Public-Health-Scotland / SBSS

Reproducible Analytical Pipeline of the Scottish Bowel Screening Programme Statistics (SBSS) publication
1 stars 0 forks source link

Readme #45

Closed jackhannah95 closed 1 year ago

jackhannah95 commented 5 years ago

Hi guys,

As promised, I added some instructions to the readme about running the publication. I mostly lifted it from the HSMR one.

I don't think it's a finished article (particularly towards the end); there are steps you guys take that I don't know the specifics of (like refreshing the Excel tables) and no doubt there are some that I'm completely unaware of. I'd suggest you add instructions on those bits (and add extra detail to the bits I put in if need be) yourselves. I'll fix any glaring errors/typos though, so let me know if you spot any.

Lastly (should have said this before, you were maybe going to do this anyway), when you're automating in-line bits of R code in the RMarkdown scripts (like x in the summary script), I'd write all the code in separate R scripts and source them into the RMarkdown scripts. It'll make them a little less cluttered. I'd also create an archive sub-folder inside the RMarkdown folder to save old copies of the .Rmd scripts, to stop the main folder from getting too cluttered. Although once you automate all the inline bits those scripts probably won't change much, so it'd maybe be easier to just keep the names of them the same for every publication and change the names of the word documents after they've been knitted instead.

Cheers,

Jack