Nothing
tree.comp <-
function (phy1, phy2, method = "prop") {
phy1 <- unroot(phy1)
phy2 <- unroot(phy2)
nphy1 <- length(phy1$tip.label)
bp1 <- prop.part(phy1)
bp1 <- lapply(bp1, function(xx) sort(phy1$tip.label[xx]))
nphy2 <- length(phy2$tip.label)
bp2.tmp <- prop.part(phy2)
bp2 <- lapply(bp2.tmp, function(xx) sort(phy2$tip.label[xx]))
bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:nphy2, xx))
bp2.comp <- lapply(bp2.comp, function(xx) sort(phy2$tip.label[xx]))
q1 <- length(bp1)
q2 <- length(bp2)
p <- 0
for (i in 1:q1) {
for (j in 1:q2) {
if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]],
bp2.comp[[j]])) {
p <- p + 1
break
}
}
}
if(method == "shallow"){
shallow <- which(node.depth(phy1)[node.depth(phy1) > 1] <= median(node.depth(phy1)[node.depth(phy1) > 1]))
p2 <- 0
for (i in shallow) {
for (j in 1:q2) {
if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]],
bp2.comp[[j]])) {
p2 <- p2 + 1
break
}
}
}
dT <- p2/length(shallow)
}
if(method == "PH85") dT <- q1 + q2 - 2 * p
if(method =="prop") dT <- p/q1
dT
}
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