This repository contains code associated with a preprint exploring COVID-19 outbreaks in classrooms, and how these might be managed with several different protocols: COVID-19's unfortunate events in schools: mitigating classroom clusters in the context of variable transmission
The model is written in Matlab, with outbreak visualization in Matlab and other plots for the manuscript in R.
The folder 'basic simulations' contains the files necessary for reproducing most of the simulations in the preprint. Simulations for the elementary schools and highschools with structures currently in place in BC are obtained by running 'generate_spreadsheet.m'. There is a variable the you set in the beginning of the file that determines whether you simulate elementary schools, highs school mornings, or high school afternoons. Numbers in the paper for high schools are obtained by summing the data from the morning and the afternoon (and adjusting for the index case being in both classes.) Simulations for the pre-COVID highschool configuration are generated by 'highschool_normal.m'.
The folder 'pooled testing' contains the files necessary for reproducing the simulations of pooled testing for elementary schools. Run the file 'generate_pooled.m'.
The folder 'outbreak plots' contains the files necessary for generating the plots of clusters under different protocols, one of which is shown in the paper. Run the file 'make_outbreaks.m'.
The folder 'model-output' contains the output files for various simulations in the paper, along with tables of results. Run figure-script-clean.R' to generate the figures in the paper using this data. The file 'how_to_read_tables.rtf' explains how to read the tables in this folder.