Evaluating all possible co-phylogenetic plots for a pair of trees

I just pushed an update to the co-phylogenetic phytools method cophylo to permit it to compute & return all possible rotated objects of class "cophylo" for a pair of trees and table of associations.

This is functionally equivalent to using allRotations to rotate both trees in all possible ways, and then cophylo to compute an object of class "cophylo" (without rotation) on each pair of trees.

This will generally result in a large number of "cophylo" objects for even a modest number of taxa in the two input trees, as follows:

X

##    N1=N2=   N(cophylo)
## 1       2            4
## 2       3           16
## 3       4           64
## 4       5          256
## 5       6         1024
## 6       7         4096
## 7       8        16384
## 8       9        65536
## 9      10       262144
## 10     11      1048576
## 11     12      4194304
## 12     13     16777216
## 13     14     67108864
## 14     15    268435456
## 15     16   1073741824
## 16     17   4294967296
## 17     18  17179869184
## 18     19  68719476736
## 19     20 274877906944

Let's try the update:

library(phytools)
t1<-rtree(n=5,tip.label=LETTERS[1:5])
t2<-rtree(n=5,tip.label=letters[1:5])
assoc<-cbind(LETTERS[1:5],letters[1:5])
obj<-cophylo(t1,t2,methods="all",assoc=assoc)

## Rotating nodes to optimize matching...
## Done.

match.score<-sapply(obj,function(x) sum(attr(x$trees[[1]],"minRotate"),
    attr(x$trees[[2]],"minRotate")))
best<-which(match.score==min(match.score))

par(mfrow=c(16,16))
par(mar=rep(0,4))

for(i in 1:length(obj)){
    if(i%in%best) par(fg="blue") else par(fg="black")
    plot(obj[[i]],
    fsize=0.4,link.lty="solid",
    link.col=if(i%in%best) "blue" else "black",
    pts=FALSE,ylim=c(-0.1,1.1))
}

Here I have plotted the best matching rotations in blue.

That's it.