build.nodes.1 <-
function(tree, tips)
{
tips <- data.frame(as.matrix(tips), stringsAsFactors = FALSE)
dimnames(tips)[[2]] <- tolower(dimnames(tips)[[2]])
tips$species <- gsub("(^[[:alpha:]])", "\\U\\1", tips$species, perl = TRUE)
tips$genus <- gsub("(^[[:alpha:]])", "\\U\\1", tips$genus, perl = TRUE)
tips$family <- gsub("(^[[:alpha:]])", "\\U\\1", tips$family, perl = TRUE)
tree$node.label <- paste("N", 1 : tree$Nnode, sep="")
node.dep <- branching.times(tree)
tips <- tips[match(tree$tip.label, tips$species), ]
tips$No. <- as.integer(dimnames(tips)[[1]])
clustF <- cluster(tips$family)
tips$numF <- clustF
clustG <- cluster(tips$genus)
tips$numG <- clustG
clustF.size <- table(clustF)
clustF.size <- data.frame(numF = as.integer(names(clustF.size)), sizeF = as.integer(clustF.size))
clustG.size <- table(clustG)
clustG.size <- data.frame(numG = as.integer(names(clustG.size)), sizeG = as.integer(clustG.size))
tips1 <- merge(tips, clustF.size, all.x=T)
tips1 <- merge(tips1, clustG.size, all.x=T)
tips1 <- tips1[, c("No.", "species", "genus", "family", "numF", "numG", "sizeF", "sizeG")]
xF <- tips1[!duplicated(tips1$numF), ]
xF <- xF[rev(order(xF$sizeF)), ]
xF <- xF[!duplicated(xF$family), ]
xx <- merge(tips1, data.frame(numF = unique(xF$numF)))
xxG <- table(xx[!duplicated(xx$genus), ]$numF)
xxG <- data.frame(numF = as.integer(names(xxG)), gen.n = as.integer(xxG))
xxS <- table(xx$numF)
xxS <- data.frame(numF = as.integer(names(xxS)), sp.n = as.integer(xxS))
xxGS <- merge(xxG, xxS)
xF1 <- xF[xF$sizeF == 1, ]
if (dim(xF1)[1] > 0)
{
Fn1 <- data.frame(level = "F", family = xF1$family, genus = "", rn = "", rn.bl = 0, bn = "", bn.bl = 0, taxa = xF1$species, stringsAsFactors = FALSE)
for (i in 1 : dim(Fn1)[1])
{
x0 <- match(Fn1$taxa[i], tree$tip.label)
x1 <- match(x0, tree$edge[, 2])
x2 <- tree$edge[x1, 1] - length(tree$tip.label)
Fn1$bn[i] <- tree$node.label[x2]
Fn1$rn[i] <- tree$node.label[x2]
Fn1$rn.bl[i] <- tree$edge.length[x1]
Fn1$bn.bl[i] <- tree$edge.length[x1]
}
}
if (dim(xF1)[1] == 0)
{
Fn1 <- NULL
}
xF2 <- xF[xF$sizeF > 1, ]
if (dim(xF2)[1] > 0)
{
tipsF <- merge(tips1, data.frame(numF = xF2$numF))
tF <- drop.tip(tree, setdiff(tree$tip.label, tipsF$species))
tipsF <- tipsF[match(tF$tip.label, tipsF$species), ]
tF$tip.label <- tipsF$family
n1 <- which(!duplicated(tF$tip.label))
n2 <- length(tF$tip.label) + 1 - which(!duplicated(rev(tF$tip.label)))
nn <- sort(unique(c(n1, n2)))
tF <- drop.tip(tF, setdiff(1 : length(tF$tip.label), nn))
Fn2 <- data.frame(level = "F", family = xF2$family, genus = "", rn = "", rn.bl = 0, bn = "", bn.bl = 0, taxa = "", stringsAsFactors = FALSE)
x <- 1 : length(tF$tip.label)
for (i in 1 : dim(Fn2)[1])
{
h <- which(tF$tip.label == Fn2$family[i])
tt <- drop.tip(tF, setdiff(x, h))
Fn2$bn[i] <- tt$node.label
Fn2$bn.bl[i] <- tt$edge.length[1]
