TreeSearch (version 0.4.0)

ICSteps: Information Content Steps

Description

This function estimates the information content of a character char when e extra steps are present, for all possible values of e.

Usage

ICSteps(char, ambiguousToken = 0, expectedMinima = 25,
  maxIter = 10000, warn = TRUE)

Arguments

char

The character in question.

ambiguousToken

Which token, if any, corresponds to the ambiguous token (?) (not yet fully implemented).

expectedMinima

sample enough trees that the rarest step counts is expected to be seen at least this many times.

maxIter

Maximum iterations to conduct.

warn

Boolean (TRUE/FALSE): display warnings when concavity functions are generated by approximation.

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. The number of trees with no extra steps can be calculated exactly; the number of trees with more additional steps must be approximated. The function samples n.iter trees, or enough trees that the trees with the minimum number of steps will be recovered at least expected.minima times, in order to obtain precise results.

References

Faith2001TreeSearch

Examples

# NOT RUN {
{
  # A character that is present in ten taxa and absent in five
  character <- c(rep(1, 10), rep(2, 5))
  ICSteps (character)
}
# }