Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates
By IMPACTT investigators
Abstract
sample size or power calculations for such study designs, appropriate within and between group distance distributions can be challenging to obtain. When available, pilot study data, or data from prior studies of similar design should provide realistic distance estimates. However, when these are not available, distances can be extracted from available studies where one can assume similar beta-diversity. Alternatively, distances can be generated by simulation methods. Here, we describe and illustrate these three strategies for obtaining realistic distance matrices. For simulation methods, we illustrate the procedures required starting from existing benchmark data, as well as how to simulate directly from population assumptions. Using data from the American Gut project, we provide tables of observed distances for use by researchers planning their own studies, as well as R codes for generating similar matrices in other datasets. Furthermore, for simulated data, we compare methods, provide R codes, and demonstrate how challenging it is to obtain realistic distance distributions without any benchmark data. This code and illustrative distance tables are provided by the IMPACTT Consortium as a resource to the microbiome research community.