inferTTree {TransPhylo}

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,
  startCTree = NA,
  updateTTree = TRUE,
  optiStart = 2,
  dateT = Inf,
  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

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)

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)