phylosamp: The Probability of Transmission Given Phylogenetic Linkage

Implements novel tools that estimate the probability of true transmission between two cases given phylogenetic linkage and the expected number of true transmission links in a sample. Methods described in Wohl, Giles, and Lessler (2021) <doi:10.1371/journal.pcbi.1009182>.

Version: 0.1.6
Depends: R (≥ 2.10), stats
Imports: reshape2, ggplot2, cowplot, RColorBrewer
Suggests: knitr, rmarkdown, testthat
Published: 2021-11-22
Author: John R Giles [aut, ctb], Shirlee Wohl [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
CRAN checks: phylosamp results

Documentation:

Reference manual: phylosamp.pdf
Vignettes: Estimating the false discovery rate from sample size
Estimating sample size from the false discovery rate
Estimating the sensitivity and specificity of a linkage criteria
Illustrative examples

Downloads:

Package source: phylosamp_0.1.6.tar.gz
Windows binaries: r-devel: phylosamp_0.1.6.zip, r-release: phylosamp_0.1.6.zip, r-oldrel: phylosamp_0.1.6.zip
macOS binaries: r-release (arm64): phylosamp_0.1.6.tgz, r-release (x86_64): phylosamp_0.1.6.tgz, r-oldrel: phylosamp_0.1.6.tgz

Linking:

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