Biography

Dr Tom Palmer, Senior Lecturer in Biostatistics

Interests

  • Causal inference
  • Medical statistics / Biostatistics
  • Mendelian randomization
  • R and Stata programming
  • Statistical methods for Epidemiology
  • PhD thesis pdf

Education

  • Postgradute Certificate in Academic Practice, 2018

    Lancaster University

  • PhD Extensions to Mendelian randomization, 2009

    University of Leicester

  • MSc in Medical Statistics, 2005

    University of Leicester

  • BSc in Mathematics and Economics, 2002

    University of Nottingham

Awards

Version 2 of the OpenSAFELY R image released

Bennett Institute, University of Oxford Apr 2025
My version 2 of the R image for the OpenSAFELY platform has been released. You can read more about it here and here.

Blog post included as a highlight in R Weekly blog and podcast

R Weekly Jan 2025
My blog post on Seven tips for creating Quarto revealjs presentations was included as a highlight in the R Weekly blogpost and podcast (episode 193). Thanks to Eric Nantz, Mike Thomas, Jon Calder, and the R Weekly team.

Secondment to software development team at the Bennett Institute

Prof. Ben Goldacre’s Bennett Institute for Applied Data Science in the Nuffield Department of Primary Care Health Sciences, University of Oxford Sep 2024 – Mar 2025
Two day per week secondment to the Reproducible Analytics Pipeline software development team in Prof. Ben Goldacre’s Bennett Institute, University of Oxford. I will work on R related projects within the OpenSAFELY programme.

Paper in top 10% of downloaded papers from Statistics in Medicine in 2022

Statistics in Medicine Jul 2024

OneSampleMR included in RStudio’s R Views November 2021: “Top 40” New CRAN Packages

R Views Dec 2021

Co-chair of the organising committe for the 5th International Mendelian randomization conference

MRC Integrative Epidemiology Unit Jul 2021

Article in Best of IJE 2019

International Journal of Epidemiology Dec 2019
Spiller, et al., Software application profile: mrrobust–a tool for performing two-sample summary Mendelian randomization analyses, IJE, 48, 3, 684–690, https://doi.org/10.1093/ije/dyy195 was the second most cited IJE paper in 2019.

Co-editor, with Prof. Jonathan Sterne, of Meta-Analysis in Stata: An Updated Collection from the Stata Journal, Second Edition

Stata Press Oct 2015

Student conference award, Alexandroupolis, Greece

International Society for Clinical Biostatistics Aug 2007

Pfizer studentship to study MSc in Medical Statistics, University of Leicester

Pfizer Sep 2004 – Aug 2005

Recent Posts

Running the nbstata Jupyter kernel within a uv virtual environment

How to setup a uv virtual environment to run the nbstata Jupyter kernel.
Last updated on May 10, 2025 Blog
Running the nbstata Jupyter kernel within a uv virtual environment

Running R on Windows on ARM on GitHub Actions

How to setup and run the AARCH64/ARM version R on Windows on ARM on GitHub Actions
Last updated on Apr 16, 2025 Blog
Running R on Windows on ARM on GitHub Actions

Amending the Git commit message of a previous commit (that isn't the most recent) in GitHub Desktop without performing an interactive rebase

How to amend previous Git commit messages, that aren’t for the most recent commit, in GitHub Desktop without performing an interactive rebase.
Last updated on Mar 8, 2025 Blog
Amending the Git commit message of a previous commit (that isn't the most recent) in GitHub Desktop without performing an interactive rebase

Checking your R packages and practicals on a schedule using GitHub Actions

How to setup automated checks on a repository containing an R package or R practical using GitHub Actions.
Last updated on Feb 24, 2025 Blog
Checking your R packages and practicals on a schedule using GitHub Actions

Creating a Finder Smart Folder of your RStudio Project files to enable super fast project launching

Create a Finder Smart Folder showing all your RStudio (and/or your VSCode/Positron) project files so you can switch between your projects fast and conveniently.
Last updated on Feb 21, 2025 Blog
Creating a Finder Smart Folder of your RStudio Project files to enable super fast project launching
See all posts

R packages

ieugwasr R package

R Mar 2024

MRCIEU R-Universe 🚀

R-Universe Jun 2023

Personal R-Universe 🚀

R-Universe Jun 2023

Statamarkdown R package

R Feb 2023

tmsens R package

R Feb 2022

OneSampleMR R package

R Nov 2021

TwoSampleMR R package

R Feb 2020

knitexercise R package

R Feb 2020

mrbayes R package

R Jul 2019

bpbounds R package

R Oct 2018

Stata packages

ivonesamplemr Stata package

Stata Sep 2021

mrrobust Stata package

Stata Sep 2018

bpbounds Stata package

Stata Oct 2011

confunnel Stata package

Stata Jun 2008

winbugsfromstata Stata package

Stata Nov 2006

Talks

Some more R, Git, and R Markdown and Quarto tips

May 7, 2025 MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
Tom Palmer
Slides

The MRC IEU R-Universe of Mendelian randomization related R packages 🚀

Jun 19, 2024 Mendelian Randomization Conference, Bristol
Tom Palmer
PDF

The MRC IEU 🚀 R-Universe of Mendelian randomization related R packages

Jan 26, 2024 Goldney House, University of Bristol, Bristol, UK
Tom Palmer
Slides

Using Git, GitHub Desktop, and GitHub for novice and experienced users

Dec 1, 2023 MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
Tom Palmer, Yi Liu
Slides

Using allele scores to identify confounding by reverse causation: Studies of alcohol consumption as an exemplar

May 22, 2023 MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
Tom Palmer, Hannah Sallis, Kate Tilling, George Davey Smith, Marcus Munafò
Slides
See all talks