read.tree: Read Tree File in Parenthetic Format

Description

This function reads a file which contains one or several trees in parenthetic format known as the Newick or New Hampshire format.

Usage

read.tree(file = "", format = "Newick", rooted = TRUE, text = NULL,
          tree.names = NULL, skip = 0, comment.char = "#", ...)

Arguments

file

a file name specified by either a variable of mode character, or a double-quoted string; if file = "" (the default) then the tree is input on the keyboard, the entry being terminated with a blank line.

format

a character giving the format of the tree file; by default "Newick". Currently only the Newick format is available.

rooted

a logical indicating whether the tree is rooted or not; defaults to TRUE. This is currently not implemented, meaning that all trees are read as rooted.

text

alternatively, the name of a variable of mode character which contains the tree(s) in parenthetic format. By default, this is ignored (set to NULL, meaning that the tree is read in a file); if text is not NUL

tree.names

if there are several trees to be read, a vector of mode character that gives names to the individual trees; if NULL (the default), the trees are named "tree1", "tree2", ...

skip

the number of lines of the input file to skip before beginning to read data (this is passed directly toscan()).

comment.char

a single character, the remaining of the line after this character is ignored (this is passed directly to scan()).

...

Further arguments to be passed to scan().

Value

an object of class "phylo" with the following components:
edgea two-column matrix of mode character where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers (these numbers are not treated as numeric, hence the mode character); the nodes are represented with negative numbers (the root being "-1"), and the tips are represented with positive numbers. For each row, the first column gives the ancestor. This representation allows an easy manipulation of the tree, particularly if it is rooted.
edge.length(optional) a numeric vector giving the lengths of the branches given by edge.
tip.labela vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in edge.
node.label(optional) a vector of mode character giving the names of the nodes (set to NULL if not available in the file).
root.edge(optional) a numeric value giving the length of the branch at the root is it exists (NULL otherwise).
If several trees are read in the file, the returned object is of class c("phylo", "multi.tree"), and is a list of objects of class "phylo".

Details

The default option for file allows to type directly the tree on the keyboard (or possibly to copy from an editor and paste in R's console) with, e.g., mytree <- read.tree().

References

http://evolution.genetics.washington.edu/phylip/newick_doc.html http://evolution.genetics.washington.edu/phylip/newicktree.html

Examples

Run this code

### An extract from Sibley and Ahlquist (1990)
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
   "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
   file = "ex.tre", sep = "")
tree.owls <- read.tree("ex.tre")
str(tree.owls)
tree.owls
unlink("ex.tre") # delete the file "ex.tre"
### Only the first three species using the option `text'
TREE <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
TREE
tree.owls.bis <- read.tree(text = TREE)
str(tree.owls.bis)
tree.owls.bis

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