TreeSearch (version 1.1.1)

StepInformation: 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 (?).

Value

StepInformation() returns a numeric vector detailing the amount of phylogenetic information (in bits) associated with the character when 0, 1, 2<U+2026> 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).

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.

See Also

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

Examples

# NOT RUN {
character <- rep(c(0:3, '?', '-'), c(8, 5, 1, 1, 2, 2))
StepInformation(character)
# }