Introduction

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.

Who am I?

I'm Dr. Daniel Weiand MBChB FRCPath RCPathME MClinEd, a Consultant Microbiologist at Newcastle upon Tyne Hospitals NHS Foundation Trust.

• I joined Newcastle upon Tyne Hospitals NHS Foundation as a Consultant Medical Microbiologist in 2015, and have a special interest 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:
  • Associate Clinical Lecturer at Newcastle University;
  • Medical Examiner for Newcastle upon Tyne Hospitals NHS Foundation Trust; and
  • Examiner for the Royal College of Pathologists (RCPath);
  • “Q” fellow at The Health Foundation.
• I am currently enrolled in the 2024/25 PG Cert in Clinical Data Science at Manchester University.

Favourite quote

"All models are wrong, but some are useful." - George Box

Website:

https://www.newcastlelaboratories.com

Twitter:

@send2dan

GitHub:

https://github.com/send2dan/public/

ORCiD

ORCiD iD 0000-0001-5854-3452

Why R?

R is a powerful, free, and open-source language for data science and statistics. This makes it a perfect tool for the NHS, where research, collaboration, and continuous quality improvement are paramount.

Open-source languages including R and Python are used in many industries, including by Dell, Walmart and (increasingly) across the NHS

Information for anyone in the NHS who is interested in learning how to code:

• R is one of the most commonly used languages for data science, together with Python.
• It is a powerful, entirely free open source data science and statistics environment, used in industry, academia and major corporations (e.g. Microsoft, Google, Facebook).
• It benefits from a worldwide community that freely shares learning and resources, through e.g. GitHub
• The Goldacre report actively promotes the use of R in the NHS.
• NUTH now actively supports the use of R at scale, and it can be installed on any work PC (simply call IT and ask to be added the “SCCM-R” group)
• 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: [email protected].
  • 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)

See what colleagues across the NHS are doing with code:

• NHS-R and NHS.pycom run the premier data science conference in the NHS, along with regular skill-based webinars

• The free-to-NHS conference is really of excellent quality, very well organised, and well attended: Book your ticket to avoid disappointment!