Sample size calculation for phylogenetic case linkage.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
02
12
2020
accepted:
14
06
2021
revised:
16
07
2021
pubmed:
7
7
2021
medline:
26
10
2021
entrez:
6
7
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34228722
doi: 10.1371/journal.pcbi.1009182
pii: PCOMPBIOL-D-20-02147
pmc: PMC8284614
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1009182Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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