get.phybreak: Accessing a phybreak object

In phybreak: Analysis of Outbreaks with Sequence Data

Description

Accessing a phybreak object

Usage

get.tree(phybreak.object, samplenr = 0)

get.parameters(phybreak.object, samplenr = 0, whichpars = "posterior")

get.mcmc(phybreak.object, thin = 1, nkeep = Inf)

get.phylo(phybreak.object, samplenr = 0, simmap = FALSE)

get.multiPhylo(phybreak.object, thin = 1, nkeep = Inf)

get.seqdata(phybreak.object)

Arguments

phybreak.object	An object of class phybreak.
samplenr	The posterior tree sample to choose. If samplenr = 0, the current state is used.
whichpars	Which parameters to return. Either a vector with parameter names, or "all" for all parameters, or "posterior" for parameters for which a posterior is sampled.
thin	Thinning interval.
nkeep	Number of samples to keep, counting from tail of the chain.
simmap	Whether to include class "simmap" elements (package phytools), colouring the branches on the tree to indicate hosts. Is used by plotPhylo.

Functions

• get.tree: A data.frame with current (samplenr = 0) or sampled infectors and infection times.

• get.parameters: A named vector with current (samplenr = 0) or sampled parameter values.

• get.mcmc: An object of class "mcmc" (package coda), with sampled parameters, infection times, and infectors.

• get.phylo: Returns an object of class phylo ans optionally of class "simmap" (package phytools).

• get.multiPhylo: Returns an object of class multiphylo.

• get.seqdata: The sequence data in class "phyDat" (package phangorn).

Author(s)

Don Klinkenberg [e-mail]

References

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

Examples

#First build a phybreak-object.
simulation <- sim.phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation)
MCMCstate <- burnin.phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample.phybreak(MCMCstate, nsample = 50, thin = 2)

get.tree(MCMCstate)
get.parameters(MCMCstate)
codaobject <- get.mcmc(MCMCstate, thin = 2)
plot.phylo(get.phylo(MCMCstate))
get.seqdata(MCMCstate)

#function from package phangorn:
phangorn::parsimony(get.phylo(MCMCstate), get.seqdata(MCMCstate))

tree0 <- get.phylo(MCMCstate)
seqdata <- get.seqdata(MCMCstate)
phangorn::pml(tree0, seqdata, 
              rate = 0.75*get.parameters(MCMCstate)["mu"]) 
logLik(MCMCstate, genetic = TRUE, withinhost = FALSE, 
       sampling = FALSE, generation = FALSE) 
              #should give the same result as 'pml'

phybreak documentation built on May 2, 2019, 3:36 p.m.