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COVID19 Campus Model Summary

The COVID19 Campus Model is a tool to guide mitigation strategies and resource needs for universities considering in-person instruction for Fall 2020. We developed a susceptible-exposed-infectious-recovered (SEIR) type of deterministic compartmental model that captures transmission process, allowing for estimates of direct and indirect (transmission-mediated) effects of control strategies.

Code in this repository was used for the simulations and results presented our paper. An interactive software tool is available for additional simulations. Links below:

Code description

Model runs for figures in paper

File Description
Transmission scenarios Explores different transmission scenarios
Screening scenarios Explores a range of screening intervals and with an outcome of total and cumulative cases in staff and students
Testing scenarios Explores a range of testing interval (time from symptom-onset to testing and subsequent isolation)
Screen and test scenarios Explores combinations of screening and testing intervals

Functions, parameters and initials

File Description
Dependencies Loads relevant packages
Model function Loads function for transmission model
Parameters & initials Loads paramemeters, initial conditions and control settings
Distribution optimizer Loads function used to optimize beta distribution for the probabilistic senstivity analysis (PSA)
PSA parameters Loads parameters and distributions used for the PSA
PSA plot function Loads plot function used for the PSA

Outputs

File Description
Plots Folder containing figures from model outputs

Shiny web app

The application is available online.

Dependencies

In order to run the app from your computer you require the following libraries:

install.packages(c(
  "shiny",
  "shinydashboard",
  "plotly",
  "EpiModel",
  "lhs",
  "tidyr",
  "purrr",
  "glue",
  "kableExtra",
  "ggplot2"
))

Alternatively if you use renv to isolate your libraries and ensure reproducibility, a "renv.lock" file is present at the root of this project.

renv::restore()

Run the app

To launch the app, either run from the R console:

shiny::runApp("shiny/app")

Or using RStudio, open either "shiny/app/ui.R" or "shiny/app/server.R" and click the "Run App" button on the top right corner of the editor.