This is a general repository for SPARRAv4 pipelines, functions and figures.

This repository contains folders:

1. Analysis: containing figures, summaries and co-ordinates
2. Pipelines: containing code to fit models and draw figures, and to demonstrate calibration estimator
3. SPARRAv4: containing functions
4. Diagrams: containing diagrams and drawings
5. Figures: containing code to draw figures used in paper.

To generate all figure panels used in the manuscript, run Figures/generate_all_figures.R with the working directory at the main directory for this repository. Figure panels are saved into the relevant subfolder in Figures/pdfs.

A small number of analyses are performed by code in

• Analysis/external/

To find the original code to generate a plot, search for its basename in these files.

Generally, for each plot X.pdf there is an associated file X.txt. This file contains all the data that was plotted. Each file firstly contains a nominally human-readable form of the data, then a line '***************', and then some lines which can be read into R directly to recreate the variables used (using dput).

Figures were drawn on the windows machine in the NSH, for which package versions are listed as part of the R script SPARRAv4/ehr_mockup.R (object ip_windows).