Create a ranked tree

Create a new, or coerce character vector or an existing tree into a ranked tree.

Usage

rankedPhylo(x)

# S3 method for default
rankedPhylo(x)

# S3 method for numeric
rankedPhylo(x)

# S3 method for character
rankedPhylo(x)

# S3 method for phylo
rankedPhylo(x)

# S3 method for multiPhylo
rankedPhylo(x)

Arguments

x

a numeric vector, character vector or a object of class phylo or multiPhylo, see details.

Value

ranked tree or trees of class rankedPhylo or multiRankedPhylo

Details

This is a wrapper for multiple functions that create a ranked tree. As such, it accepts multiple types of inputs and produce either rankedPhylo or a collated list of ranked trees as a multiRankedPhylo.

If x is a numeric vector, create n = length(x) random ranked tree using the random_tree function. If x is a character vector, try to read the character as a newick-formatted tree. If x is object of a class phylo or multiPhylo, coerce these objects into rankedPhylo or multiRankedPhylo using the as_ranked function.

Examples

# Create a single random ranked tree with 5 tips
rankedPhylo(5)
#> 
#> Phylogenetic tree with 5 tips and 4 internal nodes.
#> 
#> Tip labels:
#>   t1, t2, t3, t4, t5
#> 
#> Rooted; includes branch lengths.

# Create multiple random ranked trees with 5 tips
rankedPhylo(c(5,5,5))
#> 3 phylogenetic trees

# Convert a coalescent tree into a ranked tree
x = ape::rcoal(5) # random coalescent tree
rankedPhylo(x)
#> 
#> Phylogenetic tree with 5 tips and 4 internal nodes.
#> 
#> Tip labels:
#>   t4, t1, t2, t3, t5
#> 
#> Rooted; includes branch lengths.