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    11= Marine Geospatial Ecology Tools = 
    22 
    3 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 automatically interfacing 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. 
     3Marine 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. 
    44 
    55MGET 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.  
    66 
    7 == Key Features == 
    8  
    9  * Free, open-source software written mainly in Python, R and MATLAB 
    10  * Distributed as a self-installing setup program, for easy installation 
    11  * Each "tool" is a software subroutine designed to be invoked programmatically 
    12  * For easy execution from many environments, each tool is exposed from: 
    13    * A Python class 
    14    * A dual-interface Microsoft COM class (on Windows) 
    15    * An ArcGIS geoprocessing toolbox 
    16  * Many tools have both single-input and multi-input (batch processing) implementations 
    17  * All tools include full documentation, one version tailored to [http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/PythonReference/PythonReference.html?format=raw Python programmers] and another to [http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/ArcGISReference/ArcGISReference.html?format=raw ArcGIS users] 
    18  * A verbose [wiki:"Configuring MGET logging" logging system] eases troubleshooting of difficult failures 
    19  * All tools are written to maximize reliability, interoperability and performance 
    20  * Many tools do not require Windows or ArcGIS; we hope to issue non-Windows releases in the future 
     7Although 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. 
    218 
    229== A Simple Example == 
    … …  
    2411Many oceanography products are published in HDF format but ArcGIS still has difficulty reading this format. The [wiki:"Converting HDFs to ArcGIS rasters" 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. 
    2512 
     13There are [wiki:"MGET examples" more examples]. 
     14 
    2615== Project Status == 
    2716 
    28 ''01-Oct-08'' - MGET 0.6 beta 1 is released. MGET 0.6 provides support for ArcGIS 9.3. As of the beta 1 release, the 9.3-compatibility work is complete. Please use MGET with ArcGIS 9.3 and report any problems that you find. There are a few tools I could not make fully compatible with 9.3; please see the list of MGET 0.7 bugs for details. MGET 0.6 also includes Eric Treml's coral reef connectivity tools and tools for downloading SSH, geostrophic currents, and other data from [http://www.aviso.oceanobs.com/ Aviso] using the OPeNDAP protocol. Also, the Microsoft .NET Framework dependency has been removed from the MGET setup program. Now you no longer need to have the .NET Framework or ArcGIS .NET Support installed in order to install MGET. 
     17''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 [http://www.aviso.oceanobs.com/ Aviso] using the OPeNDAP protocol. See the [wiki:"Publications" list of publications] for a reference to Eric's work. Finally, various bugs have been fixed and improvements made; please see the [http://code.env.duke.edu/projects/mget/report/9?MILESTONE=0.6 Change List] for more information. 
    2918 
    30 ''14-Jun-08'' - MGET 0.5 is released. MGET 0.5 integrates many of Ben Best's [http://www.nicholas.duke.edu/geospatial/software 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. The final release of MGET 0.5 will be issued within a week. 
     19''14-Jun-08'' - MGET 0.5 is released. MGET 0.5 integrates many of Ben Best's [http://www.nicholas.duke.edu/geospatial/software 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. 
    3120 
    3221''14-Jan-08'' - MGET 0.4 is released. This release adds tools for creating fishnets (useful for summarizing fishing effort points using a grid), for downloading and sampling climate indices from [http://www.cdc.noaa.gov/ClimateIndices/List/ NOAA ERSL], and for converting the [http://www.soest.hawaii.edu/wessel/gshhs/gshhs.html GSHHS high-resolution shoreline database] to ArcGIS vector formats. Many bug fixes and smaller enhancements are also included. 
    … …  
    3827If you have never installed MGET before, we '''highly recommend''' you review the installation instructions before installing it. 
    3928 
    40 '''ArcGIS 9.3 users:''' MGET 0.6b1 should be fully compatible with ArcGIS 9.3, except for a few issues noted in tickets that apply to MGET 0.7. Please try out MGET 0.6b1 with 9.3 and let us know if you have any problems. 
    41  
    4229{{{ 
    4330#!rst 
    … …  
    4633| **MGET Version** | **Release Date** | **Python Version** | **Recommended For**      | **Installation Package**      | **Installation Instructions**           | **Change List**           | 
    4734+==================+==================+====================+==========================+===============================+=========================================+===========================+ 
    48 | 0.6 beta 1       | 01-Oct-08        | 2.4                | ArcGIS 9.2 users         | GeoEco-0.6b1.win32-py2.4.exe_ | `GeoEco 0.6 Installation Instructions`_ | `GeoEco 0.6 Change List`_ | 
     35| 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`_ | 
    4936|                  |                  +--------------------+--------------------------+-------------------------------+                                         |                           | 
    50 |                  |                  | 2.5                | ArcGIS 9.1 and 9.3 users | GeoEco-0.6b1.win32-py2.5.exe_ |                                         |                           | 
    51 +------------------+------------------+--------------------+--------------------------+-------------------------------+-----------------------------------------+---------------------------+ 
    52 | 0.5              | 14-Jun-08        | 2.4                | ArcGIS 9.2 users         | GeoEco-0.5.win32-py2.4.exe_   | `GeoEco 0.5 Installation Instructions`_ | `GeoEco 0.5 Change List`_ | 
    53 |                  |                  +--------------------+--------------------------+-------------------------------+                                         |                           | 
    54 |                  |                  | 2.5                | ArcGIS 9.1 users         | GeoEco-0.5.win32-py2.5.exe_   |                                         |                           | 
    55 +------------------+------------------+--------------------+--------------------------+-------------------------------+-----------------------------------------+---------------------------+ 
