December 4, 2018

Slides: https://github.com/NHS-NSS-transforming-publications/RAP-presentation

RAP companion: https://ukgovdatascience.github.io/rap_companion/

Reproducible research

  • Not a new concept
  • Encouraged and growing within academia for last 10-15 years
  • Provides evidence of the correctness of results
  • Exposes workflow to others
  • Enables others to make use of methods and results

Current publication process

  • Complex (many steps between software)
  • Prone to error
  • Manual, menial tasks carried out by highly skilled people
  • Not reproducible or sustainable

The solution

RAP companion

Combined the principles of reproducible research with data science tools and best practice.

What is RAP?

What is RAP?

Transforming Publishing test case: Hospital Standardised Mortality
Ratio publication

Levels of automation

Level Description
1 Ad hoc R code
2 R project
3 R project under version control (VC)
4a R project under VC and peer reviewed (wrangling)
4b Replicable report in Rmarkdown (publication)
5 Near RAP (VC, peer review, data quality assurance)
6 Full RAP (as above plus unit testing and documentation)
7 R package

Challenges

  • Culture change (peer review and working in the open)
  • New software such as R and git
  • Required development time
  • Range of data sources and/or unstable production process
  • IT (R server and internally hosted code repository)

Interested in RAP?…

  • How many reports do your team produce?
  • What proportion of time is spent producing reports?
  • How much copying and pasting/data movement between software is involved?
  • What proportion of your spreadsheet or report contains errors?
  • What would the impact of mistakes in production be?
  • Could your team create the report if certain team members suddenly left?
  • Could you reproduce your publication statistics from 5 years ago?

Contact the Transforming Publishing team (nss.isdtransformingpublishing@nhs.net)

Thank You