DropTip | R Documentation |
DropTip()
removes specified leaves from a phylogenetic tree, collapsing
incident branches.
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)
tree |
A tree of class |
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 |
check |
Logical specifying whether to check validity of |
This function differs from ape::drop.tip()
, which roots unrooted trees,
and which can crash when trees' internal numbering follows unexpected schema.
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.
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.
Martin R. Smith (martin.smith@durham.ac.uk)
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()
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))
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