burnin.phybreak: MCMC updating of a phybreak-object.
In phybreak: Analysis of Outbreaks with Sequence Data

Description Usage Arguments Value Author(s) References Examples

This function allows the MCMC chain to burn in. If used after samples have been taken (with sample.phybreak), these samples will be returned unchanged in the output.

1 2	burnin.phybreak(phybreak.object, ncycles, keepphylo = NULL, phylotopology_only = 0)

`phybreak.object`	An object of class `phybreak`.
`ncycles`	Number of iterations to be carried out. Each iteration does one update of all parameters and tree updates with each host as focal host once.
`keepphylo`	The proportion of tree updates keeping the phylotree intact. If there is more than one sample per host, keepphylo should be 0. If set to NULL (default), this is done automatically, otherwise it is set to 0.2.
`phylotopology_only`	The proportion of tree updates in which only the within-host minitree topology is sampled, and the transmission tree as well as coalescence times are kept unchanged.

The phybreak-object provided as input, with variables and parameters changed due to the updating.

Don Klinkenberg don@xs4all.nl

Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.

#First create a phybreak-object
simulation <- sim.phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation)

MCMCstate <- burnin.phybreak(MCMCstate, ncycles = 50)