The included materials are intended as companions to our in-person workshop held in the Spring of 2023. They may, however, be useful to participants and non-participants as references.
The install_packages_for_workshop.R file contains a few lines of code to install the dependencies for the rest of the materials. Required packages are: 'deSolve', 'R0', 'forecast', 'padr', and 'mgcv'. If you want to run shiny apps on your own computer, you will also need to install the 'shiny' package.
(1) a basic SIR simulation model (U_basic_sir.R)
(2) an example of a simple framework to estimate R0 from case data (U_estimate_r0.R)
(3) a simple SIRV simulation model (U_SIRV.R)
(4) a streamlined GAM model, including examples of fitting the model to case data and using the model to forecast (U_GAM_forecast.R)
(5) a rudimentary example of fitting an SIR model to case data (the same data as in #4) and using the fitted model to forecast (U_SIR_fit_forecast.R)
create interactive shiny applications that allow users to explore and experience key lessons from the above scripts (except #2 - R0 estimation). Use is simple - just make sure that you have the 'shiny' package downloaded by running install.packages('shiny') before you try to run any of the programs in the folder.
Each of these shiny apps are also hosted online. If you don't want to run the apps from your own computer, you can simply access them at the following URLs:
(1) https://uouiddworkshop.shinyapps.io/sir_shiny/
(2) N/A (nothing to see here)
(3) https://uouiddworkshop.shinyapps.io/sirv_shiny/
(4) https://uouiddworkshop.shinyapps.io/gam_shiny/
(5) https://uouiddworkshop.shinyapps.io/sir_ssqfit_forecast/
(6) A fancier SIRV model is also available. Relative to #3, this script adds the ability to specify the number of initial infections and outputs the total vaccine doses given. Useful for in-person workshop exercise where we explore the effects of different vaccine allocation strategies across different scenarios. https://uouiddworkshop.shinyapps.io/scenario2_sirv_shiny/
Like these shiny apps, but want to modify them or build your own? Shiny syntax can be a little confusing at first, but it goes quickly once you get the hang of it. A nice place to start is: https://mastering-shiny.org/basic-app.html
The other files in the directory are different cuts of a dataset on cases of a regional outbreak of a virus. You can safely ignore them :)
Questions? Comments? Concerns? Suggestions? Please contact us by creating an Issue or Pull Request using the tabs at the top of the page.