NHS-R Community Podcast

We discussed the upcoming HACA and NHS-R conferences and the type of paper you might take to each. HACA is focused on analytics that enhance decision quality and inform action and strategic change. NHS-R is more focused on writing code with open source tools, packages and tools, RAP, and all the other stuff readers of the NHS-R blog know and love.

HACA: https://uobevents.eventsair.com/haca-2023/

We talked about dplyr 1.1.0 dplyr 1.1.0: `pick()`, `reframe()`, and `arrange()` https://www.tidyverse.org/blog/2023/02/dplyr-1-1-0-pick-reframe-arrange/

dplyr 1.1.0: Joins https://www.tidyverse.org/blog/2023/01/dplyr-1-1-0-joins/

There is also more on YouTube: https://www.youtube.com/watch?v=9LAML4Nr1II

We discussed a recent Slack thread looking at mutate_all and described how you can future proof your code by looking at things like lifecycle badges https://lifecycle.r-lib.org/articles/stages.html 

"Code archaeology" next with a look at aes_string https://ggplot2.tidyverse.org/reference/aes_.html

We discussed the Government Data Science Community and all the ways to hear more and get involved- Slack, meetups and a newsletter https://www.gov.uk/service-manual/communities/data-science-community

Applications to data science accelerator are closed but it will return, so keep an eye out for it https://www.gov.uk/government/publications/data-science-accelerator-programme/introduction-to-the-data-science-accelerator-programme

We also discussed the graduate programme which is open to applications https://datasciencecampus.ons.gov.uk/long-read/data-science-graduate-programme/

Very special guest this time, Senior NHS-R Fellow John MacKintosh, talking about drawing pretty graphs, blogging, data.table, colour palettes, and metal. John has an incredible wealth of GitHub packages and his blog is world class so have a look through the links at the bottom, you'll be glad you did.

Editor's note: Tom has brought to my attention that I incorrectly described "Wake up dead" as a "new" song when it does in fact date all the way back to 1986. I heard the collaboration with Lamb of God and assumed it was new. Tom has also informed me that I did in fact add the album with Wake up dead on it to {rockthemes}, which makes it doubly silly. NHS-R is all about learning and making mistakes, and I'm very happy to have made a public mistake in the spirit of NHS-R, even if it is about metal and not data science. Believe me when I say I make just as many stupid mistakes when I'm doing data science, in fact possibly even more :-)

Comments? Questions? Not about Megadeth please ;-) [email protected]

Twitter: https://twitter.com/_johnmackintosh

Mastodon: https://fosstodon.org/@johnmackintosh

Blog: https://johnmackintosh.net/

Primus lyrics in an R package: https://search.r-project.org/CRAN/refmans/stringdist/html/afind.html

Some links on data.table https://www.johnmackintosh.net/tag-data-table/

XKCD on relying on open source https://xkcd.com/2347/

Patient counter https://github.com/johnmackintosh/patientcounter

Runcharter https://github.com/johnmackintosh/runcharter

Rock themes https://github.com/johnmackintosh/rockthemes

The first item of news is that The Strategy Unit is the new home of NHS-R. Chris Beeley and Zoë Turner both now work at The Strategy Unit and have NHS-R in their job descriptions. They plan to be doing much more work in the future on communicating better with members (maybe a newsletter, more blogs...), organising hacks (which would be a first for the community), and a mentoring scheme (more on which later).

Another bit of news that was teased at the NHS-R conference was the new national conference for healthcare analytics, which does not yet have a proper name. Abstract submission will open soon and NHS-R will be announcing mentoring to go alongside the conference to help people to submit abstracts and prepare their talks. The conference will be focused on strategic analysis and decision making (as opposed to NHS-R conference which tends to be more about methods) and so do be thinking about what you might like to bring to the conference. If you feel you would like help, watch the skies because NHS-R will be offering assistance all the way through the process, from getting your talk accepted to actually presenting it on the day.

We talked about the importance of having diverse voices in NHS-R and making sure we are welcoming to as many people as possible. Tech communities can often be quite white and male and NHS-R needs to make sure that it engages people from all walks of life.

