Print Summary of a Phylogeny
The first function prints a compact summary of a phylogenetic tree (an
object of class
"phylo"). The three other functions return the
number of tips, nodes, or edges, respectively.
## S3 method for class 'phylo': summary(object, \dots) Ntip(phy) Nnode(phy, internal.only = TRUE) Nedge(phy)
- object, phy
- an object of class
- further arguments passed to or from other methods.
- a logical indicating whether to return the number
of internal nodes only (the default), or of internal and terminal
(tips) nodes (if
The summary includes the numbers of tips and of nodes, summary statistics of the branch lengths (if they are available) with mean, variance, minimum, first quartile, median, third quartile, and maximum, listing of the first ten tip labels, and (if available) of the first ten node labels. It is also printed whether some of these optional elements (branch lengths, node labels, and root edge) are not found in the tree.
If the tree was estimated by maximum likelihood with
mlphylo, a summary of the model fit and the parameter
estimated is printed.
summary simply prints its results on the standard output and is
not meant for programming.
- A NULL value in the case of
summary, a single numeric value for the three other functions.
data(bird.families) summary(bird.families) Ntip(bird.families) Nnode(bird.families) Nedge(bird.families)