CRAN/E | phylosamp

phylosamp

Sample Size Calculations for Molecular and Phylogenetic Studies

Installation

About

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).

Citation phylosamp citation info
github.com/HopkinsIDD/phylosamp
Bug report File report

Key Metrics

Version 1.0.1
R ≥ 2.10
Published 2023-05-23 502 days ago
Needs compilation? no
License GPL-2
CRAN checks phylosamp results

Downloads

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Last 30 days 216 -34%
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Maintainer

Maintainer

Justin Lessler

[email protected]

Authors

Shirlee Wohl

aut / ctb

Elizabeth C Lee

aut / ctb

Lucy D'Agostino McGowan

aut / ctb

John R Giles

aut / ctb

Justin Lessler

aut / cre

Material

README
NEWS
Reference manual
Package source

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

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

phylosamp archive

Depends

R ≥ 2.10
stats

Imports

cli
lifecycle
rlang

Suggests

cowplot
ggplot2
knitr
purrr
RColorBrewer
reshape2
rmarkdown
testthat ≥ 3.0.0