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.

中文翻译：

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系统发育案例关联的样本量计算

样本量计算是科学研究设计和评估的重要组成部分。但是，缺乏确定系统发育研究所需样本量的明确指导，这已成为研究病原体传播的重要组成部分。我们介绍了一个统计框架，用于根据系统发育研究确定的真实感染者-感染者传播对的数量，并给出该研究的规模和人口覆盖率。然后，我们展示了用于确定链接和研究设计各方面的标准的特征如何以有时违反直觉的方式影响我们正确识别传输链接的能力。我们使用爆发模拟测试整体方法，并为计算关联标准的敏感性和特异性提供指导，我们方法的关键输入。该框架可作为R包phylosamp免费获得，并且广泛适用于设计和评估各种病原体系统发育研究。