ArticlePLoS computational biology2021
Sample size calculation for phylogenetic case linkage.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups.Proceedings. Biological sciences · 2026Article
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- Power and sample size calculations for testing the ratio of reproductive values in phylogenetic samples.American journal of epidemiology · 2025Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Towards a post-pandemic future for global pathogen genome sequencing.PLoS biology · 2023Article
- Sample size calculations for pathogen variant surveillance in the presence of biological and systematic biases.Cell reports. Medicine · 2023Article
- Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.Med (New York, N.Y.) · 2022Article
- Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.Nature reviews. Genetics · 2022Review
- Response: Commentary: Statistical Modeling for the Prediction of Infectious Disease Dissemination With Special Reference to COVID-19 Spread.Frontiers in public health · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies.
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Registered trials
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