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Thank you to everyone who provided advice to my question on GIS. Plenty of ideas for me to begin exploring.
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Hi Samantha et al, for geospatial networks I use two approaches:
1) For smaller networks I use Gephi's Geo Layout plugin and use a PERL script to write GEXF files with embedded lat/long coordinate attributes on the nodes. I export the final network with a transparent background and then align on top of the desired geographic basemap. You can see two examples here:
2) For extremely large to massive networks I use GraphViz and project into its coordinate space, using its rasterizer to render the final image, which I then composite against a basemap using ImageMagick. While not the absolute fastest rasterizer possible (no hardware acceleration for example), I've found GraphViz to be among the most scalable and fastest of the libraries and tools I've worked with to be able to scale to extremely large geographic networks.
I have not tried it yet, but GraphViz also has a built-in edge bundling library called "mingle" that has a lot of promise for very dense geographic networks.