makeCtreeFromPTree: Create a transmission tree compatible with the provided...
In xavierdidelot/TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

makeCTreeFromPTree

R Documentation

Create a transmission tree compatible with the provided phylogenetic tree

Description

Create a transmission tree compatible with the provided phylogenetic tree

Usage

makeCTreeFromPTree(
  ptree,
  off.r = NA,
  off.p = NA,
  neg = NA,
  pi = NA,
  w.shape = NA,
  w.scale = NA,
  ws.shape = NA,
  ws.scale = NA,
  T = NA,
  optiStart = 0
)

Arguments

`ptree`	Phylogenetic tree
`off.r`	First parameter of the negative binomial distribution for offspring number
`off.p`	Second parameter of the negative binomial distribution for offspring number
`neg`	the within-host effective population size (Ne) timesgeneration duration (g)
`pi`	probability of sampling an infected individual
`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
`T`	Date when process stops (this can be Inf for fully simulated outbreaks)
`optiStart`	Method used to optimised colored tree (0=none, 1=slow, 2=fast)