Software
A central component of my research is the development and support of open-source scientific software tools. My software work focuses on the EpiModel research platform, an integrated toolkit for infectious disease modeling in R. My team also builds web-based apps (written in Shiny) for interactive exploration of research results.
R Packages
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.
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.
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.
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.
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.
EpiABC
Approximate Bayesian Computation for EpiModel
Implementation of Approximate Bayesian Computation with Sequential Monte Carlo Methods (ABC-SMC) optimized for use with EpiModel R package epidemic simulations running on High-Performance Computing (HPC) cluster environments.
Web Apps
COVID-19 on University Campuses
Interactive transmission model of SARS-CoV-2 on university campuses, accompanying Lopman et al., Scientific Reports (2021).
STI Screening Rates
Estimates symptomatic testing and asymptomatic screening rates for bacterial STIs given demographics, risk, and geography; accompanies the Sexually Transmitted Diseases (2019) paper.
HIV Racial Disparities
Interactive exploration of sexual-mixing and activity parameters as sources of racial disparities in HIV among MSM; accompanies Goodreau et al., Lancet HIV (2017).
CDC HIV PrEP Guidelines
Lets users input local estimates of HIV PrEP coverage and adherence and returns predicted HIV incidence; accompanies Jenness et al., Journal of Infectious Diseases (2016).