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

NOW

• Working at the London School of Hygiene and Tropical Medicine in the Epiforecasts group;
• ⭐ Crafting extensions to forecast.vocs 📦;
• ✨ Crafted last epinowcast 📦;
• 🧻 Currently working on:
  • Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England
  • Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy
  • Evaluating the use of real-time sequences for short-term forecasting
  • Evaluating a new method for nowcasting right truncated count data.

BIO

• 🏢 I’m currently working at London School of Hygiene and Tropical Medicine
• 📜 I did my PhD at the University of Bristol
• ⚙️ I use daily: R, 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 R Community
• 🌱 Learning all about Julia and Turing.jl
• 📘 Reading all of China Miéville’s work.
• 💬 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: sam.abbott@lshtm.ac.uk