NHS-R Community Podcast

HACA 23rd July and 24th July, https://haca-conference.nhs.uk/

Open for abstracts till Sunday March 17th

Interested in coming to HACA as part of the NHS-R community? Contact Chris Mainey on Slack or email [email protected]

NHS-R Conference Thurs 21st and Fri 22nd November at the ICC Birmingham. Details to follow

Will be in person but streamed so people can join in remotely similar to last year

How to install R and newly added Git/GitHub Statement on Tools - https://tools.nhsrcommunity.com/technical-git.html

Finds

How to name files (Jenny Bryan) https://www.youtube.com/watch?v=ES1LTlnpLMk

Code smells and feels(Jenny Bryan) https://www.youtube.com/watch?v=7oyiPBjLAWY

Wrangling GIS data https://github.com/humaniverse/geographr; https://github.com/humaniverse/IMD

API packages for these in NHS-R called {NHSRpopulation} and {NHSRpostcodetools} > built on the API functions from Fran Barton

https://health-inequalities.nhsrcommunity.com/content/imd.html - for more information on IMD

https://resources.nhsrcommunity.com/tools.html#api - for API links

RStudio tips https://juliendiot42.github.io/RTips-Tricks/

Efficient R programming (https://csgillespie.github.io/efficientR/)

Data Science for Active Travel Planning: Streets, schemes and networks | Robin Lovelace https://www.robinlovelace.net/talk/data-science-for-active-travel-planning-streets-schemes-and-networks/

Codebar: https://codebar.io/

Unconference blogpost: https://nhsrcommunity.com/what-was-the-unconference/

Liberating structures: https://www.liberatingstructures.com/

Questions? Comments? [email protected]

History of RAP: https://nhsdigital.github.io/rap-community-of-practice/introduction_to_RAP/history_of_RAP/

Guide to the NHS: https://www.kingsfund.org.uk/audio-video/how-does-nhs-in-england-work

Matt's blog (well worth a read): https://www.rostrum.blog/

Comments? Questions? Want to come on for a scrap? Email: [email protected]

Special guests Natalie Zelenka and Huw Day join us from the Data Ethics Club for this podcast where we talked about the Data Ethics Club, the Data Hazards Project and a how the book Weapons of Math Destruction was inspiration for an outreach project for schools.

Key links :

Data Ethics Club: https://dataethicsclub.com/

Data Hazard project: https://datahazards.com/

Midlands Analyst Network Huddle: Weapons of Math Destruction: https://www.youtube.com/watch?v=bhO64ERizxU

Email with comments and questions [email protected]

## News

NHS-R/ NHSPycom conference! https://nhsrcommunity.com/events/#event_type-conferences

Real world data science: https://realworlddatascience.net/

Unconference: http://unconference.net/unconferencing-how-to-prepare-to-attend-an-unconference-2/

## Finds

glue_sql: https://glue.tidyverse.org/reference/glue_sql.html

Obligatory Xkcd: https://xkcd.com/327/

install.packages takes an Ncpus argument https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages

Citation function: https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/citation

Shiny live: https://docs.r-wasm.org/webr/latest/ & https://shiny.posit.co/py/docs/shinylive.html

Add Shiny live to deployment options here https://github.com/nhs-r-community/statements-on-tools

NHS Python Community: Software Engineering for Data Scientists https://www.youtube.com/watch?v=We1KwBIZc_s

We have this time a very special guest from PenARC and a teacher on the HSMA course, Dan Chalk.

If you're interested in the HSMA course there is a (virtual) open day we're having on 13th December - email [email protected] and ask to be added to the mailing list for more.

Key links :

HSMA YouTube for lectures and other videos : https://www.youtube.com/@hsma

HSMA GitHub for training materials : https://github.com/hsma-programme

HSMA Website : https://sites.google.com/nihr.ac.uk/hsma

If you have any questions about the programme feel free to email [email protected].

Come to the NHS-R conference, virtual and in person 17th/ 18th October, with workshops in the two weeks before https://nhsrcommunity.com/events/#event_type-conferences

Email with comments and questions [email protected]

The NHS-R 2023 Conference tickets are now available for the in-person and virtual event on 17 and 18 October https://nhsrcommunity.com/events/#event_type-conferences. We’ll be having a side room unconference and the social event was mentioned - details are all to come!

