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Drop leaves from tree

Source: R/DropTip.R
DropTip.Rd

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

Usage

DropTip(tree, tip, preorder = TRUE, check = TRUE)

# S3 method for class 'phylo'
DropTip(tree, tip, preorder = TRUE, check = TRUE)

# S3 method for class 'Splits'
DropTip(tree, tip, preorder, check = TRUE)

DropTipPhylo(tree, tip, preorder = TRUE, check = TRUE)

# S3 method for class 'multiPhylo'
DropTip(tree, tip, preorder = TRUE, check = TRUE)

# S3 method for class 'list'
DropTip(tree, tip, preorder = TRUE, check = TRUE)

# S3 method for class '`NULL`'
DropTip(tree, tip, preorder = TRUE, check = TRUE)

KeepTipPreorder(tree, tip)

KeepTipPostorder(tree, tip)

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 tree before dropping tips. Specifying FALSE saves a little time, but will result in undefined behaviour if tree is not in preorder.

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. The edges of the tree will be numbered in preorder, but their sequence may not conform to the conventions of Preorder().

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

Details

This function differs from ape::drop.tip(), which roots unrooted trees, and which can crash when trees' internal numbering follows unexpected schema.

Functions

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

  • KeepTipPreorder(): Faster version with no checks. Does not retain labels or edge weights. Edges must be listed in preorder. May crash if improper input is specified.

  • KeepTipPostorder(): Faster version with no checks. Does not retain labels or edge weights. Edges must be listed in postorder. May crash if improper input is specified.

See also

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

Other split manipulation functions: Subsplit(), TrivialSplits()

Author

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

Examples

tree <- BalancedTree(9)
plot(tree)

plot(DropTip(tree, c("t5", "t6")))


unrooted <- UnrootTree(tree)
plot(unrooted)

plot(DropTip(unrooted, 4:5))


summary(DropTip(as.Splits(tree), 4:5))
#> 4 bipartition splits dividing 7 tips, t1 .. t9
#>      1234567
#>  12  ***....
#>  13  **.....
#>  16  ...**..
#>  17  .....**
#> 
#>  Tip 1: t1	 Tip 2: t2	 Tip 3: t3	 Tip 4: t6	 Tip 5: t7	
#>  Tip 6: t8	 Tip 7: t9