Modeling robust COVID-19 intensive care unit occupancy thresholds for imposing mitigation to prevent exceeding capacities

<p>Simulation output files for &#39;Modeling robust COVID-19 intensive care unit occupancy thresholds for imposing mitigation to prevent exceeding capacities&#39;.</p> <p>Simulating COVID-19 transmission and hospital burden to assess at which intensive care unit (ICU) occupancies mitigation, that reduces transmission, needs to be triggered to avoid exceeding ICU capacity limits, using the city of Chicago, Illinois as an example.</p> <p>Manuscript is under review for scientific publication, (see&nbsp;<a href="https://www.medrxiv.org/content/10.1101/2021.06.27.21259530v1">preprint on medRxiv</a>) and scripts are available from the&nbsp;GitHub repository at&nbsp;https://github.com/numalariamodeling/ICUtrigger_covid_chicago_paper_2021.&nbsp;</p> <p>Simulation output files uploaded per scenario including projected COVIID-19 transmission and burden trajectories for Chicago city for March 2020 to May 2021 per day.</p> <p>Simulation scenarios:</p> <p>&lt;reopening % above ICU capacity&gt;_&lt;delay after reaching ICU threshold&gt;_&lt;%mitigation&gt;_&lt;common simulation name&gt;&nbsp; i.e. `50perc_1daysdelay_pr6_triggeredrollback_reopen`</p> <ul> <li>`emodl` file <ul> <li>required file for COVID-19 transmission model in the <a href="https://docs.idmod.org/projects/cms/en/latest/index.html">Compartmental Modeling Software</a> (see <a href="https://github.com/numalariamodeling/ICUtrigger_covid_chicago_paper_2021">GitHub repository</a> for details)</li> </ul> </li> <li>sampled_parameters.csv <ul> <li>simulation input and scenario parameters, (nrow=4400, 400 unique parameter combinations * 11 scenario values)</li> </ul> </li> <li>rt_trajectoriescovidregion_11.csv <ul> <li>estimated reproductive numbers per trajectory for complete timeline per day</li> </ul> </li> <li>trajectoriesDat_region_11_traces.csv <ul> <li>filtered to include top 100 trajectories fitted to ICU data</li> </ul> </li> <li>trajectoriesDat_region_trimfut.csv <ul> <li>truncated to only include projections after September 1st 2020</li> </ul> </li> </ul> <p>The folder `mainfigures_csvs.zip` includes processed simulation output data for the publication figures.</p>