Modeling species habitat with environmental predictor variables

In this example, we demonstrate how to predict the occurrence of an animal by correlating observations of it with environmental conditions, building a statistical model that expresses that correlation, and creating maps of predicted occurrence by applying the model to maps of the environmental parameters. This type of analysis is sometimes called habitat modeling, species distribution modeling, species occurrence modeling, or range mapping.

Watch the original webinar (now somewhat obsolete)

This demonstration was originally given as a one hour webinar to the EBM Tools Network on 15 October 2008 using a beta version of MGET 0.7. Since that time we have made many improvements to MGET that simplify the processing required to complete the original example. The downloadable demonstration presented below is designed for a more recent version of MGET and only roughly matches the webinar. Please keep that in mind when watching the webinar.

The webinar consisted of a short PowerPoint presentation followed by a longer demonstration showing how to perform the analysis in ArcGIS using geoprocessing tools in MGET. You can download the PowerPoint slides in either Microsoft PowerPoint format or Adobe PDF format. You can also watch a recording of the webinar (77 MB, MP4 format). We highly recommend this because the PowerPoint does not explain any details of the analysis. All of the details are captured in the ArcGIS demonstration.

At the end of the presentation, the EBM Tools Network encountered a technical problem with its conference calling system and had to terminate the audio right when I called for questions. Thus you will hear the audio cut out while the video keeps going. If you have any questions about the end of the presentation, please contact me ( jason.roberts@duke.edu).

Download the original demonstration (MGET 0.7)

If you prefer to try the original demonstration presented in the webinar, please see these instructions. You must use MGET 0.7 and ArcGIS 9.2, 9.3, or 9.3.1. Later versions of MGET and ArcGIS are not supported.

Download the updated demonstration (MGET 0.8a39 and later)

To run the updated demo, the following software must be installed. See the MGET Installation Instructions for step-by-step installation instructions. Please contact  jason.roberts@duke.edu if you need help.

• ArcGIS 9.3, 9.3.1, or 10
• ArcGIS Spatial Analyst extension
• Python 2.5 (if ArcGIS 9.3 and 9.3.1) or 2.6 (if ArcGIS 10)
• Python pywin32 package (a.k.a. Python for Windows Extensions) installed for your version of Python
• MGET 0.8a39 for your version of Python
  • Later versions of 0.8 are likely to work; earlier versions are not
• R 2.10.0 or later
  • Earlier versions might work.

Running the demo

1. Download the file HabModelExample3.zip and save it to a folder of your choice.

2. Unzip the file. A single folder called HabModelExample3 should be created.

3. Start ArcCatalog and go to that HabModelExample3 folder. It should look like this:

4. The example uses the  NOAA ETOPO1 bathymetry, which I did not include in the HabModelExample3.zip due to the bathymetry file's large size. Download the  ETOPO1 Bedrock cell-referenced georeferenced tiff and store it in the HabModelExample3\EnvironmentalData folder. Unzip the file into that folder. Now in ArcCatalog you should see a raster called ETOPO1_Bed_c_geotiff.tif:

5. You are now ready to run the geoprocessing models in the toolbox in the Survey.mdb geodatabase. In ArcCatalog, right-click on the first model and select Edit. When the model diagram comes up, open the Model menu and select Run entire model. This first model import the shapefiles seamap5.shp and seamap6.shp (downloaded from OBIS-SEAMAP) into Survey.mdb.

6. After the first model completes, run each of the remaining models in sequence using the same method. Right-click, select Edit, open the Model menu and select Run entire model. Annotations within each model describe what it is doing.

Important notes

(Under construction)