README

Control files for running tbepRSparrow

The file app.R is a version of the Shiny app for RSparrow that is hosted on https://shiny.tbeptech.org/tbepRSparrow-control/. It is similar to code in the file debugShiny.R. The file loads the required libraries that were installed manually on the shiny server. A shiny "image" file is then loaded and assigned to objects in the environment. Objects in this image file were created by running the file results/sparrow_control.R, debugging through a browser at some point, and saving all objects in the workspace that were passed to ShinyMap2(). Each of the objects in the image file are then used as arguments to the Shiny functions in RSparrow.

This repository and tbepRSparrow are loaded on the tbep-tech server at /srv/shiny-server/. The app.R file loads the tbepRSparrow package on initation using devtools::load_all() (i.e., it is not an installed package). The tbepRSparrow package includes all functions for running the model and plotting the results. A results, gis, and data folder are also included in this repository and all are used by the Shiny application. In particular, the results folder includes pre-processed results from the RSparrow model after running results/sparrow_control.R. As is, the current application includes results for a fixed run of RSparrow.

Updates to this application will include:

• Adding a new release of RSparrow that includes interactive visualizations. The current version includes some old functions I created that aren't that great. The new version of RSparrow should replace the contents of tbeRSparrow. Take special note of modifications that were made to the original repo to allow the Shiny app to work (e.g., fixing relative paths, adding a scenario_name argument to shinyScenarios and shinymap2)

• Update the gis, data, and results folders with new content for the latest version of RSparrow. In particular, the results folders is populated with files after running the model. Take note of the file sizes for upload to GitHub.

• Figure out how to integrate RSparrow directly with the shiny app. This could be done the simple way (upload a zipped file for the results folder) or the hard way by running RSparrow directly on the server. The latter could be a separate Shiny app, but I'll have to figure out how to allow Shiny to modify files on the server.