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Working from home
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Achievements

Achievement: Starstruckx2Achievement: Pair Extraordinairex4Achievement: Pull Sharkx4Achievement: Galaxy BrainAchievement: YOLOAchievement: QuickdrawAchievement: Public SponsorAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Starstruckx2Achievement: Pair Extraordinairex4Achievement: Pull Sharkx4Achievement: Galaxy BrainAchievement: YOLOAchievement: QuickdrawAchievement: Public SponsorAchievement: Arctic Code Vault Contributor

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@EpiAware

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seabbs/README.md

Hi there 👋

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

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  1. thesis thesis Public

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

    C++ 11 2

  2. epiforecasts/EpiNow2 epiforecasts/EpiNow2 Public

    Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

    R 131 38

  3. epiforecasts/covidregionaldata epiforecasts/covidregionaldata Public

    An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisa…

    R 37 16

  4. epiforecasts/forecast.vocs epiforecasts/forecast.vocs Public

    Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluatio…

    R 8 3

  5. epinowcast/epinowcast epinowcast/epinowcast Public

    Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

    R 62 22

  6. epiforecasts/scoringutils epiforecasts/scoringutils Public

    Utilities for Scoring and Assessing Predictions

    R 56 25