R: Main function

bactdate {BactDating} | R Documentation

## Main function

### Description

Main function

### 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 = "mixedgamma", 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 relaxedgamma and mixedgamma 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 relaxedgamma and mixedgamma 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)
`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

[Package BactDating version 1.0 Index]