Add a tip to a phylogenetic tree
AddTip() adds a tip to a phylogenetic tree at a specified location.
AddTip( tree, where = sample.int(tree$Nnode * 2 + 2L, size = 1) - 1L, label = "New tip", edgeLength = 0, lengthBelow = NULL, nTip = NTip(tree), nNode = tree$Nnode, rootNode = RootNode(tree) ) AddTipEverywhere(tree, label = "New tip", includeRoot = FALSE)
tree |
A tree of class |
where |
The node or tip that should form the sister taxon to the new
node. To add a new tip at the root, use |
label |
Character string providing the label to apply to the new tip. |
edgeLength |
Numeric specifying length of new edge |
lengthBelow |
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 |
nTip, nNode, rootNode |
Optional integer vectors specifying number of tips and
nodes in |
includeRoot |
Logical; if |
AddTip() extends bind.tree, which cannot handle
single-taxon trees.
AddTipEverywhere() adds a tip to each edge in turn.
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.
Martin R. Smith (martin.smith@durham.ac.uk)
Add one tree to another: bind.tree()
Other tree manipulation:
CollapseNode(),
ConsensusWithout(),
DropTip(),
EnforceOutgroup(),
LeafLabelInterchange(),
MakeTreeBinary(),
RenumberTips(),
RenumberTree(),
Renumber(),
RootTree(),
SingleTaxonTree(),
SortTree(),
Subtree()
plot(tree <- BalancedTree(10)) ape::nodelabels() ape::nodelabels(15, 15, bg='green') plot(AddTip(tree, 15, 'NEW_TIP')) oldPar <- par(mfrow=c(2, 4), mar=rep(0.3, 4), cex=0.9) 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) par(oldPar)
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