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TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) <doi:10.1093/molbev/msw275>.

Version:	1.4.5
Depends:	R (≥ 3.0.0)
Imports:	Rcpp (≥ 0.12.8), stats, graphics, ape
LinkingTo:	Rcpp
Suggests:	knitr, testthat, purrr, coda, grDevices, lattice, rmarkdown
Published:	2021-04-20
DOI:	10.32614/CRAN.package.TransPhylo
Author:	Xavier Didelot [aut, cre], Yuanwei Xu [ctb]
Maintainer:	Xavier Didelot <xavier.didelot at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	yes
SystemRequirements:	C++11
Citation:	TransPhylo citation info
Materials:	README
In views:	Epidemiology
CRAN checks:	TransPhylo results

Documentation:

Reference manual:	TransPhylo.pdf
Vignettes:	Introducing the R package TransPhylo Inference of transmission tree from a dated phylogeny Simultaneous Inference of Multiple Transmission Trees Simulation of outbreak data

Downloads:

Package source:	TransPhylo_1.4.5.tar.gz
Windows binaries:	r-devel: TransPhylo_1.4.5.zip, r-release: TransPhylo_1.4.5.zip, r-oldrel: TransPhylo_1.4.5.zip
macOS binaries:	r-release (arm64): TransPhylo_1.4.5.tgz, r-oldrel (arm64): TransPhylo_1.4.5.tgz, r-release (x86_64): TransPhylo_1.4.5.tgz, r-oldrel (x86_64): TransPhylo_1.4.5.tgz
Old sources:	TransPhylo archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.