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 ORCID iD [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.html , TransPhylo.pdf
Vignettes: Introducing the R package TransPhylo (source, R code)
Inference of transmission tree from a dated phylogeny (source, R code)
Simultaneous Inference of Multiple Transmission Trees (source, R code)
Simulation of outbreak data (source, R code)

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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