This function conducts a test for cospeciation based on tree distance, applying a distance metric selected by the user. Note that this method should be prone to be quite liberal as the null hypothesis is no similarity between trees!
cospeciation(t1, t2, distance=c("RF","SPR"),
method=c("simulation","permutation"), assoc=NULL,
nsim=100, ...)
# S3 method for cospeciation
plot(x, ...)
# S3 method for cospeciation
print(x, ...)
object of class "phylo"
.
object of class "phylo"
.
distance method to compare trees.
method to use (simulation of pure-birth trees, or permutation of tip labels on a fixed tree) to obtain a null distribution of tree distances via distance
.
matrix containing the tip labels in t1
to match to the tip labels in t2
. Note that not all labels in either tree need to be included; however, unlike cophylo
, one label in t1
cannot be matched with more than one label in t2
, nor vice versa. If NULL
then an exact match of tip labels will be sought.
number of simulations or permutations.
for plot
and print
methods, an object of class "cospeciation"
.
optional arguments.
An object of class "cospeciation"
, which includes the test-statistic, the null distribution, and a p-value for the test of the null hypothesis of no topological similarity between the two trees.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.