CRAN/E | TransPhylo

TransPhylo

Inference of Transmission Tree from a Dated Phylogeny

Installation

About

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.

Citation TransPhylo citation info
System requirements C++11

Key Metrics

Version 1.4.5
R ≥ 3.0.0
Published 2021-04-20 699 days ago
Needs compilation? yes
License GPL-2
License GPL-3
CRAN checks TransPhylo results

Downloads

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Maintainer

Maintainer

Xavier Didelot

xavier.didelot@gmail.com

Authors

Xavier Didelot

aut / cre

Yuanwei Xu

ctb

Material

README
Reference manual
Package source

In Views

Epidemiology

Vignettes

Introducing the R package TransPhylo
Inference of transmission tree from a dated phylogeny
Simultaneous Inference of Multiple Transmission Trees
Simulation of outbreak data

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

TransPhylo archive

Depends

R ≥ 3.0.0

Imports

Rcpp ≥ 0.12.8
stats
graphics
ape

Suggests

knitr
testthat
purrr
coda
grDevices
lattice
rmarkdown

LinkingTo

Rcpp