comparePhylo: Compare Two "phylo" Objects

View source: R/comparePhylo.R

comparePhyloR Documentation

Compare Two "phylo" Objects

Description

This function compares two phylogenetic trees, rooted or unrooted, and returns a detailed report of this comparison.

Usage

comparePhylo(x, y, plot = FALSE, force.rooted = FALSE,
             use.edge.length = FALSE, commons = TRUE,
             location = "bottomleft", ...)
## S3 method for class 'comparePhylo'
print(x, ...)

Arguments

x, y

two objects of class "phylo".

plot

a logical value. If TRUE, the two trees are plotted on the same device and their similarities are shown.

force.rooted

a logical value. If TRUE, the trees are considered rooted even if is.rooted returns FALSE.

use.edge.length

a logical value passed to plot.phylo (see below).

commons

whether to show the splits (the default), or the splits specific to each tree (applies only for unrooted trees).

location

location of where to position the legend.

...

further parameters used by plot.phylo, in function print.comparePhylo unused.

Details

In all cases, the numbers of tips and of nodes and the tip labels are compared.

If both trees are rooted, or if force.rooted = TRUE, the clade compositions of each tree are compared. If both trees are also ultrametric, their branching times are compared.

If both trees are unrooted and have the same number of nodes, the bipartitions (aka splits) are compared.

If plot = TRUE, the edge lengths are not used by default because in some situations with unrooted trees, some splits might not be visible if the corresponding internal edge length is very short. To use edge lengths, set use.edge.length = TRUE.

Value

an object of class "comparePhylo" which is a list with messages from the comparison and, optionally, tables comparing branching times.

Author(s)

Emmanuel Paradis, Klaus Schliep

See Also

all.equal.phylo

Examples

## two unrooted trees but force comparison as rooted:
a <- read.tree(text = "(a,b,(c,d));")
b <- read.tree(text = "(a,c,(b,d));")
comparePhylo(a, b, plot = TRUE, force.rooted = TRUE)
## two random unrooted trees:
c <- rtree(5, rooted = FALSE)
d <- rtree(5, rooted = FALSE)
comparePhylo(c, d, plot = TRUE)

ape documentation built on March 18, 2022, 5:34 p.m.