phylobase (version 0.6.8)

phylo4d-display: Display methods for phylo4d objects

Description

Methods used to display information about the data and the tree for phylo4d objects.

Usage

## S3 method for class 'phylo4d':
print(x, edgeOrder = c("pretty", "real"),
    printall=TRUE) 
    ## S3 method for class 'phylo4d':
summary(object, quiet=FALSE)
    ## S3 method for class 'phylo4d':
names(x)

Arguments

x

a phylo4d object

object

a phylo4d object

edgeOrder

Character string indicating whether the edges should be printed as ordered in the tree "real" (e.g. preorder or postorder), or "pretty" printed with tips collated together

quiet

Should the summary be displayed on screen?

printall

If TRUE all tip labels are printed

Value

• The summary method invisibly returns a list with the following components:
• name
  the name of the object
• nb.tips
  the number of tips
• nb.nodes
  the number of nodes
• mean.el
  mean of edge lengths
• var.el
  variance of edge lengths (estimate for population)
• sumry.el
  summary (i.e. range and quartiles) of the edge lengths
• degree
  (optional) type of polytomy for each node: node, terminal (all descendants are tips) or internal (at least one descendant is an internal node); displayed only when there are polytomies
• sumry.tips
  (optional) summary for the data associated with the tips
• sumry.nodes
  (optional) summary for the data associated with the internal nodes
• The names method returns a vector of characters corresponding to the names of the slots.

See Also

phylo4d constructor and phylo4d class.