inferTTree: Infer transmission tree given a phylogenetic tree

In xavierdidelot/TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Infer transmission tree given a phylogenetic tree

Description

Infer transmission tree given a phylogenetic tree

Usage

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

Arguments

ptree	Phylogenetic tree
w.shape	Shape parameter of the Gamma distribution representing the generation time
w.scale	Scale parameter of the Gamma distribution representing the generation time
ws.shape	Shape parameter of the Gamma distribution representing the sampling time
ws.scale	Scale parameter of the Gamma distribution representing the sampling time
w.mean	Mean of the Gamma distribution representing the generation time
w.std	Std of the Gamma distribution representing the generation time
ws.mean	Mean of the Gamma distribution representing the sampling time
ws.std	Std of the Gamma distribution 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
qNeg	Proposal kernel range for parameter Ne*g
qOff.r	Proposal kernel range for parameter Off.r
qOff.p	Proposal kernel range for parameter Off.p
qPi	Proposal kernel range for parameter pi
startCTree	Optional combined tree to start from
updateTTree	Whether or not to update the transmission tree
optiStart	Type of optimisation to apply to MCMC start point (0=none, 1=slow, 2=fast)
dateT	Date when process stops (this can be Inf for fully simulated outbreaks)
delta_t	Grid precision (smaller is better but slower)
verbose	Whether or not to use verbose mode (default is false)

Value

posterior sample set of transmission trees

Examples

inferTTree(ptreeFromPhylo(ape::rtree(5),2020),mcmcIterations=100)

xavierdidelot/TransPhylo documentation built on Sept. 28, 2023, 7:20 p.m.