There was a roundup of interesting issues on the NHS-R GitHub, and a discussion about how helpful tackling these issues can be, for us as a community but also for you in terms of skills development and having work in the open for your CV. Please have a look at these results and others throughout the repos:

https://github.com/nhs-r-community/NHSRplotthedots/issues/141

https://github.com/nhs-r-community/ISR-iterative-sequential-regression-/issues

https://github.com/nhs-r-community/git_training/issues/4

https://github.com/nhs-r-community/statements-on-tools/issues

If you need any help getting started, say so on the Slack and a member of the community will be sure to come along to assist you. Note also that many of these issues are about documentation, not code, so you can make a really valuable contribution without writing code.

We talked about semantic versioning and how useful it can be, for a summary see this link about semantic versioning https://semver.org/

Chris made a passing reference to the Python 2/ 3 mess, particularly in the Linux world, and as always there is an XKCD for that: https://xkcd.com/1987/

Lastly we talked about the amazing John MacKintosh's patientcounter package, https://github.com/johnmackintosh/patientcounter, as well as some more of his packages such as rock themes and pop themes:

https://github.com/johnmackintosh/rockthemes

https://github.com/johnmackintosh/popthemes

Comments? Questions? Email [email protected]

Special guests from Pfizer this time, Mike Smith and Doug Robinson talking about the Pfizer R centre of excellence. Fascinating parallels with data science and analytics in the NHS and a great example of a vibrant global community.

Find Mike and Doug on the internet:

https://www.linkedin.com/in/mikeksmith/

https://twitter.com/mikeksmith

https://mastodon.social/@MikeKSmith

https://www.linkedin.com/in/douglas-robinson-7024182/

Comments? Questions? Email [email protected]

The awesome Turing Way community on the podcast this time, talking about reproduciblity in science and with lots of useful insights into how to run an effective community.

https://the-turing-way.netlify.app/welcome

With Malvika Sharan, Arron Lacey, Anne Steele, and Chris Beeley (hosting)

Interoperability in US procurement: https://twitter.com/doctorow/status/1462830032812871680?s=20&t=zWP1RBBL2TIW_-cy_ro-nQ

Comments? Questions? Contact [email protected]

Special guest host Fraser Battye for this special episode on the Goldacre Review. With guests Léa Quentin, Jonny Pearson, Shirin Khorsandi, and Chris Beeley.

The Goldacre Review https://www.gov.uk/government/publications/better-broader-safer-using-health-data-for-research-and-analysis

Short Explainer for the Competency Framework - https://transform.england.nhs.uk/key-tools-and-info/nhsx-analytics-unit/data-and-analytics-partnership-gateway/professionalisation/

Competency Framework Booklet - https://transform.england.nhs.uk/media/documents/NCF_Framework_Booklet.pdf

SDE Lite explainer - https://transform.england.nhs.uk/key-tools-and-info/data-saves-lives/secure-data-environments/

SDE Policy - https://www.gov.uk/government/publications/secure-data-environment-policy-guidelin[…]vironment-for-nhs-health-and-social-care-data-policy-guidelines

Open project examples - https://nhsx.github.io/AnalyticsUnit/projects.html

Sharing code in the open blog - https://nhsx.github.io/AnalyticsUnit/codeintheopen.html

Open Source Tool Request Advice - https://nhsx.github.io/AnalyticsUnit/toolstackrequests.html

NHSX open source policy https://github.com/nhsx/open-source-policy

MIT licence https://opensource.org/licenses/MIT

Jess Morley podcast https://soundcloud.com/nhs-r-community/nhsr-jess-morley

Government RAP strategy https://analysisfunction.civilservice.gov.uk/policy-store/reproducible-analytical-pipelines-strategy/

NHS R Community https://nhsrcommunity.com/

NHS Pycom https://nhs-pycom.net/

Questions and comments [email protected]

For more links please see the blog post on the NHS-R community website https://nhsrcommunity.com/nhs-r-newscast-28th-october-2022/

Comments? Questions? [email protected]

## NHS-R conference

https://nhsrcommunity.com/events/nhs-r-community-conference-2022/

## Linting part deux

Static code analysis

{lintr}

diagnostics in rstudio

Linting in vs code

{styler}

Github actions to lint code

Tidyverse style guide

## Structuring projects

scripts, setwd when reading and writing local files

Projects, self-contained and simpler to use (relative filepaths, folder structures, .gitignores)

projects as packages, simple function loading, and unit testing

devtools::load_all()

usethis::use_package()

testthat::use_test()

