Purell 11Sep2006 Desktop Garp
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Transcript of Purell 11Sep2006 Desktop Garp
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The World According to GARP *or
Using presence points to map a species using theGenetic Algorithm for Rule-set Production (GARP)
Melora K. PurellTropical Conservation Biology and Environmental Science
Masters Program
University of Hawaii - Hilo
*with apologies to Mr. John Irving
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Overview
Some niche modeling theory Primer for using Desktop GARP
Practical advice and examples
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Niche Modeling
Where is species X likely to be found?
Applications:Rare/threatened/endangered species
Alien/exotic/invasive species
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Niche Modeling
Climatic or environmentalparametersPoints of known presence
Nichemodel/map
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Environmental Envelopes
Fuzzy EnvelopeCrisp Envelope vs.
Parameters are definedrelative to each other.
Example - The species is found inareas that are:
Less than 500 m, if theannual rainfall is >250 mm
and the slope is < 5%.Greater than 500m, if thereis koa forest present andannual rainfall is > 300 mm.
Exact parameters defined foreach environmentalvariable.
Example - The species is foundin areas that are always:
Above 500 m elevation
Less than 3% slope
Mesic koa and/or ohiaforest
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GARP
GARP is a genetic algorithm that creates ecologicalniche models for species.
These fuzzy envelope models describe environmentalconditions under which the species should be able tomaintain populations.
GARP uses a set of point localities where the species isknown to occur and . . .
A set of geographic layers representing theenvironmental parameters that might limit the species'capabilities to survive.
*from the Desktop GARP website
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Genetic algorithm is a search technique used in
computing to find true or approximate solutions to
optimization and search problems. It involvesmultiple iterations of rule-setting in order to best fit
the samples to the desired outcome.
GARP is creating rules about theenvironment that will make all thepoints fit into the predicted range.
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GARP inputs
1. Create MS Excel file with presencelocations
2. Choose GIS layers to use ensure allare same projection and same spatial
resolution ( ArcMap )3. Clip GIS layers in ArcView using GARP
Datasets extension4. Create a GARP Dataset using Dataset
Manager
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GARP inputs
Data points in Excel
No te:
(decimald egr ees)
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GARP inputs
Environmental Layers
Rasters/gridsAll layers must have
same projectionSpatial resolution andspatial extent dependon your study area
Kohala Mountain
10m resolution
Windward aspect raster
Rainfall grid
Main Hawaiian islands100m resolution
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GARP inputs
Making the grids that GARP likes . . .
1. In ArcView , turn on
Spatial Analyst extensionand add grids to the frame
Also add one polygon asa mask for the entirestudy area
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GARP inputs Making the grids that GARP likes . . .
2. Use the GARP Datasetsextension to clip grids and
resample to the same cellsize.
And after a few more questions. . .
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GARP inputs
Thats the ASCIIraster grid that can
be input into GARP!
Voila!
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GARP inputs
Creating a GARP Dataset using Dataset Manager
1. Put all your ASCII grids into one folder2. Copy one of your grids in the folder and
rename it mask.asc
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GARP inputs Creating a GARP Dataset using Dataset Manager
3. Load your layers by choosing one
grid in your folder
4. Type in some
dataset info thensave into thesame folder
Now you have a Dataset of Environmental Layersto use in the Desktop GARP program.
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Running GARP
Upload Excel File
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Running GARP
Load Dataset
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Running GARP Make decisions about
runs, rules and points
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Choose output formatand file locations
Running GARP
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Running GARP Run the program!
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GARP outputs
Maps as ASCII grids
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GARP outputs
Statistics as Excel file
GA
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GARP outputsSome key stats. . .
The total number of cells that werenot covered by the rules
GARP
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GARP outputsSome key stats. . .
The % of the land area that waspredicted as presence
GARP
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GARP outputsSome key stats. . .
Error: the percentage of presence points thatdid not fit in the predicted presence area
M ki ti l
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Making an optimal map
Choose 20 runs that have the best fit for% predicted area presence (commission)and the lowest omission error, as well asno non-predicted areas.
Add those 20 maps together in GIS tocreate an optimal map with cells valuesthat range from 0 to 20.
Areas with high cell values have a highprobability of being accurate.
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Examples of Optimal GARP maps
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Examples of Optimal GARP maps
Examples of Optimal GARP maps
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Examples of Optimal GARP maps
58 presencepoints from field
samplingElevation, Slope,Windward aspectand Rainfall layers
Masters thesisproject andpotential use ininvasive speciesmanagement
Examples of Optimal GARP maps
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Examples of Optimal GARP maps
Examples of Optimal GARP maps
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Examples of Optimal GARP maps
550 presence
points frommultiple sources
Elevation, Slope,Windward aspectand Rainfall layers
Cost-benefitanalysis forbiological control
Thing to Consider with GARP
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Thing to Consider with GARP
Presence Points
must be spatially independent .
need to represent the full extent of the speciesacross the range of the environmental variables:
- very difficult with rare species
- invasive species that are still spreading - field sampling vs. museum records - output range
Thing to Consider with GARP
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Thing to Consider with GARP
GIS layers
must include all available layers that mayinfluence species distribution
must be continuous/numerical variables no
classes, categories, or ranksmust be reliable : garbage in, garbage out!
Thing to Consider with GARP
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Thing to Consider with GARP
Some Important Strengths
GARP works with whatever GIS layers youhave the output spatial resolution andextent depend upon the GIS layers you use
The output from GARP is spatially complete
It is easy to run 100s of GARP models, sooutputs can be averaged, eliminatingpotential machine learning errors
Wang and Wang, 2006
Thing to Consider with GARP
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Thing to Consider with GARP
One Major Weakness
The GARP rule sets are true black boxes. Theuser can infer the rules from the output, but notin sufficient detail to make strong statementsabout ecological mechanisms that lead to thepredicted distributions.
With great appreciation to . . .
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With great appreciation to . . .My Spatial nalysis gurus
Lisa Canale, ITER program manager
Cynthia Phillips, GIS specialist
Sun Park, PhD., UH-Hilo, Dept. of Geography My graduate committee :
Becky Ostertag, PhD., UH-Hilo, Dept. of Biology
Julie Denslow, PhD., USDA Forest Service
Rosemary Sherriff, PhD., UH-Hilo, Dept. of Geography
Sheldon Furutani, PhD., UH-Hilo, CAFNRM
Research assistants/hiking companions :
Shenandoah Marr, Randee Tubal, Steve Souder
and. . all those that helped me through the Desktop GARP list-serve
Thank You!