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Scenario analyses for COVID-19 outbreak in the United Kingdom

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- - 44000_incidence.csv
  - all_matrices.rds
  - observed_cases.rds
  - structure_UK.rds
  - wpp2019_pop2020.rds
  - wuhan_dist.csv
- - fit.cpp
  - mcmc.h
  - nloptrAPI.h
- - compartment.h
  - corona.cpp
  - helper.h
  - parameters.h
  - process.h
  - Rcpp_interface.h
  - reporter.h
- - covidm.R
  - covidm_fit.R
  - covidm_interventions.R
  - covidm_misc.R
  - covidm_params.R
  - covidm_plot.R
  - covidm_run.R
  - makecontact.R
  - plan.R
- - distribution.h
  - randomizer.h
- 2-linelist_symp_fit_fIa0.5.qs
- Global_Mobility_Report.csv
.gitignore
LICENSE
README.md
runset.sh
UK-view.R
UK.R

// repository documentation

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# 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.](https://cmmid.github.io/topics/covid19/control-measures/uk-scenario-modelling.html)

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