A look at the history and future of NHS-R hosted by Professor Mohammed Mohammed and featuring Paul Stroner, Sarah Culkin, Jenny Morgan, Ellen Coughlan, and Chris Beeley

NHS-R Podcast Episode 1- the history of NHS-R

NHS-R Podcast Episode 0- pilot

Very pleased to welcome the awesome gov.uk COVID dashboard team onto the podcast talking about the open code and data that they produced for the public and decision makers to help to manage the pandemic

Thanks as always to Tom Jemmett for his excellent editing.

Links:
https://coronavirus.data.gov.uk/
https://github.com/publichealthengland/coronavirus-dashboard

https://twitter.com/statsgeekclare
https://twitter.com/Pouriaaa
https://twitter.com/Sportlondon
https://twitter.com/jbwesty

NHS-R Podcast Episode 2- PHE COVID dashboard

Episode 3, all about the Friends and Family text mining project, with Andreas Soteriades and Chris Beeley.

Thanks as always to Tom Jemmett for his fantastic editing

Links:

https://github.com/CDU-data-science-team/pxtextmining
https://github.com/CDU-data-science-team/pxtextminingdashboard
https://github.com/CDU-data-science-team/experiencesdashboard
https://github.com/nhs-r-community/pxtextmineR

https://www.linkedin.com/in/andreas-diomedes-soteriades-05b26319/
https://twitter.com/ChrisBeeley

NHS-R Podcast 3- text mining patient experience data

Episode 4, talking COVID, maps, open source, Excel, and alcohol research with Colin Angus.
Thanks as always to Tom Jemmett for his fantastic editing
Links:
https://victimofmaths.github.io/
https://github.com/VictimOfMaths
https://twitter.com/VictimOfMaths

NHS-R Podcast Episode 4- Colin Angus

This episode is all about the super awesome NHS-R package NHSRplotthedots, which is a packages to draw NHSEI style plot the dots (SPC) charts, featuring:

* Chris Reading https://twitter.com/CReadingSkilton
* Zoë Turner https://twitter.com/Letxuga007
* Tom Jemmett https://twitter.com/tomjemmett
* Tom Smith https://twitter.com/analyst42
* Chris Mainey https://twitter.com/chrismainey

* Plot the dots from NHSE- https://www.england.nhs.uk/publication/making-data-count/
* GitHub https://github.com/nhs-r-community/NHSRplotthedots
* GitHub issues https://github.com/nhs-r-community/NHSRplotthedots/issues
* CRAN package https://cran.r-project.org/web/packages/NHSRplotthedots/index.html

Install the package, have a go, file an issue, get involved!

NHS-R Podcast Episode 5- NHSR plot the dots

A conversation with Marcus Baw, General Hacktitioner, Clinician who codes, and advocate of open source across health and medicine

* Marcus on Twitter: https://twitter.com/marcus_baw  
* Post on wetware: https://drzoeneill.medium.com/watch-the-wetware-what-should-the-doctor-order-b5d1745dcf7a
* Open source medicine: https://medium.com/@marcus_baw/open-source-is-the-only-way-for-medicine-9e698de0447e
* Awesome missing NHS things: https://publicmoneypubliccode-cic.github.io/awesome-missing-nhs-things/
* Best practice as code: https://marcus-baw.medium.com/royal-colleges-3-0-best-practice-as-code-7065bce821a7
* Digital growth charts: https://github.com/rcpch/digital-growth-charts-server
* Public money, public code: https://publicmoneypubliccode.org.uk/

Comments, questions, suggestions for episodes- get in touch! 

* nhs.rcommunity@nhs.net

NHS-R Podcast Episode 6- Marcus Baw

Very special guests from NHS Pycom, a community dedicated to supporting users of Python in UK healthcare.

NHS.pycom website: https://nhs-pycom.net/
NHS.pycom main GitHub:  https://github.com/nhs-pycom
Python takes the top slot in TIOBE: https://www.tiobe.com/tiobe-index/

Mary Amanuel: https://github.com/maryamanuelnhsx

Mark Bailey: https://twitter.com/CotswoldsMaker ; https://github.com/Cotswoldsmaker ; https://github.com/spiritumduo

Adenrele Komolafe: https://twitter.com/AK_DataPharm ; https://github.com/Adenrele ; https://github.com/Adenrele/Hayfever-NHS-Prescribing-Data- ; https://github.com/Adenrele/Web_Portfolio

Sophie Williams: https://twitter.com/sophl_williams ; https://github.com/sophie-w/ONTOSERVER_api

Comments, questions, suggestions... nhs.rcommunity@nhs.net

NHS-R podcast episode 7- NHS Pycom

A conversation with Dr. Marcus Baw, Dr. Simon Chapman and Prof. Tim Cole about the Digital Growth Charts app that they have been developing for the Royal College of Paediatrics and Childhealth.

There is a demo of the app here: https://growth.rcpch.ac.uk/

You can view the app's documentation here: https://github.com/rcpch/digital-growth-charts-documentation

You can read a blog post about why the team chose python here: https://blog.bawmedical.co.uk/why-we-chose-python-for-the-rcpch-digital-growth-charts-project

Follow our guests on social:
* Marcus Baw: https://twitter.com/marcus_baw
* Simon Chapman: https://twitter.com/eatyourpeas
* Tim Cole: https://iris.ucl.ac.uk/iris/browse/profile?upi=TCOLE39 ; https://github.com/statist7

NHS-R podcast episode 8 - Growth Charts

A discussion about using R for reproducible research at Great Ormond Street Hospital, with Will Bryant and Lydia Briggs from GOSH's Digital Research Environment.

