Usage
cospeciation(t1, t2, distance=c("RF","SPR"),
method=c("simulation","permutation"), assoc=NULL,
nsim=100, ...)
"plot"(x, ...)
"print"(x, ...)
Arguments
t1
object of class "phylo".
t2
object of class "phylo".
distance
distance method to compare trees.
method
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.
assoc
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.
nsim
number of simulations or permutations.
x
for plot and print methods, an object of class "cospeciation".