bactdate: Main function of BactDating package to date the nodes of a...

In xavierdidelot/BactDating: BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

Main function of BactDating package to date the nodes of a phylogenetic tree

Description

Main function of BactDating package to date the nodes of a phylogenetic tree

Usage

bactdate(
  tree,
  date,
  initMu = NA,
  initAlpha = NA,
  initSigma = NA,
  updateMu = T,
  updateAlpha = T,
  updateSigma = T,
  updateRoot = T,
  nbIts = 10000,
  thin = ceiling(nbIts/1000),
  useCoalPrior = T,
  model = "arc",
  useRec = F,
  minbralen = 0.1,
  showProgress = F
)

Arguments

tree	Tree wih branches measured in unit of substitutions
date	Sampling dates for the leaves of the tree
initMu	Initial rate of substitutions per genome (not per site), or zero to use root-to-tip estimate
initAlpha	Initial coalescent time unit
initSigma	Initial std on per-branch substitution rate (only used in relaxed or mixed-relaxed models)
updateMu	Whether or not to update the substitution rate
updateAlpha	Whether or not to update the coalescent time unit
updateSigma	Whether or not to per-branch substitution rate (only used in relaxed or mixed-relaxed models)
updateRoot	Whether or not to use the root finding algorithm
nbIts	Number of MCMC iterations to perform
thin	Thining interval between recorded MCMC samples
useCoalPrior	Whether or not to use a coalescent prior on the tree
model	Which model to use (poisson or negbin or strictgamma or relaxedgamma or mixedgamma or arc or carc or mixedcarc)
useRec	Whether or not to use results from previous recombination analysis
minbralen	Minimum branch length of the phylogenetic tree (in number of substitutions)
showProgress	Whether or not to show a progress bar

Value

Dating results

xavierdidelot/BactDating documentation built on Nov. 23, 2023, 1:32 a.m.