Consistency Index and Retention Index

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: a phylogenetic tree, i.e. an object of class phylo.
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

Value

a scalar or vector with the CI/RI vector.

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 $$RI = \frac{MaxChanges - ObsChanges}{MaxChanges - MinChanges}$$

Examples

example(as.phylo.formula)
#> 
#> as.ph.> data(carnivora)
#> 
#> as.ph.> frm <- ~SuperFamily/Family/Genus/Species
#> 
#> as.ph.> tr <- as.phylo(frm, data = carnivora, collapse=FALSE)
#> 
#> as.ph.> tr$edge.length <- rep(1, nrow(tr$edge))
#> 
#> as.ph.> plot(tr, show.node.label=TRUE)

#> 
#> as.ph.> Nnode(tr)
#> [1] 83
#> 
#> as.ph.> ## compare with:
#> as.ph.> Nnode(as.phylo(frm, data = carnivora, collapse = FALSE))
#> [1] 83
lab <- tr$tip.label
lab[79] <- "Herpestes fuscus"
tr$tip.label <- abbreviateGenus(lab)
X <- matrix(0, 112, 3, dimnames = list(tr$tip.label, c("Canis", "Panthera",
            "Canis_Panthera")))
desc_canis <- Descendants(tr, "Canis")[[1]]
desc_panthera <- Descendants(tr, "Panthera")[[1]]
X[desc_canis, c(1,3)] <- 1
X[desc_panthera, c(2,3)] <- 1
col <- rep("black", 112)
col[desc_panthera] <- "red"
col[desc_canis] <- "blue"
X <- phyDat(X, "USER", levels=c(0,1))
plot(tr, "f", tip.color=col)

# The first two sites are homoplase free!
CI(tr, X, sitewise=TRUE)
#> [1] 1.0 1.0 0.5
RI(tr, X, sitewise=TRUE)
#> [1] 1.000 1.000 0.875