epiforecasts / covid19-uk-nowcasts-projections

Nowcasts and projections of Covid-19 in the UK

Nowcasts and Projections for COVID-19 in the UK

This repository contains the code required to:

• Download and clean public COVID-19 surveillance data.
• Estimate the time-varying reproduction number.
• Project future hospital admissions assuming no changes in transmissibility beyond reductions in susceptibility due to infections.
• Project other dependent metrics such as fatalities, Hospital bed usage, and mechanical ventilation bed occupancy as discrete scaled convolutions of hospital admissions and estimated parametric delay distributions.
• Produce a real-time report summarising these outputs.

Updating estimates

See below for how to run a manual update using the provided docker container.

1. Optionally: set up the prebuilt docker container using the instructions here. Alternatively the estimates can be created outside of docker but dependencies will have to be installed manually.

2. Run the following in the terminal (giving GitHub credentials when requested). On a 16 core cluster a full update should take approximately 3 hours. Either interactively in the container or programmatically.

bash bin/update-forecasts.sh

3. Save the estimates, for example pushing to a clone of the repo in GitHub. For an example of CRON commands required to automate this process see here.

Estimates

A summary report is available in the docs/ directory. The latest version can be accessed here. Its source is in reports/nowcast-and-projections/report.Rmd.

Individual data files and figures are available in the following locations:

• Formatted nowcasts (Rt, growth rate, etc) can be found in format-rt/data/all with plots available in format-rt/figures.
• Formatted projections can be found in format-forecast/data/all with plots available in format-forecast/figures/snapshot/<target>/<date>/<target>-using-<predictor>.png. Other plots summarising fitting and forecasting are available in the format-forecast/figures.
• Plots summarising convolution parameter values over time are available in the format-forecast/figures/parameters folder though these require careful interpretation.

Making changes

See bin/update-forecasts.sh for links to the various subscripts for different tasks. Stepping through these files may also be required for debugging.