covid-uk

Stochastic age-structured model of SARS-nCoV-2 transmission for UK scenario projections.

Quick start guide

Installing dependencies for Mac OS

You will need to install gfortran binaries from here: https://github.com/fxcoudert/gfortran-for-macOS/releases

Once installed, run gcc --version in terminal to get your current version, e.g. Target: x86_64-apple-darwin18.8.2.0. Then run below in terminal to add library path for R:

cd ~ mkdir .R cd .R echo FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm >> Makevars

Finally, install nlopt: brew install nlopt

Guide to files

Main parameter setting and model run script is in UK.R – there is option to set local path at top. Output collation and plotting functions are in UK-view.R. Underlying model code is in covidm folder.

To run UK.R, after editing the local path at the top of the script, invoke as follows from the command line: Rscript UK.R 1 50 Here, 1 is the number for the analysis you want to run (1, 2.1, 2.2, 3, 4, 5, or 6). 50 is the number of stochastic realisations to run.

1 - 12 week interventions

2.1 - national triggering

2.2 - local triggering

3 - lockdowns

4 - elder care during school closures

5 - R0 analysis

6 - leisure and sports analyses

For 50 runs, each set takes about 6-16 hours on a current laptop.

Reference

Davies NG et al. The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study. CMMID COVID-19 working group pre-print, 2020.