Simulation code associated with "Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period"

S.M. Kissler*, C. Tedijanto*, E. Goldstein, Y.H. Grad+, and M. Lipsitch+

* denotes equal contribution

+ denotes co-senior author

doi: 10.1126/science.abb5793

Correspondence: skissler@hsph.harvard.edu

figuremaker.R reproduces Figure 2 in the manuscript and demonstrates how to import and manipulate the NREVSS data.

invasion_rates.R is used within figuremaker.R for the ode simulation

invasion_ode_parallel.R is the code for the Latin Hypercube sampling procedure

license.txt contains the GNU Version 3 license for use and redistribution of this code.

nrevssCDC_ILI.csv contains the NREVSS data on the human betacoronaviruses, used in figuremaker.R

postpandemicscenarios_full.nb is a Mathematica file containing the simulation code for Figures 3-6 in the manuscript. It contains code for simulating the three-strain simulation model and the SARS-CoV-2 model with hospitalization and critical care arms.

All code is available under the GNU General Public License, version 3, included in this repository under the following terms: This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.