Marine Geospatial

Ecology Tools (MGET)

November 2013 Overview

Jason Roberts, Ben Best, Daniel

Dunn, Eric Treml, and Pat Halpin

Duke Marine Geospatial Ecology Lab

The development of MGET was funded by:

Duke Marine Geospatial Ecology Lab
Duke Main Campus
Durham, North Carolina
Washington, D.C.
Jason Roberts

Lab Director: Duke Marine Lab

Beaufort, North Carolina
Dr. Patrick N. Halpin
Dr. Ari Friedlaender
Staff and Students:
Connie Kot
Dr. Andre Boustany Corrie Curtice
Ben Donnelly Daniel Dunn
Daniel Dunn Erin LaBrecque
Ei Fujioka Jerry Moxley
Hunter Jones
Jesse Cleary
Liza Hoos
Shay Viehman
What we do
 From data
New analytic methods

Ecological research Analysis and

decision
support tools

to decisions
MGET is an ArcGIS toolbox

Over 280 Tools

It can also be invoked from many programming languages

Many users access MGET
from the ModelBuilder
capability of ArcGIS
Installation is easy!
Free, open-source software
Requires Windows + ArcGIS + a free Python lib
For full functionality, you need other free software
Open-source GIS may be supported in the future
Easy installer (just click Next, Next, Next)
Download and instructions are here:
http://mgel.env.duke.edu/mget/download
The user community as of Nov. 2013
~3800 installs since August 2009

99 countries
 Tour of the tools

Lets see some examples from each toolset

The first tools we developed:
generic HDF/netCDF converters
These
evolved
to tools
specific to
popular
products
MGET supports a growing
list of products and algorithms

Lets look at some

more examples
Sample 3D and 4D products

Chai, F, RC Dugdale, TH Peng, FP Wilkerson, and RT Barber (2002). One-dimensional ecosystem model
of the equatorial Pacific upwelling system. Part I: model development and silicon and nitrogen cycle.
Deep Sea Research Part II: Topical Studies in Oceanography 49: 2713-2745.
Application: analyzing the movements
of leatherback sea turtles tracked by
satellite telemetry
Click here to see an animation of one of the tracklines
(requires player for .wmv files)
Sampling in 4 dimensions:
lat, lon, depth, time

Black bars are the depths most frequented by turtle on that day.
Research question: are turtles choosing locations and depths based
on mesozooplankton density (ROMS-CoSiNE zz2 variable)?
 Leatherback movement modeling

Schick et al (2008) Bayesian

animal movement model

Schick RS, Roberts JJ, Eckert SA, Halpin PN, Bailey H, Chai F, Shi L, Clark JS (accepted)
Pelagic movements of Pacific Leatherback Turtles (Dermochelys coriacea) reveal the
complex role of prey and ocean currents. Movement Ecology.
Detecting SST fronts

MGET provides tools that detect

oceanographic features in remote
sensing images
These are some of the most
popular tools in MGET

Terra Aqua
Cayula & Cornillon algorithm
Daytime SST 03-Jan-2005
Step 1: Histogram analysis ArcGIS model
Mexic
Bimodal
o Optimal

Frequency
break
27.0 C

Temperature
Example output
Step 2: Spatial cohesion test Mexico

28.0 C Front

25.8 C
Strong cohesion Weak cohesion
front present no front
~120 km
Application: Modeling density of
critically endangered right whales

Roberts, Best, Halpin, et al. (in prep)

 Detecting mesoscale eddies

This tool detects eddies in SSH

images collected by NASA/CNES
radar altimeters
Gulf stream eddies

Image from http://www.oc.nps.edu/

Okubo-Weiss eddy detection

SSH anomaly Example output

Aviso DT-MSLA 27-Jan-1993

Red: Anticyclonic Blue: Cyclonic
Negative W at eddy core
Application: fisheries ecology
Are tuna and swordfish catches in the northwest
Atlantic correlated with eddies?

