In xavierdidelot/o2mod.transphylo: outbreaker2 module using the TransPhylo model

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o2mod.transphylo: an outbreaker2 module using the TransPhylo model

o2mod.transphylo is a module of outbreaker2 which uses the TransPhylo model of within-host evolution.

Installation

To install the latest version from github:

devtools::install_github("xavierdidelot/o2mod.transphylo")

Then load the package using:

library("o2mod.transphylo")

Documentation

Once loaded, the package provides a function o2mod.transphylo() which takes the same parameters as the outbreaker() function of the outbreaker2 package, so for example if data is an outbreaker2 input object, analysis under the TransPhylo model can be carried out using:

result <- o2mod.transphylo(data)

For more details, see the introductory vignette on o2mod.transphylo.

Authors

• Xavier Didelot
• Finlay Campbell
• Thibaut Jombart

xavierdidelot/o2mod.transphylo documentation built on Nov. 21, 2021, 3:29 a.m.