n <- which(tree$node.label == Fn2$bn[i]) + length(tree$tip.label)
if (n > min(tree$edge[,1]))
{
n1 <- tree$edge[which(tree$edge[,2] == n), 1] - length(tree$tip.label)
Fn2$rn[i] <- tree$node.label[n1]
Fn2$rn.bl[i] <- node.dep[Fn2$rn[i]]
}
if (n == min(tree$edge[,1]))
{
Fn2$rn[i] <- Fn2$bn[i]
Fn2$rn.bl[i] <- Fn2$bn.bl[i]
}
}
}
if (dim(xF2)[1] == 0)
{
xF2 <- NULL
}
Fn <- rbind(Fn1, Fn2)
Fn <- merge(Fn, xF[, c("family", "numF")])
Fn <- merge(Fn, xxGS)
Fn <- Fn[, c("level", "family", "genus", "rn", "rn.bl", "bn", "bn.bl", "gen.n", "sp.n", "taxa")]
xG <- tips1[!duplicated(tips1$numG), ]
xG <- xG[rev(order(xG$sizeG)), ]
xG <- xG[!duplicated(xG$genus), ]
xx <- merge(tips1, data.frame(numG = unique(xG$numG)))
xxG <- table(xx$numG)
xxG <- data.frame(numG = as.integer(names(xxG)), gen.n = 1)
xxS <- table(xx$numG)
xxS <- data.frame(numG = as.integer(names(xxS)), sp.n = as.integer(xxS))
xxGS <- merge(xxG, xxS)
xG1 <- xG[xG$sizeG == 1, ]
if (dim(xG1)[1] > 0)
{
Gn1 <- data.frame(level = "G", family = xG1$family, genus = xG1$genus, rn = "", rn.bl = 0, bn = "", bn.bl = 0, taxa = xG1$species, stringsAsFactors = FALSE)
for (i in 1 : dim(Gn1)[1])
{
x0 <- match(Gn1$taxa[i], tree$tip.label)
x1 <- match(x0, tree$edge[, 2])
x2 <- tree$edge[x1, 1] - length(tree$tip.label)
Gn1$bn[i] <- tree$node.label[x2]
Gn1$rn[i] <- tree$node.label[x2]
Gn1$rn.bl[i] <- tree$edge.length[x1]
Gn1$bn.bl[i] <- tree$edge.length[x1]
}
}
if (dim(xG1)[1] == 0)
{
Gn1 <- NULL
}
xG2 <- xG[xG$sizeG > 1, ]
if (dim(xG2)[1] > 0)
{
tipsG <- merge(tips1, data.frame(numG = xG2$numG))
tG <- drop.tip(tree, setdiff(tree$tip.label, tipsG$species))
tipsG <- tipsG[match(tG$tip.label, tipsG$species),]
tG$tip.label <- tipsG$genus
n1 <- which(!duplicated(tG$tip.label))
n2 <- length(tG$tip.label) + 1 - which(!duplicated(rev(tG$tip.label)))
nn <- sort(unique(c(n1, n2)))
tG <- drop.tip(tG, setdiff(1:length(tG$tip.label), nn))
Gn2 <- data.frame(level = "G", family = xG2$family, genus = xG2$genus, rn = "", rn.bl = 0, bn = "", bn.bl = 0, taxa = "", stringsAsFactors = FALSE)
x<-1 : length(tG$tip.label)
for (i in 1 : dim(Gn2)[1])
{
h <- which(tG$tip.label == Gn2$genus[i])
tt <- drop.tip(tG, setdiff(x, h))
Gn2$bn[i] <- tt$node.label
Gn2$bn.bl[i] <- tt$edge.length[1]
n <- which(tree$node.label == Gn2$bn[i]) + length(tree$tip.label)
if (n > min(tree$edge[,1]))
{
n1 <- tree$edge[which(tree$edge[,2] == n), 1] - length(tree$tip.label)
Gn2$rn[i] <- tree$node.label[n1]
Gn2$rn.bl[i] <- node.dep[Gn2$rn[i]]
}
if (n == min(tree$edge[,1]))
{
Gn2$rn[i] <- Gn2$bn[i]
Gn2$rn.bl[i] <- Gn2$bn.bl[i]
}
}
}
if (dim(xG2)[1] == 0)
{
Gn2 <- NULL
}
Gn <- rbind(Gn1, Gn2)
Gn <- merge(Gn, xG[, c("genus", "numG")])
Gn <- merge(Gn, xxGS)
Gn <- Gn[, c("level", "family", "genus", "rn", "rn.bl", "bn", "bn.bl", "gen.n", "sp.n", "taxa")]
nodes <- rbind(Fn, Gn)
return(nodes)
}
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