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).
- Version1.0.1
- R version≥ 2.10 stats
- LicenseGPL-2
- Needs compilation?No
- phylosamp citation info
- Last release05/23/2023
Documentation
- VignetteEstimating the linkage false discovery rate from sample size
- VignetteEstimating sample size for transmission linkage from the false discovery rate
- VignetteEstimating the sensitivity and specificity of a linkage criteria
- VignetteIllustrative examples for evaluating transmission linkage
- VignetteEstimating bias in observed variant prevalence
- VignetteEstimating the sample size needed for variant monitoring (cross-sectional sampling)
- VignetteEstimating the probability of detecting a variant (cross-sectional sampling)
- VignetteEstimating the sample size needed for variant monitoring (periodic sampling)
- VignetteEstimating the probability of detecting a variant (periodic sampling)
- VignetteVariant surveillance example
- MaterialREADME
- MaterialNEWS
Team
Justin Lessler
Shirlee Wohl
Show author detailsRolesAuthor, ContributorElizabeth C Lee
Show author detailsRolesAuthor, ContributorLucy D'Agostino McGowan
John R Giles
Show author detailsRolesAuthor, Contributor
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- Depends1 package
- Imports3 packages
- Suggests8 packages