| bactdate {BactDating} | R Documentation |
Main function
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)
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 |
Dating results