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Evaluate the concordance of information between a tree and a dataset

Source: R/Concordance.R
ConcordantInformation.Rd

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.

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.

Details

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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

data(congreveLamsdellMatrices)
myMatrix <- congreveLamsdellMatrices[[10]]
ConcordantInformation(TreeTools::NJTree(myMatrix), myMatrix)
#> dataset contains 821.038 bits, of which 280.813 signal, 540.226 noise, 78.0817 needed.  S:N = 0.519806
#> informationContent             signal              noise      signalToNoise 
#>        821.0383923        280.8125010        540.2258914          0.5198057 
#>    treeInformation       matrixToTree            ignored 
#>         78.0816559         10.5151253          0.0000000