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 will also include here Continue reading
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 of genetic sequence data from defined phylogenetic trees. Additional features including inference of phylogenetic trees, and further input/output options are planned for the near future. Check it out if you are a Julia user interested in bioinformatics!
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 the covariate and disease state information of individuals to infer disease transmission pathways, external disease pressure, and infectivity parameters.
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. Continue reading
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: Continue reading
For the last year or so I have been researching and developing an agent based model for fisheries management applications. Continue reading
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. Continue reading