bind.tip | R Documentation |
Adds a new tip to the tree.
bind.tip(tree, tip.label, edge.length=NULL, where=NULL, position=0,
interactive=FALSE, ...)
tree |
receptor tree. |
tip.label |
a string containing the species name for the new tip. |
edge.length |
edge length for the new tip (a scalar). |
where |
node number to attach new tip. If |
position |
distance rootward of the node to add the new tip. |
interactive |
logical value indicating whether or not the species should be added interactively. (Defaults to |
... |
arguments to be passed to |
If the tree is ultrametric and no branch length is specified, then edge.length
is scaled so that the tree remains ultrametric after the new tip is added.
Wrapper function for ape bind.tree
. Note that interactive=TRUE
works only for right-facing phylograms.
An object of class "phylo"
.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
set.seed(123)
par(mfrow=c(3,1))
## generate tree
tree<-pbtree(b=0.1, n=10)
## plot original tree
plotTree(tree,mar=c(2.1,0.1,2.1,0.1))
axisPhylo()
mtext("a)",adj=0)
## add an extant tip ("t_extant") sister to taxon 't5'
## with divergence time of 4.5 Ma
node <- which(tree$tip.label=="t5")
tree <- bind.tip(tree, tip.label="t_extant",
where=node, position=4.5)
# plot to see the result
plotTree(tree,mar=c(2.1,0.1,2.1,0.1))
axisPhylo()
mtext("b)",adj=0)
## add an extinct tip ("t_extinct") sister to 't2' with
## divergence time of 7.8 Ma and duration (edge length) of
## 3.3 Ma
node <- which(tree$tip.label=="t2")
tree <- bind.tip(tree, tip.label="t_extinct", where=node,
position=7.8, edge.length=3.3)
## plot to see the result
plotTree(tree,mar=c(2.1,0.1,2.1,0.1))
axisPhylo()
mtext("c)",adj=0)
par(mar=c(5.1,4.1,4.1,2.1),mfrow=c(1,1))
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