internalLengths: Growth rate estimate using the sum of internal lengths

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Growth rate estimate using the sum of internal lengths

Description

internalLengths() provides an estimate for the net growth rate of the clone with confidence bounds, using the internal lengths method.

Usage

internalLengths(tree, alpha = 0.05)

Arguments

tree	An ultrametric tree subset to include only the clone of interest. Alternatively, a list with several such trees.
alpha	Used for calculation of confidence intervals. 1-alpha confidence intervals used with default of alpha = 0.05 (95 percent confidence intervals)

Value

A dataframe including the net growth rate estimate, the sum of internal lengths and other important details (clone age estimate, runtime, n, etc.)

See Also

maxLikelihood(), sharedMuts() for other growth rate methods.

Examples

internalLengths(cloneRate::exampleUltraTrees[[1]])

cloneRate documentation built on Sept. 22, 2023, 5:09 p.m.