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The quality of the inferences we make from pathogen sequence data isdetermined by the number and composition of pathogen sequences that make up thesample used to drive that inference. However, there remains limited guidance onhow to best structure and power studies when the end goal is phylogeneticinference. One question that we can attempt to answer with molecular data iswhether some people are more likely to transmit a pathogen than others. Here wepresent an estimator to quantify differential transmission, as measured by theratio of reproductive numbers between people with different characteristics,using transmission pairs linked by molecular data, along with a sample sizecalculation for this estimator. We also provide extensions to our method tocorrect for imperfect identification of transmission linked pairs,overdispersion in the transmission process, and group imbalance. We validatethis method via simulation and provide tools to implement it in an R package,phylosamp.

Power and sample size calculations for testing the ratio of reproductive values in phylogenetic samples