Open AccessSample size calculation for phylogenetic case linkage
Author(s) -
Shirlee Wohl,
J Giles,
Justin Lessler
Publication year - 2021
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.1009182
Subject(s) - sample size determination , phylogenetic tree , linkage (software) , counterintuitive , sample (material) , computer science , statistics , component (thermodynamics) , population , transmission (telecommunications) , econometrics , data mining , biology , mathematics , genetics , physics , gene , thermodynamics , telecommunications , philosophy , chemistry , demography , epistemology , chromatography , sociology
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.