R: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

# Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

## Documentation for package ‘treedater’ version 1.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

treedater-package | treedater fits a molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.
boot | Estimate of confidence intervals of molecular clock parameters with user-supplied set of bootstrap trees
dater | Estimate a time-scaled tree and fit a molecular clock
gibbs_jitter | Sample node dates conditional on root time using Gibbs sampling and date prior
goodnessOfFitPlot | Produce a goodness of fit plot
outlierLineages | Detect lineages with unusually large evolutionary divergence under the fitted treedater model
outlierTips | Detect terminal lineages with unusually large evolutionary divergence under the fitted treedater model
parboot | Estimate of confidence intervals using parametric bootstrap for molecular clock dating.
plot.bootTreedater | Plots lineages through time and confidence intervals estimated by bootstrap.
relaxedClockTest | Use parametric bootstrap to test if relaxed clock offers improved fit to data.
rootToTipRegressionPlot | Plot evolutionary distance from root to sample times and estimated internal node times and regression lines
sampleYearsFromLabels | Compute a vector of numeric sample times from labels in a sequence alignment or phylogeny
treedater | treedater fits a molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.