phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

Implements novel tools for estimating sample sizes needed for phylogenetic studies, including studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).

Package overview README.md Estimating bias in observed variant prevalence Estimating sample size for transmission linkage from the false discovery rate Estimating the linkage false discovery rate from sample size Estimating the probability of detecting a variant Estimating the probability of detecting a variant Estimating the sample size needed for variant monitoring Estimating the sample size needed for variant monitoring Estimating the sensitivity and specificity of a linkage criteria Illustrative examples for evaluating transmission linkage Variant surveillance example

Vignettes Man pages API and functions Files

Package details
Author	Shirlee Wohl [aut, ctb], Elizabeth C Lee [aut, ctb], Lucy D'Agostino McGowan [aut, ctb] (<https://orcid.org/0000-0002-6983-2759>), John R Giles [aut, ctb], Justin Lessler [aut, cre]
Maintainer	Justin Lessler <jlessler@unc.edu>
License	GPL-2
Version	1.0.1
URL	https://github.com/HopkinsIDD/phylosamp
Package repository	View on CRAN
Installation	Install the latest version of this package by entering the following in R: `install.packages("phylosamp")`