Convert a tree to ranked treeSource:
Convert a tree of class "phylo" to a ranked tree of class "rankedPhylo".
To convert a tree to a ranked tree, the tree needs to be binary (i.e., fully resolved), be rooted, and ultrametric. Typically, such tree would be produced by coalescent process.
Ranked trees are similar to time-trees, only instead of time, we care about the order of the splits.
# this will throw an error, the tree is not ultrametric x = ape::rtree(5) try(as_ranked(x)) #> Error in as_ranked(x) : Input tree must be ultrametric. # coalescent trees can be converted without problem y = ape::rcoal(5) as_ranked(y) #> #> Phylogenetic tree with 5 tips and 4 internal nodes. #> #> Tip labels: #> t4, t5, t1, t3, t2 #> #> Rooted; includes branch lengths.