ConcordantInformation: 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)
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.
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.