nardus/covid-uk

A fork of LSHTM's COVID-19 model to adapt to our data

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.

SCRC Development

Please see the Wiki for this repository for more information on the developments to this model for SCRC usage.

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.