Description Usage Arguments Details Value Author(s) References See Also Examples
Compares the clades between two trees.
1  tree.comp(phy1, phy2, method = "prop")

phy1, phy2 
Trees of class ‘phylo’ to compare. 
method 
One of the following options:

This function is a modification of the dist.topo
function in
ape
to give similarity between the two trees as a proportion, and to
account for the unreliable resolution of deeper nodes that affect some
methods of tree construction (such as NJ).
It is important that the tip labels of the two trees are the same. If the tip labels are different between the two trees, the method will not recognise any similarity between them.
This function does not take into account differences in branch length. The
"score"
method in dist.topo
does this if desired.
Numeric vector of length 1.
If method = "prop"
, the number returned is the proportion of nodes in
the first tree for which there is a node in the second that contains the
same tips. Higher number represents greater similarity. If it is 1, the
trees are identical. If 0, the trees have no similarity whatsoever.
When method = "shallow"
, only those nodes tipwards of the median node
depth are taken into account. This will not be useful for small trees, but
may be helpful with larger datasets.
"PH85"
is the Penny and Hendy (1985) distance. This measure is the
default of dist.topo
. In this measure, the smaller the number,
the closer the trees are. If the trees are identical, this results in 0.
Samuel Brown <[email protected]>
Penny, D. and Hendy, M. D. (1985) The use of tree comparison metrics. _Systematic Zoology_ *34* 7582.
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