phylo4d-display {phylobase}R Documentation

Display methods for phylo4d objects

Description

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

Usage

    ## S4 method for signature 'phylo4d':
    print(x, edgeOrder = c("pretty", "real"),
    printall=TRUE) 
    ## S4 method for signature 'phylo4d':
    summary(object, quiet=FALSE)
    ## S4 method for signature '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.

Methods

print
signature(x = "phylo4d"): print method
show
signature(object = "phylo4d"): show method
summary
signature(object = "phylo4d"): summary method
names
signature(x = "phylo4d"): gives the slots names
head
signature(object = "phylo4d"): show first few nodes
tail
signature(object = "phylo4d"): show last few nodes

Author(s)

Ben Bolker, Thibaut Jombart

See Also

phylo4d constructor and phylo4d class.


[Package phylobase version 0.5 Index]