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## as.phylo.R (2021-05-05)
## Conversion Among Tree Objects
## Copyright 2005-2021 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
old2new.phylo <- function(phy)
{
mode(phy$edge) <- "numeric"
phy$Nnode <- -min(phy$edge)
n <- length(phy$tip.label)
NODES <- phy$edge < 0
phy$edge[NODES] <- n - phy$edge[NODES]
phy
}
new2old.phylo <- function(phy)
{
NTIP <- length(phy$tip.label)
NODES <- phy$edge > NTIP
phy$edge[NODES] <- NTIP - phy$edge[NODES]
mode(phy$edge) <- "character"
phy$Nnode <- NULL
phy
}
as.phylo <- function (x, ...)
{
if (identical(class(x), "phylo")) return(x)
UseMethod("as.phylo")
}
as.phylo.default <- function(x, ...)
{
if (inherits(x, "phylo")) return(x)
stop('object does not inherit the class "phylo": found no appropriate method to convert it')
}
as.phylo.hclust <- function(x, ...)
{
N <- dim(x$merge)[1]
edge <- matrix(0L, 2*N, 2)
edge.length <- numeric(2*N)
## `node' gives the number of the node for the i-th row of x$merge
node <- integer(N)
node[N] <- N + 2L
cur.nod <- N + 3L
j <- 1L
for (i in N:1) {
edge[j:(j + 1), 1] <- node[i]
for (l in 1:2) {
k <- j + l - 1L
y <- x$merge[i, l]
if (y > 0) {
edge[k, 2] <- node[y] <- cur.nod
cur.nod <- cur.nod + 1L
edge.length[k] <- x$height[i] - x$height[y]
} else {
edge[k, 2] <- -y
edge.length[k] <- x$height[i]
}
}
j <- j + 2L
}
if (is.null(x$labels))
x$labels <- as.character(1:(N + 1))
obj <- list(edge = edge, edge.length = edge.length / 2,
tip.label = x$labels, Nnode = N)
class(obj) <- "phylo"
reorder(obj)
}
as.phylo.phylog <- function(x, ...)
{
tr <- read.tree(text = x$tre)
n <- length(tr$tip.label)
edge.length <- numeric(dim(tr$edge)[1])
term <- which(tr$edge[, 2] <= n)
inte <- which(tr$edge[, 2] > n)
edge.length[term] <- x$leaves[tr$tip.label]
edge.length[inte] <- x$nodes[tr$node.label][-1]
tr$edge.length <- edge.length
if (x$nodes["Root"] != 0) {
tr$edge.root <- x$nodes["Root"]
names(tr$edge.root) <- NULL
}
tr
}
as.hclust.phylo <- function(x, ...)
{
if (!is.ultrametric(x)) stop("the tree is not ultrametric")
if (!is.binary.phylo(x)) stop("the tree is not binary")
if (!is.rooted(x)) stop("the tree is not rooted")
n <- length(x$tip.label)
if (n == 1) stop("needs n >= 2 observations for a classification")
is_tip <- x$edge[,2] <= n
order <- x$edge[is_tip, 2]
if (n == 2) {
m <- matrix(c(-1L, -2L), 1, 2)
bt <- x$edge.length[1]
} else {
x$node.label <- NULL # by Jinlong Zhang (2010-12-15)
bt <- branching.times(x)
N <- n - 1L
x <- reorder(x, "postorder")
m <- matrix(x$edge[, 2], N, 2, byrow = TRUE)
anc <- x$edge[c(TRUE, FALSE), 1]
bt <- bt[as.character(anc)] # 1st, reorder
## 2nd, sort keeping the root branching time in last (in case of
## rounding error if there zero-lengthed branches nead the root)
bt <- c(sort(bt[-N]), bt[N])
o <- match(names(bt), anc)
m <- m[o, ]
## first renumber the tips:
TIPS <- m <= n
m[TIPS] <- -m[TIPS]
## then renumber the nodes:
oldnodes <- as.numeric(names(bt))[-N]
m[match(oldnodes, m)] <- 1:(N - 1)
names(bt) <- NULL
}
obj <- list(merge = m, height = 2*bt, order = order, labels = x$tip.label,
call = match.call(), method = "unknown")
class(obj) <- "hclust"
obj
}
if (getRversion() >= "2.15.1") utils::globalVariables(c("network", "network.vertex.names<-"))
as.network.phylo <- function(x, directed = is.rooted(x), ...)
{
if (is.null(x$node.label)) x <- makeNodeLabel(x)
res <- network(x$edge, directed = directed, ...)
network.vertex.names(res) <- c(x$tip.label, x$node.label)
res
}
as.igraph.phylo <- function(x, directed = is.rooted(x), use.labels = TRUE, ...)
{
## local copy because x will be changed before evaluating is.rooted(x):
directed <- directed
if (use.labels) {
if (is.null(x$node.label)) x <- makeNodeLabel(x)
## check added by Klaus:
if (anyDuplicated(c(x$tip.label, x$node.label)))
stop("Duplicated labels!")
x$edge <- matrix(c(x$tip.label, x$node.label)[x$edge], ncol = 2)
}
igraph::graph_from_edgelist(x$edge, directed = directed)
}
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