AddTip()
adds a tip to a phylogenetic tree at a specified location.
AddTip(
tree,
where = sample.int(tree[["Nnode"]] * 2 + 2L, size = 1) - 1L,
label = "New tip",
nodeLabel = "",
edgeLength = 0,
lengthBelow = NULL,
nTip = NTip(tree),
nNode = tree[["Nnode"]],
rootNode = RootNode(tree)
)
AddTipEverywhere(tree, label = "New tip", includeRoot = FALSE)
A tree of class phylo
.
The node or tip that should form the sister taxon to the new
node. To add a new tip at the root, use where = 0
. By default, the
new tip is added to a random edge.
Character string providing the label to apply to the new tip.
Character string providing a label to apply to the newly
created node, if tree$node.label
is specified.
Numeric specifying length of new edge. If NULL
,
defaults to lengthBelow
.
This will become the default behaviour in a
future release; please manually specify the desired behaviour in your code.
Numeric specifying length below neighbour at which to
graft new edge. Values greater than the length of the edge will result
in negative edge lengths. If NULL
, the default, the new tip will be added
at the midpoint of the broken edge. If inserting at the root (where = 0
),
a new edge of length lengthBelow
will be inserted.
Optional integer vectors specifying number of tips
and nodes in tree
, and index of root node.
Not checked for correctness: specifying values here yields a marginal speed
increase at the cost of code safety.
Logical; if TRUE
, each position adjacent
to the root edge is considered to represent distinct edges; if FALSE
,
they are treated as a single edge.
AddTip()
returns a tree of class phylo
with an additional tip
at the desired location.
AddTipEverywhere()
returns a list of class multiPhylo
containing
the trees produced by adding label
to each edge of tree
in turn.
AddTip()
extends bind.tree
, which cannot handle
single-taxon trees.
AddTipEverywhere()
adds a tip to each edge in turn.
Add one tree to another: bind.tree()
Other tree manipulation:
CollapseNode()
,
ConsensusWithout()
,
DropTip()
,
EnforceOutgroup()
,
ImposeConstraint()
,
KeptPaths()
,
KeptVerts()
,
LeafLabelInterchange()
,
MakeTreeBinary()
,
Renumber()
,
RenumberTips()
,
RenumberTree()
,
RootTree()
,
SortTree()
,
Subtree()
,
TipTimedTree()
,
TrivialTree
tree <- BalancedTree(10)
# Add a leaf below an internal node
plot(tree)
ape::nodelabels()
node <- 15
ape::nodelabels(bg = ifelse(NodeNumbers(tree) == node, "green", "grey"))
plot(AddTip(tree, 15, "NEW_TIP"))
# Add edge lengths for an ultrametric tree
tree$edge.length <- rep(c(rep(1, 5), 2, 1, 2, 2), 2)
# Add a leaf to an external edge
leaf <- 5
plot(tree)
ape::tiplabels(bg = ifelse(seq_len(NTip(tree)) == leaf, "green", "grey"))
plot(AddTip(tree, 5, "NEW_TIP", edgeLength = NULL))
# Set up multi-panel plot
oldPar <- par(mfrow = c(2, 4), mar = rep(0.3, 4), cex = 0.9)
# Add leaf to each edge on a tree in turn
backbone <- BalancedTree(4)
# Treating the position of the root as instructive:
additions <- AddTipEverywhere(backbone, includeRoot = TRUE)
xx <- lapply(additions, plot)
par(mfrow = c(2, 3))
# Don't treat root edges as distinct:
additions <- AddTipEverywhere(backbone, includeRoot = FALSE)
xx <- lapply(additions, plot)
# Restore original plotting parameters
par(oldPar)