Before incorporating the use of genomic data in the inference methods of Pathogen.jl, we needed to see how well the standard individual level model (ILM) of disease transmission performed at the task of transmission pathway inference.
Pathogen.jl is a package that provides utilities for the simulation and inference of pathogen phylodynamics, built in the Julia language. Specifically, Pathogen.jl presents an extension to the individual level infectious diesase transmission models (ILMs) of Deardon et al. (2010), to simultaneously model infectious disease transmission and evolution. Pathogen genomic sequences are used in conjunction with […]
If it weren’t for visualization, statistics would be pretty boring. One of the ways I like to celebrate project milestones is by producing plots. This gives my left brain a break from the programming and mathematics involved in my work and hands the reins over to the right side to consider visualization aesthetics.