Introduction to Pathogen.jl

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 […]

Plotting progress

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.