profiles: Empirically counted profiles for small trees

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Empirically counted profiles for small trees

Description

The base 2 logarithm of the number of trees containing s steps, calculated by scoring a character on each n-leaf tree.

Usage

profiles

Format

A list with the structure ⁠profiles[[number of leaves]][[number of tokens]][[tokens in smallest split]]⁠ The list entry returns a named numeric vector; each entry lists log2(proportion of n-leaf trees with s or fewer steps for this character).

See Also

Other profile parsimony functions: Carter1(), PrepareDataProfile(), StepInformation(), WithOneExtraStep()

Examples

data(profiles)

# Load profile for a character of the structure 0 0 0 1 1 1 1 1
profile3.5 <- profiles[[8]][[2]][[3]]

# Number of trees with _s_ or fewer steps on that character
TreeTools::NUnrooted(8) * 2 ^ profile3.5

TreeSearch documentation built on Aug. 26, 2023, 9:06 a.m.