Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification
Peter Ashcroft, Sonja Lehtinen, Sebastian Bonhoeffer
Manuscript currently online at https://doi.org/10.1101/2020.12.04.20244004
The manuscript is created by the ttiq.Rmd R-markdown file, which contains (almost) all code required to generate the data and figures.
Running knitr on this file will create a PDF manuscript file.
We include serial interval data and modified code from Ferretti et al. medRxiv (2020) [https://doi.org/10.5281/zenodo.4033022], which is used to generate parameter estimates for the infectivity profile and generation time distribution.
The files savedDistributions.RData and savedDistributionsLLH.RData need to be generated by running the ttiq.Rmd file as they are too large to attach.
To generate confidence intervals in some plots, we need to run a separate R script for a few hours, as described below.
The script TTIQ-CIscript.R is used for generating confidence intervals (CI).
It takes an info file as an argument, and returns a .RData file containing the CI dataframe.
The info files are automatically generated when executing the manuscript file.
To run the script, use R --vanilla --slave < TTIQ-CIscript.R --args INFO-FILENAME-HERE run.
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
