TreeTools (version 1.6.0)

DropTip: Drop tips from tree

Description

DropTip() removes specified tips from a phylogenetic tree, collapsing incident branches.

Usage

DropTip(tree, tip, preorder = TRUE, check = TRUE)
# S3 method for phylo
DropTip(tree, tip, preorder = TRUE, check = TRUE)
DropTipPhylo(tree, tip, preorder = TRUE, check = TRUE)
# S3 method for multiPhylo
DropTip(tree, tip, preorder = TRUE, check = TRUE)
KeepTip(tree, tip, preorder = TRUE, check = TRUE)

Arguments

tree

A tree of class phylo.

tip

Character vector specifying labels of leaves in tree to be dropped, or integer vector specifying the indices of leaves to be dropped. Specifying the index of an internal node will drop all descendants of that node.

preorder

Logical specifying whether to Preorder the tree before dropping tips. Necessary if a tree's edges may be unconventionally numbered.

check

Logical specifying whether to check validity of tip. If FALSE and tip contains entries that do not correspond to leaves of the tree, undefined behaviour may occur.

Value

DropTip() returns a tree of class phylo, with the requested leaves removed.

KeepTip() returns tree with all leaves not in tip removed, in preorder.

Functions

• DropTipPhylo: Direct call to DropTip.phylo(), to avoid overhead of querying object's class.

Details

This function is more robust than ape::drop.tip() as it does not require any particular internal node numbering schema.

See Also

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

Examples

# NOT RUN {
tree <- BalancedTree(8)
plot(tree)
plot(DropTip(tree, c('t4', 't5')))

# }