Welcome to Dr. Daniel Weiand's Public GitHub Repository!
This repository includes presentations I’ve delivered (and the code used to deliver them), including:
- an online workshop on Producing Parameterised Reports using purrr and Quarto; and
- a plenary talk on Predicting Antimicrobial Resistance Rates (AMR) using R and Sharing the Results in the form of Parameterised Reports produced using Quarto.
- a plenary talk on Patient-Level Analytics That Work: Using R to Achieve Rapid, Sustained MRSA Screening Compliance Improvements (delivered @ RPySOC 2025, the NHS-R/NHS.pycom Open Source Conference)
My name is Dr. Daniel Weiand MBChB FRCPath RCPathME MClinEd MBCS PGCertClinicalDataScience and I work as a Consultant Medical Microbiologist at Newcastle upon Tyne Hospitals NHS Foundation Trust.
- I joined Newcastle upon Tyne Hospitals NHS Foundation (NUTH) as a Consultant in 2015, and have special interests in nephrology, urology, solid organ transplantation (kidney and pancreas), vascular surgery, medical education, clinical informatics (#RStats @NHSrCommunity) and quality improvement.
- Before moving to the North East of England, I trained in Aberdeen, Sheffield, York, Hull and Leeds.
- My additional roles and responsibilities include:
- Clinical Informatics Lead for Clinical and Diagnostic Services (Board 8) at NUTH; and
- Associate Clinical Lecturer at Newcastle University; and
- Examiner for the Royal College of Pathologists (RCPath); and
- “Q” fellow at The Health Foundation; and
- Member of The British Computer Society (BCS); and
- Member of the Data Access Committee (DAC) for the North East and North Cumbria (NENC) Secure Data Environment (SDE).
- In 2025, I was awarded the Postgraduate Certificate (PGCert) in Clinical Data Science by the University of Manchester:
- NHS England commissioned the University of Manchester to develop a flexible Clinical Data Science Postgraduate Certificate programme in collaboration with the National School of Healthcare Science and clinical partners at The Christie Hospital, to support NHS long-term workforce development plans.
- The Clinical Data Science Programme aims to empower healthcare professionals to apply data science in practice and translate data into patient benefit.
"All models are wrong, but some are useful." - George Box
Integrated Laboratory Medicine at Newcastle upon Tyne Hospitals NHS Foundation Trust
https://github.com/send2dan/public/
- NUTH now actively supports the use of R at scale, and it can be installed on any work PC (simply call IT on ext 21000 and ask to be added to the “SCCM-R” group).
- The NUTH-R Teams channel has been set up to as a place for anyone in the Trust working in, or interested in data science – whether it’s for research, business analytics, service improvement, or any other purpose. The group has started with a focus on R, but everything data science – Python, SQL, Git, even Excel – is fair game. Use it to find out more about each other’s work, share resources, help each other out, and support new people who are dipping their toes in the world of R.
Background information
- R is one of the most commonly used languages for data science, together with Python.
- Open-source (free) data science programming languages, including R and Python, are used in many industries, including by Dell, Walmart and (increasingly) across the NHS
- Both R and Python benefit from a worldwide community that freely shares peer-reviewed learning and resources, e.g. through GitHub, for anyone to use
- The Goldacre report actively promotes the use of open-source data science programming languages across the NHS. This is with a view to increasing adoption of RAP (Reproducible Analytical Pipelines). The vision is for modern, open-source tools to support better, broader, safer care
- Lord Darzi's report on the state of the National Health Service in England emphasises we are on the precipice of an artificial intelligence (AI) revolution that could transform care for patients.
- Investing in additional data science capacity is essential to meet national policy expectations, improving diagnostic capabilities, and ensuring our Trust is positioned to deliver the "better, broader, safer care" that the NHS 10-year plan demands.
Resources
- Great resources to learn how to code include:
- NHS-R delivers free-to-NHS-staff online introductory training on R and RStudio/Posit. It’s free to register. These courses are really popular and spaces are limited to about 20 per session. Sessions are scheduled once a month. For further information, please contact: nhs.rcommunity@nhs.net.
- The NHS-R community also runs the premier data science conference in the NHS, along with regular skill-based webinars.
- Also see NHS-R community blog: https://nhsrcommunity.com/blog/
- There are also many (!) excellent, free textbooks (e.g. R4DS)
- NHS-R supports a thriving Slack community, which is an excellent resource for when you get stuck (most useful if you are able to share a reproducible example of the problem you're encountering)