treespace (version 1.1.4.3)

tipDiff: Find tip position differences

Description

Find the topologicial differences between two trees with the same tip labels. The function returns a data frame of the tips and the number of differences in their ancestry between the two trees. Called by plotTreeDiff, which highlights the differing tips in a plot of the two trees.

Usage

tipDiff(tr1, tr2, vec1 = NULL, vec2 = NULL, sizeOfDifferences = FALSE)

Value

A data frame of the tree tips and the number of ancestral differences between them in the two trees, in order of increasing difference. A tip is said to have zero difference if each of its ancestral nodes admits the same tip partition in the two trees.

Arguments

tr1

an object of the class phylo: the first tree to compare.

tr2

an object of the class phylo: the second tree to compare.

vec1

an optional input, the result of treeVec(tr1, lambda=0), to speed up the computation.

vec2

an optional input, the result of treeVec(tr2, lambda=0), to speed up the computation.

sizeOfDifferences

a logical (default FALSE) specifying whether the size of the differences in the vectors per tip is also computed

Author

Michelle Kendall

See Also

medTree plotTreeDiff

Examples

## simple example on trees with five tips:
tr1 <- read.tree(text="((A:1,B:1):1,((C:1,D:1):1,E:1):1):1;")
tr2 <- read.tree(text="((A:1,B:1):1,(C:1,(D:1,E:1):1):1):1;")
tipDiff(tr1,tr2)

## example on larger woodmice trees
data(woodmiceTrees)
tipDiff(woodmiceTrees[[1]],woodmiceTrees[[2]])