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Hi there ๐Ÿ‘‹

I'm an infectious disease researcher interested in real-time analysis, forecasting, semi-mechanistic modelling, and open-source tool development.
NOW
BIO
  • ๐Ÿข 2024-: Assistant professor in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
  • ๐Ÿข 2023-: Contractor supporting the CDC Centre for Forecast and Outbreak Analytics
  • ๐Ÿข 2020-2023: Postdoc in real-time modelling of infectious disease w/ Sebastian Funk at the London School of Hygiene and Tropical Medicine
  • ๐Ÿข 2017-2019: Data Scientist at Funding Circle
  • ๐Ÿ“œ 2016-2019: PhD at the University of Bristol on modelling the use of the BCG vaccine in the UK
  • โš™๏ธ I use daily: R, julia, stan
  • ๐Ÿ—๏ธ I like to perform analysis using novel models on interesting data and generalise those approaches into software ๐Ÿ“ฆs
  • ๐ŸŒ I'm mostly active within the epinowcast community
  • ๐ŸŒฑ Learning all about Julia and Turing.jl - currently wondering why in the world you would use callables.
  • ๐Ÿ“˜ Reading: Probability and random processes
  • ๐Ÿ’ฌ Ping me about statistical modelling of infectious diseases, real-time analysis of infectious diseases, estimating transmission dynamics in real-time, and team science opportunities
  • ๐Ÿ“ซ Reach me: [email protected] prob

Sam Abbott's Projects

showmeperseus icon showmeperseus

A shiny app aiming to remove some of the potential friction for users of the rperseus package

stacktweetbot icon stacktweetbot

Tools for quickly and easily creating twitter StackOverflow bots

tb_england_wales icon tb_england_wales

Dashboards visualising publicly available Tuberculosis incidence data in England and Wales

thepebblegame icon thepebblegame

The pebble game: A simple game that can be used to understand epidemics and vaccination

thesis icon thesis

PhD thesis submitted to the University of Bristol. Title: Modelling BCG vaccination in the UK: What is the impact of changing policy?

tidyverse-gpu icon tidyverse-gpu

Adding in support for GPU acceleration via CUDA to rocker/tidyverse

touchstone icon touchstone

Smart benchmarking of pull requests with statistical confidence

trendsinpapers icon trendsinpapers

A simple R package to load, clean and analysis trends in publications - with TB modelling papers as an example

wuhanseedingvstransmission icon wuhanseedingvstransmission

The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis

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