CharacterInformation {TreeTools}

Character information content

Description

CharacterInformation() calculates the cladistic information content (Steel and Penny 2006) of a given character, in bits. The total information in all characters gives a measure of the potential utility of a dataset (Cotton and Wilkinson 2008), which can be compared with a profile parsimony score (Faith and Trueman 2001) to evaluate the degree of homoplasy within a dataset.

Usage

CharacterInformation(tokens)

Arguments

tokens

Character vector specifying the tokens assigned to each taxon for a character. Example: c(0, 0, 0, 1, 1, 1, "?", "-").

Note that ambiguous tokens such as (01) are not supported, and should be replaced with ⁠?⁠.

Value

CharacterInformation() returns a numeric specifying the phylogenetic information content of the character (sensu Steel and Penny 2006), in bits.

Author(s)

Martin R. Smith ([e-mail])

References

Cotton JA, Wilkinson M (2008). “Quantifying the potential utility of phylogenetic characters.” Taxon, 57(1), 131–136.

Faith DP, Trueman JWH (2001). “Towards an inclusive philosophy for phylogenetic inference.” Systematic Biology, 50(3), 331–350. doi:10.1080/10635150118627.

Steel MA, Penny D (2006). “Maximum parsimony and the phylogenetic information in multistate characters.” In Albert VA (ed.), Parsimony, Phylogeny, and Genomics, 163–178. Oxford University Press, Oxford.

See Also

Other split information functions: SplitInformation(), SplitMatchProbability(), TreesMatchingSplit(), UnrootedTreesMatchingSplit()