| StepInformation {TreeSearch} | R Documentation |
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 (martin.smith@durham.ac.uk)
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)