## summary.phylo.R (2010-11-03)
## Print Summary of a Phylogeny and "multiPhylo" operators
## Copyright 2003-2010 Emmanuel Paradis, and 2006 Ben Bolker
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
Ntip <- function(phy)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
length(phy$tip.label)
}
Nnode <- function(phy, internal.only = TRUE)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
if (internal.only) return(phy$Nnode)
phy$Nnode + length(phy$tip.label)
}
Nedge <- function(phy)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
dim(phy$edge)[1]
}
summary.phylo <- function(object, ...)
{
cat("\nPhylogenetic tree:", deparse(substitute(object)), "\n\n")
nb.tip <- length(object$tip.label)
nb.node <- object$Nnode
cat(" Number of tips:", nb.tip, "\n")
cat(" Number of nodes:", nb.node, "\n")
if (is.null(object$edge.length))
cat(" No branch lengths.\n")
else {
cat(" Branch lengths:\n")
cat(" mean:", mean(object$edge.length), "\n")
cat(" variance:", var(object$edge.length), "\n")
cat(" distribution summary:\n")
print(summary(object$edge.length)[-4])
}
if (is.null(object$root.edge))
cat(" No root edge.\n")
else
cat(" Root edge:", object$root.edge, "\n")
if (nb.tip <= 10) {
cat(" Tip labels:", object$tip.label[1], "\n")
cat(paste(" ", object$tip.label[-1]), sep = "\n")
}
else {
cat(" First ten tip labels:", object$tip.label[1], "\n")
cat(paste(" ", object$tip.label[2:10]), sep = "\n")
}
if (is.null(object$node.label))
cat(" No node labels.\n")
else {
if (nb.node <= 10) {
cat(" Node labels:", object$node.label[1], "\n")
cat(paste(" ", object$node.label[-1]), sep = "\n")
}
else {
cat(" First ten node labels:", object$node.label[1], "\n")
cat(paste(" ", object$node.label[2:10]), sep = "\n")
}
}
if (!is.null(attr(object, "loglik"))) {
cat("Phylogeny estimated by maximum likelihood.\n")
cat(" log-likelihood:", attr(object, "loglik"), "\n\n")
npart <- length(attr(object, "para"))
for (i in 1:npart) {
cat("partition ", i, ":\n", sep = "")
print(attr(object, "para")[[i]])
if (i == 1) next
else cat(" contrast parameter (xi):",
attr(object, "xi")[i - 1], "\n")
}
}
}
### by BB:
print.phylo <- function(x, printlen = 6,...)
{
nb.tip <- length(x$tip.label)
nb.node <- x$Nnode
cat(paste("\nPhylogenetic tree with", nb.tip, "tips and", nb.node,
"internal nodes.\n\n"))
cat("Tip labels:\n")
if (nb.tip > printlen) {
cat(paste("\t", paste(x$tip.label[1:printlen],
collapse=", "), ", ...\n", sep = ""))
} else print(x$tip.label)
if (!is.null(x$node.label)) {
cat("\tNode labels:\n")
if (nb.node > printlen) {
cat(paste("\t", paste(x$node.label[1:printlen],
collapse=", "), ",...\n", sep = ""))
} else print(x$node.label)
}
rlab <- if (is.rooted(x)) "Rooted" else "Unrooted"
cat("\n", rlab, "; ", sep="")
blen <- if (is.null(x$edge.length)) "no branch lengths." else
"includes branch lengths."
cat(blen, "\n", sep = "")
}
print.multiPhylo <- function(x, details = FALSE, ...)
{
N <- length(x)
cat(N, "phylogenetic trees\n")
if (details)
for (i in 1:N)
cat("tree", i, ":", length(x[[i]]$tip.label), "tips\n")
}
"[[.multiPhylo" <- function(x, i)
{
class(x) <- NULL
phy <- x[[i]]
if (!is.null(attr(x, "TipLabel")))
phy$tip.label <- attr(x, "TipLabel")
phy
}
`$.multiPhylo` <- function(x, name) x[[name]]
"[.multiPhylo" <- function(x, i)
{
oc <- oldClass(x)
class(x) <- NULL
structure(x[i], TipLabel = attr(x, "TipLabel"),
class = oc)
}
str.multiPhylo <- function(object, ...)
{
class(object) <- NULL
cat('Class "multiPhylo"\n')
str(object, ...)
}
c.phylo <- function(..., recursive = FALSE)
structure(list(...), class = "multiPhylo")
## only the first object in '...' is checked for its class,
## but that should be OK for the moment
c.multiPhylo <- function(..., recursive = FALSE)
{
obj <- list(...)
n <- length(obj)
x <- obj[[1L]]
N <- length(x)
i <- 1L
while (i < n) {
a <- N + 1L
N <- N + length(obj[[i]])
## x is of class "multiPhylo", so this uses the operator below:
x[a:N] <- obj[[i]]
i <- i + 1L
}
x
}
.uncompressTipLabel <- function(x)
{
Lab <- attr(x, "TipLabel")
if (is.null(Lab)) return(x)
class(x) <- NULL
for (i in 1:length(x)) x[[i]]$tip.label <- Lab
class(x) <- "multiPhylo"
attr(x, "TipLabel") <- NULL
x
}
`[<-.multiPhylo` <- function(x, ..., value)
{
## recycling is allowed so no need to check: length(value) != length(..1)
## check that all elements in 'value' inherit class "phylo"
test <- unlist(lapply(value, function(xx) !inherits(xx, "phylo")))
if (any(test))
stop("at least one element in 'value' is not of class \"phylo\".")
oc <- oldClass(x)
class(x) <- NULL
if (is.null(attr(x, "TipLabel"))) {
x[..1] <- value
class(x) <- oc
return(x)
}
x[..1] <- 0L # in case x needs to be elongated
class(x) <- oc
j <- 1L
for (i in ..1) {
## x is of class "multiPhylo", so this uses the operator below:
x[[i]] <- value[[j]]
j <- j + 1L
}
x
}
`[[<-.multiPhylo` <- function(x, ..., value)
{
if (!inherits(value, "phylo"))
stop('trying to assign an object not of class "phylo" into an object of class "multiPhylo".')
oc <- oldClass(x)
class(x) <- NULL
Lab <- attr(x, "TipLabel")
if (!is.null(Lab)) {
n <- length(Lab)
if (n != length(value$tip.label))
stop("tree with different number of tips than those in the list (which all have the same labels; maybe you want to uncompress them)")
o <- match(value$tip.label, Lab)
if (any(is.na(o)))
stop("tree tip labels do not match with those in the list; maybe you want to uncompress them.")
value$tip.label <- NULL
ie <- match(o, value$edge[, 2])
value$edge[ie, 2] <- 1:n
}
x[[..1]] <- value
class(x) <- oc
x
}
`$<-.multiPhylo` <- function(x, ..., value)
{
x[[..1]] <- value
x
}
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