Overview for the EBM Tools NetworkJason Roberts and Ben Best, Duke University

15-Oct-2008

Duke Marine Geospatial Ecology Lab

Lab Director:Lab Director:Dr. Patrick N. HalpinDr. Patrick N. Halpin

Duke Main CampusDuke Main CampusDurham, North CarolinaDurham, North Carolina

Staff and Students:Staff and Students:Ben BestBen BestAndre BoustanyAndre BoustanyAndrew DimatteoAndrew DimatteoBen DonnallyBen DonnallyAri FriedlaenderAri FriedlaenderEi FujiokaEi FujiokaRob SchickRob Schick

Washington, D.C.Washington, D.C.

Caroline GoodCaroline GoodConnie KotConnie KotElliott HazenElliott HazenErin LaBrecqueErin LaBrecque

Duke Marine LabDuke Marine LabBeaufort, North CarolinaBeaufort, North Carolina

Sarasota, FloridaSarasota, FloridaDaniel DunnDaniel Dunn

Jason RobertsJason Roberts

Eric TremlEric Treml

University of QueenslandUniversity of QueenslandBrisbane, AustraliaBrisbane, Australia

Talk outlineOverview of Marine Geospatial Ecology Tools

(MGET)Live demonstration of habitat modeling in

ArcGISQuestions

What is MGET?A collection of geoprocessing tools for marine ecology

Oceanographic data management and analysisHabitat modeling, connectivity modeling, statisticsHighly modular; designed to be used in many scenariosEmphasis on batch processing and interoperability

Free, open sourceWritten in Python, R, MATLAB, and C++Designed mainly for intermediate-skill ArcGIS usersMinimum requirements: Win XP, ArcGIS 9.1, Python

2.4 ArcGIS and Windows are only non-free requirements

MGET interface in ArcGISThe MGET toolbox appears in the ArcToolbox window

MGET interface in ArcGISDrill into the toolbox to find the toolsDouble-click tools to execute directly, or drag

to geoprocessing models to create a workflow

InteroperabilityMGET “tools” are really just Python functions.MGET exposes them to several types of external callers.

pythoncom2x.dll

IDispatchIMyTool

MyToolCOM class

MyTool.py

MGET ArcGIS Toolbox

Python programsArcGIS 9.x

Early-bound COM clients (e.g. C++)

Late-bound COM clients

(e.g. VBScript)

MGET

(a.k.a. the GeoEco Python Package)

External callers

win32com module

MGET COM module

Integration

The Python function that implements an MGET tool can invoke C++, MATLAB, R, ArcGIS, and COM classes.

R interpreter

MyTool.m MyTool.r

MyTool.py

Python extension DLL

MyTool.cpp

C++

MyTool.pyd

Python extension DLL

MyToolMatlab.pyd

MATLAB Component Runtime (MCR)

rpy module

MGET COM module

win32com module

R packagesMATLAB toolboxes

IDispatch

COM Automation

classes

MGET ArcGIS module

arcgisscripting or win32com

module

ArcGIS geoprocessor

C libraries

ArcGIS toolboxes

Python packages

MGET R module

Habitat modeling example

Chlorophyll

SST

Bathymetry

Presence/absence observations

Sampled environmental data

Multivariate statistical model

Probability of occurrence predicted from environmental covariates

Binary classification

Live demonstrationPurpose: show how MGET can assist you with habitat

modeling Not a training on how to do habitat modeling!Not enough time to delve deeply into hard problems, such as:

Selecting environmental predictors appropriate for the speciesDealing with missing environmental data (e.g., caused by clouds)Generating absence points when none are availableSelecting a suitable statistical approach (e.g. GLM, GAM, CART)Selecting predictors for the model and how they should be fitted Interpreting the statistics and plots output by the modelEvaluating the model’s performanceMaking management decisions based on the model’s output

The demonstration uses real data but the analysis is not intended to be scientifically defensible; it is just a demo of the tools!

If you missed the live demonstration, please check the MGET web site http://code.env.duke.edu/projects/mget for a written example.

AcknowledgementsThanks to NOAA SEFSC for making the 1999 Atlantic Survey data available, the observers and crew of NOAA Ship Oregon II Cruise OT 99-05 (236) for collecting it, and to OBIS-SEMAP for hosting it.

Thanks to our funders:http://seamap.env.duke.edu

For more informationDownload MGET:

http://code.env.duke.edu/projects/mget

Contact us:jason.roberts@duke.edu, bbest@duke.edu

Learn more about habitat modeling:Guisan, A., Zimmermann, N.E., 2000. Predictive habitat distribution models in ecology. Ecological Modelling 135, 147–186.

Thanks for attending!