## MIT vs GPL

https://choosealicense.com/

https://www.tidyverse.org/blog/2021/12/relicensing-packages/

NHS-R newscast

NHS-R conference– Keynotes: Heather Turner from R Ladies, Jess Morley, and others. Python track. Free to all UK public sector. Fully hybrid remote/ in person

Rstudioconf. Alice Walsh talk on creativity, quilting, and R. Really useful analogy: do you want to be a pizza delivery business, or a plumber? Pizza delivery – choose from a picture, it arrives and looks like it should. We do a lot of dashboard pizza – asked for a chart here, there, summary table, no creativity. Plumber is domain expert. Turns up and asks questions about the problem. Brings tools and fittings to fix, but doesn’t focus on them. Focus on understanding the customer’s problem. Then gets on with work, and trusted to deliver result. https://www.rstudio.com/conference/2022/talks/quilting-in-r-becoming-creative/

Software carpentry and linting https://github.com/r-lib/lintr

RStudio becomes Posit to broaden focus to Python and VS Code https://posit.co/

VS Code for R. Live share. Git lens. GitHub co pilot https://twitter.com/_ColinFay/status/1556656199885529090?s=20&t=V-MENMBfJLbBbpLGVh4cVA

We had some feedback from the drop in that it should be easier to find training materials. GitHub can be quite confusing for beginners and in particular it is actively blocked in some NHS Trusts. We need to have a top level “training” view on the main website which has clear signposting to what all the courses are and where to find them. We will take this feedback away and try to work on it.

Website: https://nhsrcommunity.com/

Comments? Questions? [email protected]

Blog post about this newscast: https://nhsrcommunity.com/nhs-r-newscast-15th-august/

Thanks as always to Tom J for the editing

An interview with Jess Morley, self confessed Health Data Nerd, co-author of the Goldacre review, and Policy Lead at the Bennett Institute for Applied Data Science. All about ethics, AI, data, patient and public involvement, and Jess's thoughts on the Goldacre review and next steps.

Twitter: https://twitter.com/jessRmorley

Website: https://www.healthdatanerd.org/

Website: https://www.bennett.ox.ac.uk/about-us/jess-morley/

Goldacre review: https://www.gov.uk/government/publications/better-broader-safer-using-health-data-for-research-and-analysis

I can't find the tweet I mentioned with the open sourced code however hard I try, sorry! It was great, whoever you are.

NHS-R website https://nhsrcommunity.com/

Comments? Questions? [email protected]

# NHS-R podcast 6th July notes

## Goldacre review

Really good 1hr overview video from the Oxford Internet Institute to the Goldacre Morley report, gov initial response, and some good Q&A.

https://twitter.com/jessRmorley/status/1542110796540428289

### What does NHS-R and what can it do in the future?

Community building

* Two weekly drop in sessions

* Regular updates on GitHub issues and work triage

* More involvement of and communication with fellows

* Regular, structured communication programme featuring tweets, blogs, and podcasts

Experiential learning

* Mentoring scheme

* NHS data science acceletator launched

* Run and co-run NHS-R training

* NHS-R solutions can include a component where training/ supervising/ assisting the team delivering them is included

Writing code, software, and training

* Offer an “out of the box” NHS-R solution where software is provided to organisations that request it

Contributing to policy

## NHSRplotthedots

Going to have a bit of a push towards version 0.2 by conference time.

Any users who have quibbles / potential bugs, now's the time to talk / raise issues / get them understood and addressed.

Auto-rebasing. Discussion about pros and cons https://github.com/nhs-r-community/NHSRplotthedots/issues/151

Any users who have some time to help with writing material for a training workshop?

https://github.com/nhs-r-community/NHSRplotthedots/issues

## Drop in

Drop in session was a great success, next one Tuesday 2nd of August at 2pm, for details see #announcements in Slack

## R Screencasts

Great for learning, this is a curated list of screencasts following #tidytuesday solutions, indexed in various ways so you can find the things that might interest you, or that you want to learn about.

https://twitter.com/OscarBaruffa/status/1526154552201854977

Big Book of R https://www.bigbookofr.com/

## RAP

RAP strategy https://analysisfunction.civilservice.gov.uk/policy-store/reproducible-analytical-pipelines-strategy/

## Demand and capacity

Demand and capacity. Very early days, some code here https://github.com/nhs-r-community/shinyDemand . Join the #demand-and-capacity channel on Slack to get involved

Send an email! [email protected]