mrc-ide / sarscov2-severity-england

sarscov2-severity-england

This is an orderly repository which contains the analysis to our preprint

Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

Running

A sequence of tasks needs to be run with a set of parameters to generate the final results. This is sketched out in the run.R script, though this is provided only as a form of documentation. In practice these were run over several days on a HPC.

• regions: c("north_west", "north_east_and_yorkshire", "midlands", "east_of_england", "london", "south_west", "south_east")

1. Run the severity_parsed_data task to prepare the raw data for fitting.
2. Run the severity_parameters task.
3. Run the severity_fits task for each of the seven regions.
4. Run the severity_fits_combined task.
5. Run the severity_sensitivity_analysis task.

Requirements

The core requirement is our sircovid package and its dependencies. Because that package is in constant development you will probably want to pin your versions of the software to the versions we used for preparation:

remotes::install_github(c(
  "mrc-ide/dust@v0.13.2",
  "mrc-ide/mcstate@v0.9.14",
  "mrc-ide/sircovid@0.14.11",
  "mrc-ide/spimalot@v0.8.24"))

However, you can always install the versions that we are using with

drat:::add("ncov-ic")
install.packages(c("sircovid", "spimalot"))

You will also need a recent orderly which can be installed with

drat:::add("vimc")
install.packages("orderly")

License

MIT © Imperial College of Science, Technology and Medicine