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Rawson-spatial-covid

orderly

This is an orderly project, holding the analysis for our manuscript

"The impact of health inequity on regional variation of COVID-19 infection 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 Master_script.R script, though this is provided only as a form of documentation. In practice these were run over several days on a HPC.

  1. Run the 01_Prepare_Data task to prepare the raw data for fitting.
  2. Run the 02_model_fit_A task to fit the model.
  3. Run the 03_model_summaries_A task to produce model summaries.
  4. Run the 04_nb_CI_output task to prepare credible intervals for plotting.
  5. Run the 05_manuscript_figures task to produce figures seen in the manuscript.

Requirements

You will need a recent orderly which can be installed with

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

You will also need to follow the specific install instructions for rstan.

License

MIT © Imperial College of Science, Technology and Medicine