Links, resources and additional information

Infectious disease modelling work

R packages for recent papers and publications

(See github/dajmcdon or my publications page for others)

  • {fkf}: Fast Kalman Filter. Very fast Kalman filtering and smoothing.
  • {sparsegl} Sparse Group Lasso. Efficient implementation of sparse group lasso with optional bound constraints on the coefficients. It supports the use of a sparse design matrix as well as returning coefficient estimates in a sparse matrix. Furthermore, it correctly calculates the degrees of freedom to allow for information criteria rather than cross-validation with very large data. Finally, the interface to compiled code avoids unnecessary copies and allows for the use of long integers.
  • {dpf}: Discrete particle filtering. This package greedily estimates switching Kalman filters fast. Also useful for analysis of musical tempos.
  • {AIMER}: Amplified, Initially Marginal, Eigenvector Regression. As described in Ding, L. and McDonald, D.J., “Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression”. A better version of supervised principal components analysis.
  • {cplr}: Compressed penalized linear regression. As described in Homrighausen, D. and McDonald, D.J., “Compressed and penalized linear regression.”

Additional resources

Resources for R and basic analysis

(see also my course materials on the Teaching page)

Artwork and other attributions

The artwork throughout this website is generated using R and additional packages. In principle, it will change randomly whenever the site is updated. Some of these use the {aRtsy} package built by Koen Derks. Others use some custom functions that I occasionally work on in my spare time. These have benefited from reading Danielle Navarro’s excellent blog and other material, as well as some posts by Tyler Hobbs.

This website was built with Quarto along with some custom CSS inspired by the Hugo Apéro theme. Building the site in Quarto removes some flexibility that I used to have with my old Jekyll site, but it also allows for much easier integration of R code.

If any of this seems useful, see the underlying GitHub repo for the code. There are script files that control the artwork as well as autogenerating the list of publications (a massive headache in other static site generators).


I still play cello occasionally, both privately and with the Vancouver Philharmonic. And I enjoy listening to classical music whenever I get the chance. I’ve only once successfully connected research and music, but this leaves music to be a nice hobby, a total diversion from academic work.

I should also point to my partner’s website: Tamara Mitchell. She does great work in Hispanic literature, and we’re lucky to be at the same institution. We also have a wonderful cat that we spoil rotten.