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).

Version:	1.0.1
Depends:	R (≥ 2.10), stats
Imports:	cli, lifecycle, rlang
Suggests:	cowplot, ggplot2, knitr, purrr, RColorBrewer, reshape2, rmarkdown, testthat (≥ 3.0.0)
Published:	2023-05-23
DOI:	10.32614/CRAN.package.phylosamp
Author:	Shirlee Wohl [aut, ctb], Elizabeth C Lee [aut, ctb], Lucy D'Agostino McGowan [aut, ctb], John R Giles [aut, ctb], Justin Lessler [aut, cre]
Maintainer:	Justin Lessler <jlessler at unc.edu>
BugReports:	https://github.com/HopkinsIDD/phylosamp/issues
License:	GPL-2
URL:	https://github.com/HopkinsIDD/phylosamp
NeedsCompilation:	no
Citation:	phylosamp citation info
Materials:	README NEWS
CRAN checks:	phylosamp results

Documentation:

Reference manual:

phylosamp.pdf

Vignettes:

Estimating the linkage false discovery rate from sample size Estimating sample size for transmission linkage from the false discovery rate Estimating the sensitivity and specificity of a linkage criteria Illustrative examples for evaluating transmission linkage Estimating bias in observed variant prevalence Estimating the sample size needed for variant monitoring (cross-sectional sampling) Estimating the probability of detecting a variant (cross-sectional sampling) Estimating the sample size needed for variant monitoring (periodic sampling) Estimating the probability of detecting a variant (periodic sampling) Variant surveillance example

Downloads:

Package source:	phylosamp_1.0.1.tar.gz
Windows binaries:	r-devel: phylosamp_1.0.1.zip, r-release: phylosamp_1.0.1.zip, r-oldrel: phylosamp_1.0.1.zip
macOS binaries:	r-release (arm64): phylosamp_1.0.1.tgz, r-oldrel (arm64): phylosamp_1.0.1.tgz, r-release (x86_64): phylosamp_1.0.1.tgz, r-oldrel (x86_64): phylosamp_1.0.1.tgz
Old sources:	phylosamp archive

Linking:

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