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Marine Geospatial Ecology Tools
Marine Geospatial Ecology Tools (MGET), also known as the GeoEco Python package, is an open source geoprocessing toolbox designed for coastal and marine researchers and GIS analysts who work with spatially-explicit ecological and oceanographic data in scientific or management workflows. MGET includes over 150 tools useful for a variety of tasks, such as converting oceanographic data to ArcGIS formats, identifying fronts in sea surface temperature images, fitting and evaluating statistical models such as GAMs and GLMs by integrating ArcGIS with the R statistics program, analyzing coral reef connectivity by simulating hydrodynamic larval dispersal, and building grids that summarize fishing effort, CPUE and other statistics. Currently under development are tools for identifying rings and eddy cores in sea surface height images, for analyzing connectivity networks, for estimating fishing effort when no effort data are available, for predicting hard bottom habitat from coarse grain bathymetry, and much more.
MGET may be accessed from ArcGIS as a toolbox in the ArcToolbox window and from programming languages as a set of Python modules and COM components.
Although much of MGET is written to be platform independent, the current version is only packaged for installation on Microsoft Windows (XP or later). Many tools also require ArcGIS Desktop 9.1 or later.
Page Contents
- A Simple Example
- Project Status
- Download and Installation
- Help, Feedback, and Mailing List
- Citation Instructions
- More Information
- Software License
- Acknowledgements
A Simple Example
Many oceanography products are published in HDF format but ArcGIS still has difficulty reading this format. The HDF SDS to ArcGIS Raster tool efficiently converts a Scientific Data Set in an HDF file to ArcGIS raster format and performs common post-processing steps.
There are more examples.
Project Status
19-Mar-09 - MGET 0.7 alpha 12 is released. So far, in MGET 0.7 we have added tools to convert SIR files published by the BYU MERS lab to ArcGIS formats, tools for downloading data from DiGIR servers, and a tool for computing biodiversity indices for species points contained by polygons, support for the latest versions of R (up to 2.8.1). We also fixed some user-reported bugs and requested enhancements in the statistical modeling tools, simplified MGET setup by prepackaging some needed Python modules with the setup program, and fixed an important bug (#315) in the SST front identification tools and a series of bugs in the GSHHS conversion tools. If you use these tools, please upgrade to this release.
14-Oct-08 - MGET 0.6 is released. MGET 0.6 provides support for ArcGIS 9.3. All tools will work, but some run slower on 9.3 than 9.2 or 9.1 due to the apparent ArcGIS bug described in MGET ticket #284. If you have 9.3, please try this out and let us know how it goes. MGET 0.6 also includes Eric Treml's coral reef connectivity tools and tools for downloading SSH, geostrophic currents, and other data from Aviso using the OPeNDAP protocol. See the list of publications for a reference to Eric's work. Finally, various bugs have been fixed and improvements made; please see the Change List for more information.
14-Jun-08 - MGET 0.5 is released. MGET 0.5 integrates many of Ben Best's ArcRStats/HabMod tools for exploring and modeling statistical data using GLMs and GAMs. Also included: tools for converting 2-dimensional netCDF variables, with no requirement that the netCDF file adhere to a particular netCDF metadata convention (ArcGIS 9.2's built-in tools have that requirement); improvement of the MGET tools that invoke R, including the ability to easily load ArcGIS tables into R (all data types are supported, including dates!); additional simplification of MGET setup, including automatic installation of all R packages used by MGET; and many bug fixes.
Download and Installation
If you have never installed MGET before, we highly recommend you review the installation instructions before installing it.
| MGET Version | Release Date | Python Version | Recommended For | Installation Package | Installation Instructions | Change List |
|---|---|---|---|---|---|---|
| 0.7 alpha 12 | 19-Mar-09 | 2.4 | ArcGIS 9.2 users | GeoEco-0.7a12.win32-py2.4.exe | GeoEco 0.7 Installation Instructions | GeoEco 0.7 Change List |
| 2.5 | ArcGIS 9.1 and 9.3 users | GeoEco-0.7a12.win32-py2.5.exe | ||||
| 0.6 | 14-Oct-08 | 2.4 | ArcGIS 9.2 users | GeoEco-0.6.win32-py2.4.exe | GeoEco 0.6 Installation Instructions | GeoEco 0.6 Change List |
| 2.5 | ArcGIS 9.1 and 9.3 users | GeoEco-0.6.win32-py2.5.exe |
Note: The proper file names end in .exe. Internet Explorer may mangle the file name to end with [1] instead. For example, it may turn "GeoEco?-0.6.win32-py2.4.exe" into "GeoEco?-0.6.win32-py2.4[1]". If this happens, save the file to your desktop, using the correct name, and run it from there. (This is a bug in the Trac Wiki system we use. It has been fixed but we have not installed the new version of Trac yet.)
You can also download old releases.
Help, Feedback, and Mailing List
To get help, suggest an improvement, or send us feedback, please email mget-help@nicholas.duke.edu. We will reply as soon as possible. You may also browse the archive or subscribe to the list to see what others are saying.
To receive notification of new releases of MGET and upcoming presentations related to MGET, please subscribe to our annoucements mailing list.
If you have any privacy concerns, please review our Privacy Policy before emailing or subscribing.
Citation Instructions
If you use Marine Geospatial Ecology Tools for a project that results in a peer-reviewed paper or other scientific report, please cite it as follows:
Roberts, J.J., B.D. Best, D.C. Dunn, E.A. Treml, and P.N. Halpin (in review) Marine Geospatial Ecology Tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. Environmental Modelling & Software. Available online: http://mgel.env.duke.edu/tools.
Your citations help us obtain funding for additional development and allow us to continue to offer MGET as free software. Thank you for your support.
More Information
- MGET Overview for NOAA Coastal GeoTools 2009 Conference (Microsoft PowerPoint format)
- MGET examples
- Publications about MGET and projects that used it
- Online documentation
Software License
Marine Geospatial Ecology Tools is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Marine Geospatial Ecology Tools program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License (available in the file LICENSE.TXT) for more details.
Acknowledgements
Marine Geospatial Ecology Tools is built atop a lot of other software, much of it free. We would particularly like to thank these developers? for making their excellent work freely reusable. Without your work, MGET would never have gotten off the ground. Cheers to all of you!
Development of Marine Geospatial Ecology Tools is funded by:
