Function reference • cloneRate

All functions

birthDeathMCMC(): Growth rate estimate using MCMC

cloneRate-package 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)