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@geoepi

Geographical Epidemiology

The GeoEpi Group investigates animal disease transmission and outbreak dynamics.

Welcome to the GeoEpi Group's GitHub

The GeoEpi Notebook is a resource designed for and by group members and collaborators engaged in geographical epidemiology and data science. Its purpose is to share and refine the best practices, standards, and guidelines essential for ensuring reproducible science across the domains of scientific computing, coding, data management, and modeling. Importantly, this notebook is envisioned as a living document—continually updated to reflect the latest insights, solutions, and efficiencies. It is not a compendium of rigid requirements but a collection of recommended approaches designed to enhance the quality and integrity of our work.

The GeoEpi Group investigates animal disease transmission and outbreak dynamics. Leveraging statistical and mathematical modeling, bioinformatics, and artificial intelligence, our work aims to bridge the molecular and landscape scales to reveal insights into the ecology and spatiotemporal dynamics of foreign, transboundary, emerging, and zoonotic animal diseases.

The GeoEpi Open Science Framwork site provides a comprehensive suite of tools and features to support and enhance group projects. OSF provides project Management tools, data storage and sharing, document version control, and permanent Digital Object Identifiers for archiving data.

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  1. seir-vector Public

    R 2

  2. vs-epizootics Public

    Spatiotemporal analysis of U.S. Vesicular stomatitis outbreak (2014-2016)

    R

Repositories

Showing 10 of 13 repositories
  • pak-coinfection Public

    FMDV co-infection and recombination in Asian water buffalo

    R 0 0 0 0 Updated Jan 21, 2025
  • Python 0 0 0 0 Updated Jan 17, 2025
  • sandbox Public

    Meeting notes, vignettes, tutorials, and demos for general group use.

    R 0 0 0 0 Updated Jan 17, 2025
  • challengeABM Public

    Agent Based Model (ABM) simulating transmission and within-host virus dynamics during a challenge experiment.

    R 1 0 0 0 Updated Nov 18, 2024
  • phylo-tutorial Public

    Code and exercises for phylogenetics in R.

    HTML 0 0 0 0 Updated Sep 13, 2024
  • geoepi.github.io Public

    GeoEpi Landing Page

    JavaScript 0 MIT 0 0 0 Updated Aug 19, 2024
  • seir-vector Public
    R 2 GPL-3.0 0 0 0 Updated Aug 18, 2024
  • vs-epizootics Public

    Spatiotemporal analysis of U.S. Vesicular stomatitis outbreak (2014-2016)

    R 0 MIT 0 0 0 Updated Aug 9, 2024
  • fmdv-preclinical Public

    Analysis of FMDV preclinical transmission study in bovine

    R 1 0 0 0 Updated Jul 25, 2024
  • .github Public
    JavaScript 0 0 0 0 Updated Jul 7, 2024