Information content of a character known to contain e steps

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

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… 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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

character <- rep(c(0:3, "?", "-"), c(8, 5, 1, 1, 2, 2))
StepInformation(character)
#>         3         4         5         6         7 
#> 9.9203529 5.5280354 2.5784492 0.7618403 0.0000000