NHS-R Community Podcast: Recent Episodes
NHS-R Community
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.
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.netNHS-R Conference Thurs 21st and Fri 22nd November at the ICC Birmingham. Details to followWill be in person but streamed so people can join in remotely similar to last yearHow to install R and newly added Git/GitHub Statement on Tools - https://tools.nhsrcommunity.com/technical-git.htmlFindsHow 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 Bartonhttps://health-inequalities.nhsrcommunity.com/content/imd.html - for more information on IMDhttps://resources.nhsrcommunity.com/tools.html#api - for API linksRStudio 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? nhs.rcommunity@nhs.net
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-workMatt's blog (well worth a read): https://www.rostrum.blog/Comments? Questions? Want to come on for a scrap? Email: nhs.rcommunity@nhs.net
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
NewsNHS-R/ NHSPycom conference! https://nhsrcommunity.com/events/#event_type-conferencesReal world data science: https://realworlddatascience.net/Unconference: http://unconference.net/unconferencing-how-to-prepare-to-attend-an-unconference-2/## Findsglue_sql: https://glue.tidyverse.org/reference/glue_sql.htmlObligatory Xkcd: https://xkcd.com/327/ install.packages takes an Ncpus argument https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packagesCitation function: https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/citationShiny live: https://docs.r-wasm.org/webr/latest/ & https://shiny.posit.co/py/docs/shinylive.htmlAdd Shiny live to deployment options here https://github.com/nhs-r-community/statements-on-toolsNHS 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 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/@hsmaHSMA GitHub for training materials : https://github.com/hsma-programmeHSMA Website : https://sites.google.com/nihr.ac.uk/hsmaIf 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-conferencesEmail with comments and questions nhs.rcommunity@nhs.net
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
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
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
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-submissionsWe have had the first NHS-R conference committee, and the minutes will be posted in the conference channel on Slack when they are readyChris’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/nhsrcommunityWebinar 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 flexibilityBase 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/issuesWebpages to help you learn GitHub https://github.com/firstcontributions/first-contributions and GitHub Minesweeper - https://profy.dev/project/github-minesweeper#start-project
Another newscast for the month of February, a quick summary for those of you who do not do the whole podcast thing: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=9LAML4Nr1IIWe 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_.htmlWe 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-communityApplications 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-programmeWe 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 ;-) nhs.rcommunity@nhs.net Twitter: https://twitter.com/_johnmackintoshMastodon: https://fosstodon.org/@johnmackintoshBlog: https://johnmackintosh.net/Primus lyrics in an R package: https://search.r-project.org/CRAN/refmans/stringdist/html/afind.htmlSome 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/patientcounterRuncharter https://github.com/johnmackintosh/runcharterRock 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/141https://github.com/nhs-r-community/ISR-iterative-sequential-regression-/issueshttps://github.com/nhs-r-community/git_training/issues/4https://github.com/nhs-r-community/statements-on-tools/issuesIf 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/rockthemeshttps://github.com/johnmackintosh/popthemesComments? Questions? Email nhs.rcommunity@nhs.net
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/mikeksmithhttps://mastodon.social/@MikeKSmithhttps://www.linkedin.com/in/douglas-robinson-7024182/Comments? Questions? Email nhs.rcommunity@nhs.net
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 Malkiva 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
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
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
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
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 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
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
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
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
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
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
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
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!
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
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
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
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