Origin/fix hospitalisation&icu model

[katiebechman]

@AnnaB45 - here are the new files 003 define covariates & 202 cox models

[AnnaB45]

@katiebechman - would you be able to save the changed define covariates file as the same name as the previous one (000_define_covariates.do) rather than saving as a new file? This means that the changes between the current define covariates file and the updated one you've made will be really easy to review.

[AnnaB45]

@katiebechman - on the cox models file, the current versions in the master branch remove the first loop (over the 13 different datasets) so that the models for each dataset can be run in parallel in the job server - which is much quicker. I think the changes you've made add this loop back in, is this for a particular reason?

Looking at the code the models run against four outcomes:

• hospital admission date (with positive test within date restrictions)
• icu admission or death (with positive test within date restrictions based on hospital admissions flag)
• hospital admission date sensitivity analysis (with positive test but positive result can occur at anytime pre admission)
• icu admission sensitivity analysis (icu admission only with positive test within date restrictions)

These are on top of the two existing outcomes that don't need to be rerun (death and positive COVID test), is that right?

[katiebechman]

@AnnaB45 I ahve uploaded baseline covariates saved as 000

[AnnaB45]

Have moved changes to another branch/pull request so can close this one without merging