StepInformation: Information content of a character known to contain _e_ steps

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Information content of a character known to contain e steps

Description

StepInformation() calculates the phylogenetic information content of a character char when e extra steps are present, for all possible values of e.

Usage

StepInformation(char, ambiguousTokens = c("-", "?"))

Arguments

char	Vector of tokens listing states for the character in question.
ambiguousTokens	Vector specifying which tokens, if any, correspond to the ambiguous token (⁠?⁠).

Details

Calculates the number of trees consistent with the character having e extra steps, where e ranges from its minimum possible value (i.e. number of different tokens minus one) to its maximum.

Value

StepInformation() returns a numeric vector detailing the amount of phylogenetic information (in bits) associated with the character when 0, 1, 2… extra steps are present. The vector is named with the total number of steps associated with each entry in the vector: for example, a character with three observed tokens must exhibit two steps, so the first entry (zero extra steps) is named 2 (two steps observed).

Author(s)

Martin R. Smith ([e-mail])

See Also

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

Examples

character <- rep(c(0:3, "?", "-"), c(8, 5, 1, 1, 2, 2))
StepInformation(character)

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