Identify vertices retained when leaves are dropped

Identify vertices retained when leaves are dropped

Usage

KeptVerts(tree, keptTips, tipLabels = TipLabels(tree))

# S3 method for class 'phylo'
KeptVerts(tree, keptTips, tipLabels = TipLabels(tree))

# S3 method for class 'numeric'
KeptVerts(tree, keptTips, tipLabels = TipLabels(tree))

Arguments

tree

Original tree of class phylo, in Preorder.

keptTips

Either:

• a logical vector stating whether each leaf should be retained, in a sequence corresponding to tree[["tip.label"]]; or

• a character vector listing the leaf labels to retain; or

• a numeric vector listing the indices of leaves to retain.

tipLabels

Optional character vector naming the leaves of tree, if keptTips is not logical. Inferred from tree if unspecified.

See also

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), EnforceOutgroup(), ImposeConstraint(), KeptPaths(), LeafLabelInterchange(), MakeTreeBinary(), Renumber(), RenumberTips(), RenumberTree(), RootTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

master <- BalancedTree(12)
master <- Preorder(master) # Nodes must be listed in Preorder sequence
plot(master)
nodelabels()


allTips <- master[["tip.label"]]
keptTips <- sample(allTips, 8)
plot(KeepTip(master, keptTips))

kept <- KeptVerts(master, allTips %in% keptTips)

map <- which(kept)
# Node `i` in the reduced tree corresponds to node `map[i]` in the original.