ConcordantInformation: Evaluate the concordance of information between a tree and a...

In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data

Evaluate the concordance of information between a tree and a dataset

Description

Details the amount of information in a phylogenetic dataset that is consistent with a specified phylogenetic tree, and the signal:noise ratio of the character matrix implied if the tree is true.

Usage

ConcordantInformation(tree, dataset)

Evaluate(tree, dataset)

ConcordantInfo(tree, dataset)

Arguments

tree	A tree of class phylo.
dataset	A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree.

Details

Presently restricted to datasets whose characters contain a maximum of two parsimony-informative states.

Value

ConcordantInformation() returns a named vector with elements:

• informationContent: cladistic information content of dataset

• signal, noise: amount of cladistic information that represents phylogenetic signal and noise, according to tree

• signalToNoise: the implied signal:noise ratio of dataset

• treeInformation: the cladistic information content of a bifurcating tree on dataset; this is the minimum amount of information necessary to resolve a bifurcating tree, assuming no duplicate information or noise

• matrixToTree: the ratio of the cladistic information content of the matrix to the cladistic information content of the tree, a measure of the redundancy of the matrix

• ignored: information content of characters whose signal and noise could not be calculated (too many states) and so are not included in the totals above.

Author(s)

Martin R. Smith ([e-mail])

Examples

data(congreveLamsdellMatrices)
myMatrix <- congreveLamsdellMatrices[[10]]
ConcordantInformation(TreeTools::NJTree(myMatrix), myMatrix)

ms609/TreeSearch documentation built on April 7, 2024, 7:06 p.m.