as.Node.phylo: Convert a 'phylo' object from the ape package to a 'Node'

In data.tree: General Purpose Hierarchical Data Structure

Convert a phylo object from the ape package to a Node

Description

Convert a phylo object from the ape package to a Node

Usage

## S3 method for class 'phylo'
as.Node(
  x,
  heightName = "plotHeight",
  replaceUnderscores = TRUE,
  namesNotUnique = FALSE,
  ...
)

Arguments

x	The phylo object to be converted
heightName	If the phylo contains edge lengths, then they will be converted to a height and stored in a field named according to this parameter (the default is "height")
replaceUnderscores	if TRUE (the default), then underscores in names are replaced with spaces
namesNotUnique	if TRUE, then the name of the Nodes will be prefixed with a unique id. This is useful if the children of a parent have non-unique names.
...	any other parameter to be passed to sub-implementations

See Also

Other ape phylo conversions: GetPhyloNr(), as.phylo.Node()

Other as.Node: as.Node.data.frame(), as.Node.dendrogram(), as.Node.list(), as.Node.rpart(), as.Node()

Examples

#which bird familes have the max height?
library(ape)
data(bird.families)
bf <- as.Node(bird.families)
height <- bf$height
t <- Traverse(bf, filterFun = function(x) x$level == 25)
Get(t, "name")

data.tree documentation built on Nov. 13, 2023, 1:08 a.m.