click
the direct link below:
http://www.lifemapper.org/desktopgarp/Default.asp?Item=3&Lang=1#bib
I hope this clarified things a bit.
Cheers,
Ricardo
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/
>> >>
>> >>
>> >>
>> >> --
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>> >>
>> >> _______________________________________________
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>> >> seek-beam at ecoinformatics.org
>> >> http://www.ecoinformatics.org/mailman/listinfo/seek-beam
>> >>
>> >>
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>> >>
>> >>
>> >
>>
>
>
--
Ricardo Scachetti Pereira
Gerente de Pesquisa
Centro de Referência em Informação Ambiental - CRIA
http://www.cria.org.br/
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