Tom Smith gave an update on the HACA 2023 conference as, although he hadn’t made it to the event himself due to work commitments, he had seen some of the posters. One poster stood out to him from someone in his own Trust who he hadn’t realised was working on a similar project and it showed the power of connections that conferences like this can have in connecting people and projects.

Zoë mentioned (a few times!) about the pull request she’d had accepted from Hadley Wickham for the inclusion of back ticks in the second edition R for Data Science https://github.com/hadley/r4ds/pull/1522. And on the theme of “small changes” to famous repositories she had also had a pull requested accepted to the {NHSRplotthedots} for text change to remove a reference to here and a link https://github.com/nhs-r-community/NHSRplotthedots/pull/183/files, making the text more readable for screen readers.

Tom updated on a few recent, bigger, changes to {NHSRplotthedots} in preparation for a new release ahead of this year’s NHS-R Community Conference. This has included some {plotly} code from a colleague who could contribute with their knowledge of {plotly} to help make {NHSRplotthedots} more interactive in its charts.

Tom put out a plea to everyone to get in touch via NHS-R Slack or email if you use {NHSRplotthedots} and what you have used it for.

Finds from the Slack group

Chris shared his life hack of ordering GitHub notifications by repository instead of the default of by date. It’s possible to subscribe and watch any repository on GitHub and notifications can build up rapidly if you are part of teams repositories like NHS-R Community. Having them grouped by repository can help manage those messages.

Tom gave his regular shout out to John Mackintosh’s {patientcounter} package. If you work with patient level data this package is likely to help you at some point with your analysis:

How many patients were in the hospital at 10 AM yesterday?

How many were in during each 15 minute spell between 2pm and 6pm?

How many were in during the last week, by hour?

This package aims to make answering these questions easier and quicker.

No SQL? No problem!

If you have time in, time out, a unique patient identifier, and optionally, a grouping variable to track moves between departments, this package will tell you how many patients were ‘IN’ at any time, at whatever granularity you need.

Zoë started by mentioning the {pivotr} package:

A shiny implementation of Excel’s PivotTables. Perform your aggregation/pivoting in the GUI, then copy the dplyr/tidyr code into your R script but quickly changed to talking about Matt Dray’s {quartostamp} because she uses it as regularly now as {tidyverse} as she’s creating Quarto slides and books. The package changes the RStudio IDE so that add ins can be selected to put the required text into your code for Quarto so you don’t have to remember the formats.

Chris talked about a function in {purrr} called pluck() which gets and sets elements within nested structures. Allison Horst has also drawn a lovely image to explain pluck() https://allisonhorst.com/r-packages-functions. Chris also mentioned that page breaks in Quarto can be made really simply:

{{< pagebreak >}}

Email us on [email protected]

We had our first email! On the subject of tidyverse versus base R, from the excellent Matt Dray. Links follow

http://varianceexplained.org/r/teach-tidyverse/

https://github.com/matloff/TidyverseSkeptic/blob/master/README.md

https://r4ds.hadley.nz/base-r

If you would like to email the show, especially if you learned tidyverse first, and then base, email us on [email protected]

NHSRepisodes https://github.com/nhs-r-community/NHSRepisodes

We're not open for abstracts any more, sorry! We have absolutely loads though, so keep an eye out for the conference 17th/ 18th October

Code speed up thread https://github.com/JosiahParry/pathattr/issues/1

Thanks again to Tim Taylor for an excellent podcast, and thanks to him for all of his wonderful contributions to the community

We have another newscast from the podcast, if you don’t do the whole podcast thing here are the notes and links from what we talked about.

The NHS-R Conference call for abstracts has been extended to 23rd June 2023 https://www.smartsurvey.co.uk/s/7FLFRY/

we’ve started an NHSR-Way book https://nhs-r-community.github.io/NHSR-way/ and also published through Netlify because some organisations block GitHub published pages. This book is inspired by The Turing Way and The GDS Way with more technical elements coming from the Statement on Tools book. For example, on licences we’ve detailed a lot of the options in the Statement on Tools but then said what NHS-R Community use in the NHS-R Way https://nhs-r-community.github.io/statements-on-tools/open-code-in-the-nhs.html#how-to-use-licences.

