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Software

Open-source software from the EpiModel Research Lab, including the EpiModel R package for infectious disease modeling and its extensions.

A central component of my research is the development and support of open-source scientific software. The work centers on EpiModel, a research platform for infectious disease modeling in R, with extension packages for particular disease areas and supporting packages for performance, scale, and calibration.

The platform

EpiModel

Flagship R platform for infectious disease modeling

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models using temporal exponential random graph models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of packages. Standard templates cover SI, SIR, and SIS disease types, with an easy API for extending to novel research aims.

WebsiteCRANGitHubMethods Paper (JSS 2018)

Extensions

Disease-area packages

Built on EpiModel, each carrying the parameters and mechanics of a particular pathogen system.

  • EpiModelHIV

    HIV and bacterial STI transmission

    Extension package to EpiModel for simulating network models for HIV and bacterial STI (gonorrhea, chlamydia, syphilis) transmission dynamics in key target populations, with a focus on assessing emerging biomedical HIV/STI prevention and treatment technologies.

    GitHub

  • EpiModelCOVID

    SARS-CoV-2 and respiratory pathogen transmission

    Extension package to EpiModel for simulating network models for SARS-CoV-2 and related respiratory infection transmission dynamics, with a focus on assessing both vaccines and non-pharmaceutical prevention and treatment strategies.

    GitHub

Infrastructure

Performance, scale, and calibration

Supporting packages that make the platform faster to run, larger to scale, and easier to fit to data.

  • networkLite

    Fast sparse-matrix dynamic networks

    Methods for simulating dynamic contact networks with ERGMs using a sparse matrix representation, resulting in a substantial improvement in the efficiency and speed of epidemic models.

    GitHub

  • EpiModelHPC

    Large-scale models on HPC clusters

    Supports simulating large-scale stochastic network models on modern high-performance computing systems. Functionality provided to simulate models in parallel using single-node, multiple-core, or multiple-node setups.

    GitHub

  • ARTnet

    Model parameterization from ARTnet network data

    Methods for parameterizing epidemic and network models of HIV/STI transmission among men who have sex with men with data from the ARTnet study, a national web-based survey of sexual networks and HIV-related behaviors in the United States.

    GitHub

  • EpiModel.Gallery

    Worked examples for extending EpiModel

    A curated collection of annotated tutorials for extending EpiModel with custom modules to model infectious disease dynamics over networks.

    WebsiteGitHub