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