    56 | 0.4              | 14-Jan-08        | 2.4                | ArcGIS 9.2 users         | GeoEco-0.4.win32-py2.4.exe_   | `GeoEco 0.4 Installation Instructions`_ | `GeoEco 0.4 Change List`_ | 
    57 |                  |                  +--------------------+--------------------------+-------------------------------+                                         |                           | 
    58 |                  |                  | 2.5                | ArcGIS 9.1 users         | GeoEco-0.4.win32-py2.5.exe_   |                                         |                           | 
    59 +------------------+------------------+--------------------+--------------------------+-------------------------------+-----------------------------------------+---------------------------+ 
    60 | 0.3              | 20-Sep-07        | 2.4                | ArcGIS 9.2 users         | GeoEco-0.3.win32-py2.4.exe_   | `GeoEco 0.3 Installation Instructions`_ | `GeoEco 0.3 Change List`_ | 
    61 |                  |                  +--------------------+--------------------------+-------------------------------+                                         |                           | 
    62 |                  |                  | 2.5                | ArcGIS 9.1 users         | GeoEco-0.3.win32-py2.5.exe_   |                                         |                           | 
    63 +------------------+------------------+--------------------+--------------------------+-------------------------------+-----------------------------------------+---------------------------+ 
    64 | 0.2              | 20-Jun-07        | 2.4                | ArcGIS 9.2 users         | GeoEco-0.2.win32-py2.4.exe_   | `GeoEco 0.2 Installation Instructions`_ | Not available             | 
    65 |                  |                  +--------------------+--------------------------+-------------------------------+                                         |                           | 
    66 |                  |                  | 2.5                | ArcGIS 9.1 users         | GeoEco-0.2.win32-py2.5.exe_   |                                         |                           | 
     37|                  |                  | 2.5                | ArcGIS 9.1 and 9.3 users | GeoEco-0.6.win32-py2.5.exe_   |                                         |                           | 
    6738+------------------+------------------+--------------------+--------------------------+-------------------------------+-----------------------------------------+---------------------------+ 
    6839 
    69 .. _GeoEco-0.6b1.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/GeoEco-0.6b1.win32-py2.4.exe?format=raw 
    70 .. _GeoEco-0.6b1.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/GeoEco-0.6b1.win32-py2.5.exe?format=raw 
     40.. _GeoEco-0.6.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/GeoEco-0.6.win32-py2.4.exe?format=raw 
     41.. _GeoEco-0.6.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/GeoEco-0.6.win32-py2.5.exe?format=raw 
    7142.. _GeoEco 0.6 Installation Instructions: http://code.env.duke.edu/projects/mget/browser/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html?format=raw#Installation 
    7243.. _GeoEco 0.6 Change List: http://code.env.duke.edu/projects/mget/report/9?MILESTONE=0.6 
    73 .. _GeoEco-0.5.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.5/PythonPackage/dist/GeoEco-0.5.win32-py2.4.exe?format=raw 
    74 .. _GeoEco-0.5.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.5/PythonPackage/dist/GeoEco-0.5.win32-py2.5.exe?format=raw 
    75 .. _GeoEco 0.5 Installation Instructions: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.5/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html?format=raw#Installation 
    76 .. _GeoEco 0.5 Change List: http://code.env.duke.edu/projects/mget/report/9?MILESTONE=0.5 
    77 .. _GeoEco-0.4.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.4/PythonPackage/dist/GeoEco-0.4.win32-py2.4.exe?format=raw 
    78 .. _GeoEco-0.4.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.4/PythonPackage/dist/GeoEco-0.4.win32-py2.5.exe?format=raw 
    79 .. _GeoEco 0.4 Installation Instructions: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.4/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html?format=raw#Installation 
    80 .. _GeoEco 0.4 Change List: http://code.env.duke.edu/projects/mget/report/9?MILESTONE=0.4 
    81 .. _GeoEco-0.3.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.3/PythonPackage/dist/GeoEco-0.3.win32-py2.4.exe?format=raw 
    82 .. _GeoEco-0.3.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.3/PythonPackage/dist/GeoEco-0.3.win32-py2.5.exe?format=raw 
    83 .. _GeoEco 0.3 Installation Instructions: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.3/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html?format=raw#Installation 
    84 .. _GeoEco 0.3 Change List: http://code.env.duke.edu/projects/mget/report/9?MILESTONE=0.3 
    85 .. _GeoEco-0.2.win32-py2.4.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.2/PythonPackage/dist/GeoEco-0.2.win32-py2.4.exe?format=raw 
    86 .. _GeoEco-0.2.win32-py2.5.exe: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.2/PythonPackage/dist/GeoEco-0.2.win32-py2.5.exe?format=raw 
    87 .. _GeoEco 0.2 Installation Instructions: http://code.env.duke.edu/projects/mget/browser/MGET/Tags/GeoEco-0.2/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html?format=raw#Installation 
    8844}}} 
    8945 
    90 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-0.3.win32-py2.4.exe" into "GeoEco-0.3.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 the new version of Trac has not been released yet.) 
     46Note: 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.) 
     47 
     48You can also download [wiki:"MGET releases" old releases] of MGET. 
    9149 
    9250== Citation Instructions == 
    … …  
    9452If 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: 
    9553 
    96 Roberts, J.J., B.D. Best, D.C. Dunn, E.A. Treml, and P.N. Halpin. (In prep) Marine Geospatial Ecology Tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. ''Environmental Modelling & Software''. Software available online: http://mgel.env.duke.edu/tools. 
     54Roberts, J.J., B.D. Best, D.C. Dunn, E.A. Treml, and P.N. Halpin. (In prep) 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. 
    9755 
    9856Your citations help us obtain funding for additional development and allow us to continue to offer MGET as free software. Thank you for your support.