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## which.edge.R (2017-10-04)
## Identifies Edges of a Tree
## Copyright 2004-2017 Emmanuel Paradis, 2017 Joseph W. Brown, 2017 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
getMRCA <- function(phy, tip) {
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
if (length(tip) < 2) return(NULL)
Ntip <- length(phy$tip.label)
## <FIXME> do we need to check the value(s) in 'tip'?
##if (any(tip > Ntip + phy$Nnode) || any(tip < 1))
## stop("value(s) out of range in 'tip'")
## </FIXME>
rootnd <- Ntip + 1L
pars <- integer(phy$Nnode) # worst case assignment, usually far too long
tnd <- if (is.character(tip)) match(tip, phy$tip.label) else tip
done_v <- logical(Ntip + phy$Nnode)
## build a lookup table to get parents faster
pvec <- integer(Ntip + phy$Nnode)
pvec[phy$edge[, 2]] <- phy$edge[, 1]
## get entire lineage for first tip
nd <- tnd[1]
for (k in 1:phy$Nnode) {
nd <- pvec[nd]
pars[k] <- nd
if (nd == rootnd) break
}
pars <- pars[1:k] # delete the rest
mrcind <- integer(max(pars))
mrcind[pars] <- 1:k
mrcand <- pars[1]
## traverse lineages for remaining tips, stop if hit common ancestor
for (i in 2:length(tnd)) {
cnd <- tnd[i]
done <- done_v[cnd]
while(!done){
done_v[cnd] <- TRUE
cpar <- pvec[cnd] # get immediate parent
done <- done_v[cpar] # early exit if TRUE
if (cpar %in% pars) {
if (cpar == rootnd) return(rootnd) # early exit
if(mrcind[cpar] > mrcind[mrcand]) mrcand <- cpar
done_v[cpar] <- TRUE
done <- TRUE
}
cnd <- cpar # keep going!
}
}
mrcand
}
which.edge <- function(phy, group)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
if (is.character(group))
group <- which(phy$tip.label %in% group)
if (length(group) == 1)
return(match(group, phy$edge[, 2]))
n <- length(phy$tip.label)
sn <- .Call(seq_root2tip, phy$edge, n, phy$Nnode)[group]
i <- 2L
repeat {
x <- unique(unlist(lapply(sn, "[", i)))
if (length(x) != 1) break
i <- i + 1L
}
d <- -(1:(i - 1L))
x <- unique(unlist(lapply(sn, function(x) x[d])))
match(x, phy$edge[, 2L])
}
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