Ap phs pub linkage

[abigap01]

Hi Monica,

Another update to a shiny app for the ScotPHO website. I have revived this one which used an old Health Protection publication which PHS picked up post-covid. Hopefully everything looks good on the data prep side of things too as this needed reworking a bit to account for missing data years etc.

Thanks,
Abbie

[monicamcgibbon]

Thanks for this @abigap0. I've just made a few changes. Firstly, the data for the shiny app needs to be saved within the repository itself. It works fine when pointing to data saved on the network when you're running the app locally but it wouldn't work if it was deployed because it wouldn't know how to access those filepaths. When you deploy the app you also need to include the data that's required for it too. The data prep code also needs to be commented out for deploying for the same reasons. Also, nothing to do with you but the code was a little confusing to follow so I've re-organised it and adding some analyst notes at the top for the next person - can you please add to/amend the notes to make it easier for whoever needs to update next year? Let me know if you have any questions.