Two-population Model of SARS-CoV-2 within a University and Community Populations for Pullman, WA

A repository for the code and data for the "Estimating SARS-CoV-2 transmission parameters between coinciding outbreaks in a university population and the surrounding community" manuscript.

Parameter Estimation using pMCMC

"Param_Est_pMCMC.R" runs the model simulations using pMCMC and processes the posterior distributions from 5-chain random walks for each parameter being estimated.

Requires the "weekly_wide.csv" dataset.

Figure 2. Epi Curves

"Figure 2 - Epi Curves.R" produces both figures depicting the epidemic curve (weekly) for the case population (2a) and the epidemic curve for each subpopulation.

Requires both the "weekly_wide.csv" and the "weekly_long_ext.csv" dataset.

Figure 3. Rt Estimates

"Figure 3 - Rt Est.R" produces the time-varying reproduction numbers for the total cases (Figure 3a) and the sub-population cases (Figure 3b) using the EpiEstim R package from (Cori et al.)

Requires the "WSU_Pullman_wide.csv" dataset, which is not available here due to data sensitivity requirements.

To reproduce the plots, the datasets generated from the EpiEstim package are provided (R_total.csv, R_wsu.csv, & R_pul.csv)

Figure 4. Posterior Distributions & Figure S1. Trace Plots

"Figure 4 - PostDist_TracePlots.R" produces both the trace plots and the posterior distribution figures.

The MCMC results are provided "mcmc_results.csv" for the analysis. These are the results produced by the output of the parameter estimation using pMCMC program. Note this file is compressed in the GitHub repository, and will need to be unzipped before use.