sort_tips {rrnni} | R Documentation |
Sort tip labels
Description
Sort tip labels in a tree or a collection of trees.
Usage
sort_tips(x)
## S3 method for class 'phylo'
sort_tips(x)
## S3 method for class 'multiPhylo'
sort_tips(x)
Arguments
x |
a tree of class "phylo" or a collection of trees of class "multiPhylo" |
Details
The rnni
function assumes tip labels in an unambiguous order.
This is due to the internal implementation not having tip labels,
tip/leave are instead identified by the index in the node matrix.
The sort_tips
orders the tip labels and change the node indices
in the node matrix so that the tips for two different trees of the
same taxa have the same node id.
Value
an input tree with sorted tips
Examples
# generate random trees
# use rcoal(5) instead of rankedPhylo(5)
# as ranked phylo always generate tip.labels
# in the same order.
t1 = ape::rcoal(5) |> rankedPhylo()
t2 = ape::rcoal(5) |> rankedPhylo()
t1s = sort_tips(t1)
t2s = sort_tips(t2)
all(tips(t1s) == tips(t2s))
# for collection of trees:
trees = c(t1, t2)
sort_tips(trees)
[Package rrnni version 0.1.1 Index]