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CI

Consistency Index and Retention Index

Description

CI and RI compute the Consistency Index (CI) and Retention Index (RI).

Usage

CI(tree, data, cost = NULL, sitewise = FALSE)

RI(tree, data, cost = NULL, sitewise = FALSE)

Arguments

tree

tree to start the nni search from.
data

A object of class phyDat containing sequences.
cost

A cost matrix for the transitions between two states.
sitewise

return CI/RI for alignment or sitewise

Details

The Consistency Index is defined as minimum number of changes divided by the number of changes required on the tree (parsimony score). The Consistency Index is equal to one if there is no homoplasy. And the Retention Index is defined as

RI = (MaxChanges - ObsChanges) / (MaxChanges - MinChanges)

See Also

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0
GPL (>= 2)
Authors
Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]
Initial release

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