The NHSR book club have started reading the R4DS second edition and created an unofficial solutions book https://nhs-r-community.github.io/r4ds-ed2-exercise-solutions/.

Zoë Turner will be talking next month at the Government Data Science Community Meet-Up: The Data Science Toolshed Tue 13 Jun 2023 1.30 to 3pm. Title tbc but about how people can contribute to NHS-R open repositories or even pass them to NHS-R as has happened with the quarto NHS theme from Craig Shenton and {NHSRepisodes} package from Tim Taylor. Sign up to the event is free for Public Sector and Civil Service

Quarto theme: https://github.com/nhs-r-community/quarto-nhs-theme

NHSRepisodes: https://github.com/nhs-r-community/NHSRepisodes

Chris Beeley spoke at the DataConnect23 Government launch event and gave a taster session of text mining of patient experience data. Sign up to DataConnect events can be found at https://www.gov.uk/government/news/dataconnect23-is-on-its-way

Finds from the Slack group

Python linter: https://github.com/charliermarsh/ruff

Look at this great guidance on pie charts, unfairly maligned Pie charts from the Government Analysis Function https://analysisfunction.civilservice.gov.uk/support/communicating-analysis/introduction-to-data-visualisation-e-learning/module-9-pie-charts/.

A retro graphic to brighten up the Python exception messages - https://github.com/James-Ansley/cowexcept (can feature a dragon as well as a cow!).

For an extension of retro visuals then check out Star Wars in the Linux Terminal - https://www.linuxfordevices.com/tutorials/linux/ascii-star-wars-linux-terminal

Send questions and comments to [email protected]

There has been an extension of HACA abstract dates- new deadline is midnight on 14th April, see here for more https://uobevents.eventsair.com/haca-2023/abstract-submissions

We have had the first NHS-R conference committee, and the minutes will be posted in the conference channel on Slack when they are ready

Chris’s emergency webinar is not uploaded yet but keep an eye out for it on NHS-R YouTube if you are interested in Shiny and golem https://www.youtube.com/c/nhsrcommunity

Webinar change- Introduction to Quarto for R Users rescheduled to Friday 21st April 2023, 1.00 pm – 2.00 pm https://nhsrcommunity.com/events/april-2023-webinar-introduction-to-quarto-for-r-users-filippo-cavallari-data-science-lecturer-office-for-national-statistics-ons/

April 2023 Webinar: Chat with your data via RTutor and ChatGPT – Dr. Xijin “Steven” Ge – Professor of Bioinformatics at South Dakota State University Friday 14th April 2023, 3.00 pm – 4.00 pm https://nhsrcommunity.com/events/april-2023-webinar-chat-with-your-data-via-rtutor-and-chatgpt-dr-xijin-steven-ge-professor-of-bioinformatics-at-south-dakota-state-university/

New training for introduction to R and R Studio https://nhsrcommunity.com/events/nhs-r-introduction-to-r-and-r-studio/, focused on data manipulation, available in shorter chapters to give greater flexibility

Base vs dplyr pipe (https://twitter.com/_ColinFay/status/1640440512006987787).

Living library Living Library expression of interest (https://forms.office.com/Pages/ResponsePage.aspx?id=vweIB4LOiEa84A2BFoTcRqyZH350RK5LoLYHS7ST_B9UQkZRQ0VBWTRaMURLRExQMkxGTVhLWURIUC4u) from Government Data Science Community “The Living Library provides a space for staff to connect with people outside their work area to encourage knowledge sharing across government and the public sector.”

We talked about code style- the use of library(tidyverse) as well as namespacing packages with "::". Obligatory XKCD https://xkcd.com/2730/

Our SU discussions about style https://github.com/The-Strategy-Unit/data_science/issues

Webpages to help you learn GitHub https://github.com/firstcontributions/first-contributions and

GitHub Minesweeper - https://profy.dev/project/github-minesweeper#start-project