o2mod.transphylo is a module of outbreaker2 which uses the TransPhylo model of within-host evolution.
To install the latest version from github:
devtools::install_github("xavierdidelot/o2mod.transphylo")
Then load the package using:
library("o2mod.transphylo")
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.