Publications (15)
Evaluating undercounts in epidemics: response to Maruotti et al. 2022
Michael Li, Jonathan Dushoff, David J. D. Earn +1
Maruotti et al. 2022 used a mark-recapture approach to estimate bounds on the true number of monkeypox infections in various countries. These approaches are fundamentally flawed; i…
Synonymous codon usage and selection on proteins
Joshua B. Plotkin, Jonathan Dushoff, Michael M. Desai +1
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `vol…
pcoxtime: Penalized Cox Proportional Hazard Model for Time-dependent Covariates
Steve Cygu, Jonathan Dushoff, Benjamin M. Bolker
The penalized Cox proportional hazard model is a popular analytical approach for survival data with a large number of covariates. Such problems are especially challenging when cova…
Toward a comprehensive system for constructing compartmental epidemic models
Darren Flynn-Primrose, Steven C. Walker, Michael Li +3
Compartmental models are valuable tools for investigating infectious diseases. Researchers building such models typically begin with a simple structure where compartments correspon…
I can see clearly now: reinterpreting statistical significance
Jonathan Dushoff, Morgan P. Kain, Benjamin M. Bolker
Null hypothesis significance testing remains popular despite decades of concern about misuse and misinterpretation. We believe that much of the problem is due to language: signific…
Robust estimation of microbial diversity in theory and in practice
Bart Haegeman, Jérôme Hamelin, John Moriarty +3
Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renew…