inferTTree: Infer transmission tree given a phylogenetic tree

In yuanwxu/TransPhyloC: Inference of Transmission Tree under a Within-Host Evolution Model

Description

Infer transmission tree given a phylogenetic tree

Usage

inferTTree(ptree, w.shape = 2, w.scale = 1, ws.shape = w.shape,
  ws.scale = w.scale, mcmcIterations = 1000, thinning = 1,
  startNeg = 100/365, startOff.r = 1, startOff.p = 0.5, startPi = 0.5,
  updateNeg = T, updateOff.r = T, updateOff.p = F, updatePi = T,
  startCTree = NA, updateTTree = TRUE, optiStart = T, dateT = Inf)

Arguments

ptree	Phylogenetic tree
w.shape	Shape parameter of the Gamma probability density function representing the generation time
w.scale	Scale parameter of the Gamma probability density function representing the generation time
ws.shape	Shape parameter of the Gamma probability density function representing the sampling time
ws.scale	Scale parameter of the Gamma probability density function representing the sampling time
mcmcIterations	Number of MCMC iterations to run the algorithm for
thinning	MCMC thinning interval between two sampled iterations
startNeg	Starting value of within-host coalescent parameter Ne*g
startOff.r	Starting value of parameter off.r
startOff.p	Starting value of parameter off.p
startPi	Starting value of sampling proportion pi
updateNeg	Whether of not to update the parameter Ne*g
updateOff.r	Whether or not to update the parameter off.r
updateOff.p	Whether or not to update the parameter off.p
updatePi	Whether or not to update the parameter pi
startCTree	Optional combined tree to start from
updateTTree	Whether or not to update the transmission tree
optiStart	Whether or not to optimise the MCMC start point
dateT	Date when process stops (this can be Inf for fully simulated outbreaks)

Value

posterior sample set of transmission trees

yuanwxu/TransPhyloC documentation built on May 4, 2019, 6:35 p.m.