ICSteps: Information Content Steps

In ms609/ProfileParsimony: Phylogenetic Inference by Profile Parsimony

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 ambigious 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.

Author(s)

Martin R. Smith

References

Faith, D. P. & Trueman, J. W. H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology 50:3, 331-350, doi: 10.1080/10635150118627

Examples

{
  # A character that is present in ten taxa and absent in five
  character <- c(rep(1, 10), rep(2, 5))
  ICSteps (character)
}

ms609/ProfileParsimony documentation built on May 23, 2019, 7:49 a.m.