Identify vertices retained when leaves are dropped
Original tree of class phylo
, in Preorder
.
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.
Optional character vector naming the leaves of tree
,
if keptTips
is not logical. Inferred from tree
if unspecified.
Other tree manipulation:
AddTip()
,
CollapseNode()
,
ConsensusWithout()
,
DropTip()
,
EnforceOutgroup()
,
ImposeConstraint()
,
KeptPaths()
,
LeafLabelInterchange()
,
MakeTreeBinary()
,
RenumberTips()
,
RenumberTree()
,
Renumber()
,
RootTree()
,
SortTree()
,
Subtree()
,
TipTimedTree()
,
TrivialTree
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.