# Estimate Growth Rates from Phylogenetic Trees

## Documentation for package ‘cloneRate’ version 0.2.3

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

## Help Pages

cloneRate-package | The 'cloneRate' package.
birthDeathMCMC | Growth rate estimate using MCMC
cloneRate | The 'cloneRate' package.
coal_to_tree | Generate tree from coalescence times
exampleMutTrees | Example mutation tree data
exampleUltraTrees | Example ultrametric tree data
internalLengths | Growth rate estimate using the sum of internal lengths
longitudinalData | Longitudinal validation data
maxLikelihood | Growth rate estimate using Maximum Likelihood
realCloneData | Real clone data from human blood
sharedMuts | Growth rate estimate using the sum of shared mutations assuming a mutation tree
simMut | Simulate mutation-based birth and death branching trees
simUltra | Simulate ultrametric birth and death branching trees
siteFrequency | Get site frequency spectrum of a tree
ultra2mut | Add poissonian mutations to an ultrametric tree(s)