Eddies

Hsu A, Boustany AM, Roberts JJ, Halpin PN (in review) The

effects of mesoscale eddies on tuna and swordfish catch in
the U.S. northwest Atlantic longline fishery. Fish. Oceanogr.
Results
CPUE in eddy Effects of Other Parameters on CPUE
Species habitats SST Bait Depth Lightsticks
Bluefin A>N>C
Yellowfin C>N +
Bigeye C>A>N
Swordfish N>C>A + + +
A = In anticyclonic eddies + = positively correlated with CPUE
C = In cyclonic eddies = negatively correlated with CPUE
N = Not in eddies

For tunas, CPUE is higher inside eddies than outside eddies (p < 0.05)
For swordfish, CPUE is lower inside eddies than outside eddies (p < 0.05)
Cheltons eddy database
MGET also includes tools
that provide easy access to
data products published by
other NASA grantees
By improving access to these
products from GIS, we hope
to increase use by ecologists

Chelton, DB, MG Schlax, and RM Samelson (2011). Global observations of nonlinear

mesoscale eddies. Progress in Oceanography 91: 167-216.
Spatiotemporal analysis
of fisheries
Bigeye CPUE highest
Swordfish exhibits
in full moon
annual periodicity
Daniel Dunn, et al. (2013)
Empirical move-on rules
to inform fishing
strategies: a New England
case study. Fish and
Fisheries.

To avoid damage by
slime eels, move on
by 3 km for 5 days
Model larval connectivity
Habitat patches Ocean currents data Larval density rasters

Tool downloads data for the

region and dates you specify

Edge list feature class representing

dispersal network

Methods described in Treml et al. (2008, 2012)

Application: modeling dispersal of coral
larvae in the Caribbean to assist in
systematic conservation planning
Click here to see a simulation of the dispersal of coral larvae
(requires player for .mp4 files)
Animation by George Raber
Schill S, Raber G, Roberts JJ, Treml EA, Brenner J (in prep) Designing for Resilience: A
regional coral marine connectivity model for the Caribbean Basin and Gulf of
Mexico based on NOAAs Real-Time Ocean Forecast System (RTOFS).
Invoke R from ArcGIS
Predictive species distribution modeling
Point observations of species Probability of occurrence predicted
from environmental covariates

Predictive model

Gridded environmental data

Binary classification

Bathymetry
SST
Chlorophyll
Application: rockfish habitat models

Young MA, Iampietro PJ,

Kvitek RG, Garza CD (2010)
Multivariate bathymetry-
derived generalized linear
model accurately predicts
rockfish distribution on
Cordell Bank, California,
USA. Marine Ecology
Progress Series 415: 247
261.
Bathymetry-derived predictor variables

Young et al. (2010)

Results: yellowtail rockfish

Young et al. (2010)

 MGET is not just useful for marine species. How about a
terrestrial example involving homo sapiens sapiens habitat?
Using Predictive Modeling Methods as a Way of Examining Past
Settlement Patterns: An Example From Southern Poland
Anna Luczak, University of Wroclaw, Institute of Archaeology, Wroclaw, Poland
Results:
Predicted
Neolithic
Sites
Anna Luczak
Acknowledgements
A special thanks to the many developers of the open source software that
MGET is built upon, including:
Guido van Rossum and his many collaborators; Mark Hammond; Travis Oliphant
and his collaborators; Walter Moreira and Gregory Warnes; Peter Hollemans; David
Ullman, Jean-Francois Cayula, and Peter Cornillon; Stephanie Henson; Tobias Sing,
Oliver Sander, Niko Beerenwinkel, and Thomas Lengauer; Frank Warmerdam and
his collaborators, Howard Butler; Timothy H. Keitt, Roger Bivand, Edzer Pebesma,
and Barry Rowlingson; Gerald Evenden; Jeff Whitaker; Roberto De Almeida and his
collaborators; Joe Gregorio; David Goodger and his collaborators; Daniel Veillard and
his collaborators; Stefan Behnel, Martijn Faassen, and their collaborators; Paul
McGuire and his collaborators; Phillip Eby, Bob Ippolito, and their collaborators;
Jean-loup Gailly and Mark Adler; the developers of netCDF; the developers of HDF

Thanks to our funders:

Thank you!
Download MGET:
http://mgel.env.duke.edu/mget (or Google MGET)
Email me:
jason.roberts@duke.edu
If you use MGET, please cite our paper:
Roberts, JJ, Best BD, Dunn DC, Treml EA, Halpin PN (2010)
Marine Geospatial Ecology Tools: An integrated framework for
ecological geoprocessing with ArcGIS, Python, R, MATLAB, and
C++. Environmental Modelling & Software 25: 1197-1207.