R/Concordance.R
ConcordantInformation.RdDetails 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.
ConcordantInformation(tree, dataset)
Evaluate(tree, dataset)
ConcordantInfo(tree, dataset)A tree of class phylo.
A phylogenetic data matrix of phangorn class
phyDat, whose names correspond to the labels of any accompanying tree.
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.
Presently restricted to datasets whose characters contain a maximum of two parsimony-informative states.
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