Estimate Growth Rates from Phylogenetic Trees

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Documentation for package ‘cloneRate’ version 0.2.3.9000

• 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
truncate_tree	Truncate a tree at a distance dist from the root. Useful for identifying subclones and especially for embryonic development rate estimation. Imagine taking a tree, drawing a line across it at a time dist, and only evaluating the tree from above that line.
ultra2mut	Add poissonian mutations to an ultrametric tree(s)