artlesshao / 2020-cov-tracing

Accompanying code for: Kucharski AJ, Klepac P et al. Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study. Lancet Infectious Diseases, 2020

2020-cov-tracing

Code for modelling combined isolation, tracing and physical distancing measures.

Note: this is working repository, so non-archived code and data are likely to change over time

Quick start guide

First, set local path in R to GitHub directory, e.g.: setwd("~/Documents/GitHub/2020-cov-tracing/") Data loading and main model run script are in scripts/contact_model.r. This calls the following R file:

R/model_functions.R - Function to sample individual contact networks, calculate secondary infections and effect of control measures.

Archived versions

• Code to accompany medRxiv V1 pre-print is in V1_code, with file paths as above. An independent reproducibility CODECHECK has been performed on this version: http://doi.org/10.5281/zenodo.3767060

• Code to accompany peer-reviewed paper published in Lancet Infectious Diseases is in V2_code, with file paths as above.

Citation

Kucharski AJ, Klepac P, Conlan AJK et al. Effectiveness of isolation, testing, contact tracing and physical distancing on reducing transmission of SARS-CoV-2 in different settings. Lancet Infectious Diseases, 2020