CI and RI compute the Consistency Index (CI) and Retention
Index (RI).
CI(tree, data, cost = NULL, sitewise = FALSE)RI(tree, data, cost = NULL, sitewise = FALSE)
tree to start the nni search from.
A object of class phyDat containing sequences.
A cost matrix for the transitions between two states.
return CI/RI for alignment or sitewise
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 $$RI = \frac{MaxChanges - ObsChanges}{MaxChanges - MinChanges}$$