On May 16 and 17th, 2016, Guelph hosted the annual conference of the Canadian Association of Veterinary and Preventative Medicine. The theme of the conference was “Thinking Outside the Epidemiological Tool Box”, and saw presentations on disease surveillance, risk profiles, modelling, and other topics. I contributed a poster to the conference on phylodynamic modelling, which […]
I’ve been working on a Julia package for working with phylogenetic trees for the last month or so. This package is called PhyloTrees.jl. I’ve made a small introduction to its use in an IJulia notebook, check it out here, and let me know what you think of the interface! PhyloTrees.jl will primarily be used for the simulation […]
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 […]
In a previous post I gave a simple exercise to illustrate the sampling distribution. I figured it would be of interest to some to show how this exercise could be completed in R, or the language which I now use more frequently, Julia.
A good friend of mine has been learning how to use R for his research in community ecology for the last year. He reminded me today of an exercise I wrote up for him awhile back to introduce the use of for loops. The exercise is a demonstration of the sampling distribution and goes as such:
For the last year or so I have been researching and developing an agent based model for fisheries management applications.
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.