I am a Research Software Engineer, and currently run the RESIDE research software group within the MRC Centre for Global Infectious Disease Analysis. I am excited about ways to break down the barriers between domain experts and code and help people do more science per line of code written.

Previously, I have:

• developed software to evolve traits in virtual tropical forests,
• designed and implemented new methods for comparative phylogenetic methods, then explained these methods through the medium of puppetry,
• investigated potential environmental impacts of genetically modified crops, which involved hunting turnips from helicopters (and building databases).

Writing

Occasionally, I blog on my group's blog, or contribute to rOpenSci's blog. This post from 2014 in particular remains very relevant. Academic writing via Google Scholar, though I've not actively published for many years now.

I occasionally tweet as @rgfitzjohn and am on Mastodon at @richfitz@fosstodon.org.

Previously, I wrote a teaching blog at with Daniel Falster called nicercode.

Projects

My current professional work can be found on the RESIDE pages, and my software can be found on my GitHub page, as well as the organisations mrc-ide, vimc, jameel-institute, bacpop, and reside-ic.

Currently I am working on:

• The next iteration of orderly, our continually-reproducible reporting framework (as outpack and orderly2), which will be more powerful, flexible, and polylingual with first class Python support.
• Our framework for dynamical modelling built around the odin DSL, dust simulation engine and mcstate inference package; currently we are implementing automatic differentiation. Current work is in the odin2, dust2 and monty packages.
• Friendly approaches to high-throughput and high-performance computing, via hipercow.
• Designing robust approaches to deploy research software to the web.

Active projects that are more personal include

• redux, the most fully featured Redis client for R.
• stevedore, a complete docker client for R, automatically generated from the docker OpenAPI specification.
• thor, a very fast key-value store for R, implemented using lmdb.

Very occasionally, I code outside of work:

• rainbowrite - more colourful replacements to message and cat, inspired by lolcat.
• stegasaur - encode arbitrary R objects in cat pictures.
• rfiglet - a complete, pure-R, implementation of the FIGlet system for fancy terminal writing.

I am a huge fan of Advent of Code, and we use this to expose Centre researchers to programming concepts each December:

• Solutions to several years in R, and 2023 in Python.
• Progress solving 2022 in Rust.

Previous projects include:

• diversitree - a large suite of phylogenetic methods, developed and implemented during my PhD. No longer in active development but still in wide use
• geiger, arbutus - packages with Matt Pennell for comparative phylogenetics.
• plant, a framework for eco-evolutionary modelling with Daniel Falster, still under development in his lab
• TRAMPR, a package for analysing T-RFLP data in fungal communities before the advent of next generation sequencing. My first publicly released R package, and still in use after more than 15 years.

Talks

I'm always interested in speaking opportunities, especially around reproducibility, software processes in multidisciplinary teams or directly on any of the projects above - please get in touch.

Some representative talks:

• 2024 RSECon24 - slides, video
  • A talk about orderly2 (the first since we rewrote the tool) focussing on what it means to the reproducible and why I think our thinking about it has become stuck in unproductive areas.
• 2023 Research Software Engineering in Data and AI workshop, Warwick University/Alan Turing Institute - slides
  • Our approach to handling ever changing data streams during the UK COVID-19 response, creating reproducible pipelines with automatic provenance tracking.
• 2022 RSLondonSE - slides
  • An overview of the technologies used in the UK COVID-19 response, from the simulation and inference tools to our approach to data management and reproducibility.
• 2020 Research Software Engineer Stories Podcast - recording
  • In the relatively quiet period after the first wave of the COVID-19 pandemic, I talked with Peter Schmidt about the roles that software and software engineering had played in the response so far, and the role of best practices as they applied in different parts of the process.
• 2020 Bioinformatics London (b2b with Matt Dray) - slides
  • On the eve of the COVID-19 pandemic, my last in person talk for over two years with an ominous graph showing growth in infection numbers. The next iteration of my reproducibility/orderly talk.
• 2019 rOpenSci Community call on testing - slides, recording and resources
  • A tutorial-style presentation and discussion on best use of software testing for those new to the idea, or those who struggle to effectively integrate it into their workflows.
• 2019 UseR! Toulouse - slides, video
  • Description of odin, focusing on solving complex systems of differential equations. At this point we were pleased with the system, but had no idea how it would change over the next 12 months!
• 2019 RSLondonSE - slides
  • Challenges in reproducible research, and how simple workflows can help. My first attempt at describing the problem that orderly tries to solve.
• 2018 Oxford R User Group - slides
  • A discussion of three projects where exploiting peculiarities of the R language (such as “non standard evaluation”) can build highly expressive user interfaces. Discusses cyphr, odin and stevedore.
• 2014 Sydney Users of R Forum (SURF) - slides
  • My first public attempt to outline practical issues facing researchers trying to work in a reproducible way, outlining the tools they might use and challenges they might face.
• 2013 ESEB keynote - slides
  • One of the last science-focused talks I ever gave, in receipt of the John Maynard Smith prize.

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