sharedMuts: Growth rate estimate using the sum of shared mutations...

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Growth rate estimate using the sum of shared mutations assuming a mutation tree

Description

sharedMuts() provides an estimate for the net growth rate of the clone with confidence bounds, using the shared mutations method.

Usage

sharedMuts(tree, nu = NULL, alpha = 0.05)

Arguments

tree	A non-ultrametric ape tree subset to include only the clone of interest
nu	The mutation rate. If none given, sharedMuts() will first look for a nu column in a metadata data.frame of the tree, and then look for a nu in the tree itself. Will throw error if no nu given or found.
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

internalLengths() which is the ultrametric/time-based analogue

Examples

sharedMuts(cloneRate::exampleMutTrees[[1]])

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