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arnold-c/README.md

Hi! I'm Callum, a 4th year PhD candidate in the Biology department at Penn State, studying infectious disease epidemiology. I spend a lot of my day thinking about respiratory viruses (currently SARS-CoV-2 and measles), using traditional epidemiological methods and mathematical transmission models to better understand the burden of disease. More specifically, I am exploring how the choices we make when discretizing continuous and complex phenomena, such as assigning individuals into different transmission risk groups or turning an serological IgG optical density value into a binary positive/negative result, affects our ability to prevent, detect, and even understand outbreaks.

I mainly work in R and Julia, but sometimes dabble with Python for personal projects, and am currently learning Javascript (and D3) for web development and interactive plots and books, and Rust for CLI tools.

  • 🔭 I’m currently working on:
    • The Data4Action cohort study to better understand SARS-CoV-2 transmission dynamics in University communities
    • Measles burden estimation, and a vaccination campaign effectiveness evaluation, in the Democratic Republic of Congo, in collaboration with the Epicentre team from Médecins Sans Frontières
    • Developing methods for better detection measles outbreak in settings with limited resources and test capabilities
    • Creating a handbook about Julia for epidemiologists, inspired by the excellent EpiRHandbook
  • 🌱 I’m currently learning:
    • Javascript
    • Rust
  • 👯 I’m always looking to collaborate on any interesting epidemiology projects
  • 📫 How to reach me:
    • At my twitter (although I'm not particularly active, I will respond to DMs)
    • Via email (contact at callumarnold dot com)

Top Langs

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  1. JuliaEpiHandbook JuliaEpiHandbook Public

    Trying to recreate a version of the EpiRHandbook for new Julia users

    HTML 6 1

  2. SISMID-Module-02_2023 SISMID-Module-02_2023 Public

    Contains materials for Module 2 of the 2023 SISMID workshop

    HTML 3 2

  3. psu-intro-to-git psu-intro-to-git Public

    Book for the introduction to git and GitHub short course at Penn State University

    SCSS 3

  4. website website Public

    HTML

  5. garmin-backups garmin-backups Public

    Scripts to download Garmin activities, and download and clean Concept2 Logbook (ErgData) and Painsled rowing files for GoldenCheetah import

    Python