ConcordantInformation | R Documentation |
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.
ConcordantInformation(tree, dataset)
Evaluate(tree, dataset)
ConcordantInfo(tree, dataset)
tree |
A tree of class |
dataset |
A phylogenetic data matrix of phangorn class
|
Presently restricted to datasets whose characters contain a maximum of two parsimony-informative states.
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.
Martin R. Smith (martin.smith@durham.ac.uk)
data(congreveLamsdellMatrices)
myMatrix <- congreveLamsdellMatrices[[10]]
ConcordantInformation(TreeTools::NJTree(myMatrix), myMatrix)
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