I’m an infectious disease researcher interested in real-time analysis, forecasting, semi-mechanistic modelling, and open-source tool development.

NOW

• Working @Epiforecasts (part of the London School of Hygiene and Tropical Medicine);
• ⭐ Contributing to the epinowcast community developing tools and methods for current surveillance of infectious disease and preparing for future outbreaks;
• 🧻 Currently working on:
  • If we want an estimate of the reproduction number do we need the renewal process? and associated Julia modelling toolkit.
  • Developing a workbench for real-time and outbreak infectious disease modelling
  • Course materials on nowcasting, forecasting, and evaluation
  • 😴 🔌 🐑

BIO

• 🏢 2024-: Assistant professor in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
• 🏢 2023-2025: Contractor supporting the US CDC Centre for Forecast and Outbreak Analytics
• 🏢 2020-2023: Postdoc in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
• 🏢 2017-2019: Data Scientist at Funding Circle
• 📜 2016-2019: PhD at the University of Bristol on modelling the use of the BCG vaccine in the UK
• ⚙️ I use daily: R, julia, stan
• 🏗️ I like to perform analysis using novel models on interesting data and generalise those approaches into software 📦s
• 🌍 I’m mostly active within the epinowcast community
• 🌱 Learning all about Julia and Turing.jl - currently wondering why in the world you would use callables.
• 📘 Reading: Probability and random processes
• 💬 Ping me about statistical modelling of infectious diseases, real-time analysis of infectious diseases, estimating transmission dynamics in real-time, and team science opportunities
• 📫 Reach me: contact@samabbott.co.uk prob