My colleague and I recently published a technical note in the Journal of the American Water Resources Association (JAWRA) on automating a hydrodynamic model of the Delaware Estuary. The automation process harvests data from the internet, processes it into a model input file, and runs the model overnight. You can see the abstract at:
http://onlinelibrary.wiley.com/doi/10.1111/jawr.12185/abstract
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I am very excited about R at the moment. Here is an example of an app I constructed for one of the long term monitoring projects at my full time place of employment.
https://johnyagecic.shinyapps.io/BoatRunExplorer/
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