phylo2ggphy

phylo

a vector containing the sample dates of
 the tip in "Date" format, the dates must be ordered like
 the tips

tip.dates

the unit of the branch. Either "year",
 "month", "day" or "subst". If a time unit is provided,
 together with tip.dates, then the x-axis of the phylogeny
 will be in the Date format

branch.unit

if <code>TRUE</code> additional information is
 provided at execution

verbose

Function to convert phylogenies from the class 'phylo' to
 the class 'ggphy'

Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.

phylo2ggphy: Convert phylogenies from the class 'phylo' to the class 'ggphy'

Description

Usage

Arguments