This repository provides a collection of curated outbreak analytics pipelines using different infrastructures for automation.
The analyses presented here are largely automated, and should be of use to any outbreak analyst. A basic R literacy will be required to adapt the report to other datasets, most importantly for identifying the variables to be used for dates of events and stratification. The data used in this report are daily case incidence. For raw linelists, alternative commands will be supplied in the section on building epicurves.
To illustrate the different analyses, we use real data reporting daily numbers of COVID-19 hospitalisations in England as of the 24 October 2020, broken down to the hospital and National Health Service (NHS) region level. The data is available online from the NHS England's website. The dataset analysed here is a simplified version, providing incidence of hospital admissions by NHS trust, stored in the file covid_admissions_uk_2020_10_24.xlsx.
The most basic command to create a report, without tweaking any of the default settings is to run:
rmarkdown::render("reports/transmissibility.Rmd")You can, however, modify some of the settings, and re-create a new report in a single line of code. For instance, to generate a report with epicurves showing daily incidence, instead of weekly, one can use:
rmarkdown::render("reports/transmissibility.Rmd",
params = list(epicurve_unit = "day"))