Carter1: Number of trees with _m_ steps

In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data

Number of trees with m steps

Description

Calculate the number of trees in which Fitch parsimony will reconstruct m steps, where a leaves are labelled with one state, and b leaves are labelled with a second state.

Usage

Carter1(m, a, b)

Log2Carter1(m, a, b)

LogCarter1(m, a, b)

Arguments

m	Number of steps.
a, b	Number of leaves labelled 0 and 1.

Details

Implementation of theorem 1 from \insertCiteCarter1990;textualTreeTools

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See also:

\insertRef

Steel1993TreeSearch

\insertRef

Steel1995TreeSearch

(\insertRefSteel1996TreeSearch)

See Also

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

Examples

# The character `0 0 0 1 1 1`
Carter1(1, 3, 3) # Exactly one step
Carter1(2, 3, 3) # Two steps (one extra step)

# Number of trees that the character can map onto with exactly _m_ steps
# if non-parsimonious reconstructions are permitted:
cumsum(sapply(1:3, Carter1, 3, 3))

# Three steps allow the character to map onto any of the 105 six-leaf trees.

ms609/TreeSearch documentation built on April 7, 2024, 7:06 p.m.