Digital Research, Informatics, Virtual Environments unit (DRIVE): https://twitter.com/drivegosh
Will: https://www.linkedin.com/in/william-a-bryant/
Lydia: https://twitter.com/lrb93
GitHub: https://github.com/gosh-dre

Find out more about the NHS-R Community here: https://nhsrcommunity.com/
Comments, questions? nhs.rcommunity@nhs.net

NHS-R podcast episode 9 - reproducible research at GOSH

Innovative data science with individuals from what was at the time of recording NHSX (now NHS Transformation directorate), with Amadeus Stevenson, Matthew Cooper, and Jennifer Hall, discussing:

* Productionisation of data science and ML
* Finding projects and communicating about them
* Disseminating models
* Synthetic data
* Scheduling algorithms

https://www.nhsx.nhs.uk/ai-lab/ai-lab-programmes/skunkworks/working-with-us/

https://govdatascience.slack.com/ - Slack channel within here called MLOps

https://www.adalovelaceinstitute.org/project/algorithmic-impact-assessment-healthcare/ - Algorithmic Impact Assessment with Ada Lovelace Institute

https://github.com/nhsx/SynthVAE - SynthVAE, variational autoencoder for generation of synthetic data

https://physionet.org/content/mimiciii/1.4/ - MIMIC-III, dataset used as an input for the synthetic data pipeline

https://kedro.readthedocs.io/en/stable/  - QuantumBlack Kedro, pipelining package used on Synthetic Data project

https://cran.r-project.org/web/packages/synthpop/index.html - Synthpop, R package for synthetic data

https://www.nhsx.nhs.uk/ai-lab/explore-all-resources/develop-ai/using-machine-learning-to-identify-patients-at-risk-of-long-term-hospital-stays/ - Long Stayers Case Study

https://github.com/nhsx/skunkworks-long-stayer-risk-stratification - Code for the Long Stayers project

https://nhsx.github.io/nhsx-internship-projects/ - NHSX Analytics Unit PhD internships

Code repositories for Synthetic Data project and Nursing Schedule Optimisation project are coming soon

Find out more about the NHS-R Community here: nhsrcommunity.com/
Comments, questions? nhs.rcommunity@nhs.net

NHS-R Podcast Episode 10 - NHS-X AI

A conversation with NHS-R Community trainers, many of whom have delivered the NHS-R Introduction to R and R Studio workshop, amongst other courses. The panel are:

Anastasiia Zharinova - Senior Economic Manager in NHS England and Improvement. In her previous role in the Strategy Unit, Anastasiia has provided training on Evaluating Complex Interventions and Simulation in R. She also was a project-manager of NHS-R community, so she is passionate about the training and knowledge sharing.

Annie Yu - Epidemiological Programmer at Hertfordshire County Council. She works in the development of shiny dashboards, automated reporting, and visualisations for public health management and COVID-19 surveillance. She does internal R training and held a workshop about interactive plotting for NHS-R.

Simon Wellesley-Miller - Senior Analytical Manager, NHS England and Improvement, lead for primary care, public health, mental health and quality in South West. He runs training in R, analytical and statistical techniques and is keen to get to more meaningful analytics as Business As Usual.

Presented by Zoë Turner, thanks to Tom Jemmett for editing

NHS-R community training

# 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! nhs.rcommunity@nhs.net

NHS-R newscast 6th July 2022

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? nhs.rcommunity@nhs.net

NHS-R podcast: Jess Morley

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

Thanks as always to Tom J for the editing

NHS-R Newscast 15th August 2022

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? nhs.rcommunity@nhs.net

## 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- 28th October 2022

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 nhs.rcommunity@nhs.net

Goldacre Review

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 nhs.rcommunity@nhs.net

NHS-R Podcast: The Turing Way

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 nhs.rcommunity@nhs.net

Pfizer R Centre of excellence

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 nhs.rcommunity@nhs.net

NHS-R Newscast- 16th January 2023

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 ;-) nhs.rcommunity@nhs.net 

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

John MacKintosh

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/

NHS-R Newscast 24th February 2023

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

NHS-R newscast 28th March 2023

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 nhs.rcommunity@nhs.net

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

NHS-R podcast with Tim Taylor 25th May 2023

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 nhs.rcommunity@nhs.net

NHS-R newscast 25th May 2023

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 nhs.rcommunity@nhs.net

NHS-R Newscast 20th July 2023

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 penchord@exeter.ac.uk 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 penchord@exeter.ac.uk.

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 nhs.rcommunity@nhs.net

Learning open source data science on the HSMA course with Dan Chalk

## 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

NHS-R/ NHS Pycom conference newscast 10th October 2023

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 nhs.rcommunity@nhs.net

NHSR - Data - Ethics

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: nhs.rcommunity@nhs.net

NHS-R podcast, 1st December, Matt Dray

Codebar: https://codebar.io/
Unconference blogpost: https://nhsrcommunity.com/what-was-the-unconference/
Liberating structures: https://www.liberatingstructures.com/

Questions? Comments? nhs.rcommunity@nhs.net

NHS-R Podcast, 14th December- Unconferences

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 nhs.rcommunity@nhs.net

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/

NHS-R podcast- conference roundup 4th March 2024

The NHS-R community aims to support the learning, application and exploitation of R in the NHS through workshops, video tutorials and providing a platform for discussion and sharing of developing best practice solutions to NHS problems.

NHS-R Community

Popular tracks