Growth rate estimate using the sum of internal lengths

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]])
#>   lowerBound estimate upperBound cloneAgeEstimate sumInternalLengths
#> 1  0.8729623 1.085769   1.298576         20.83863           92.10061
#>   sumExternalLengths extIntRatio   n alpha runtime_s  method
#> 1           1547.141    16.79838 100  0.05     0.004 lengths