A simple SEIR for on/off-campus transmission of SARS-CoV-2 with delays in testing, behavioral modifiers, and infection/transmission modifiers. This stems from orginal work by Dr. Matt Ferrari at PSU .
uni_sim_par_function.R and uni_sim_cost_par_function.R are functions that bundle the SEIR files and allow for comparison across multiple scenarios with additional ability to run processes in parallel. uni_sim_function.R and uni_sim_cost_function.R are the wrappers for the SEIR model that store output after each time step. sir_simple_step_function.R is a function that allows disease progession in individuals who have been tested but are not yet isolated. sir_lamp_function.R and sir_lamp_cost_function.R are functions that manage the inputs from the wrapper, uni_sim_function.R and uni_sim_cost_function.R, and generate disease progression. Functions which contain cost are used in cost-limited testing investment scenarios, whereas functions lacking cost operate on test-limited scenarios (limited by X number of tests per day. Results.RMD and Supp_Info.Rmd provide the graphics described in our paper, and show how to run functions.
Please reach out if you have comments or questions (rogerswill47@gmail.com).