ape (version 1.8-4)

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 = "#", ...)

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 if it exists (NULL otherwise).If several trees are read in the file, the returned object is of class c("multi.tree", "phylo"), 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().

`read.tree' tries to represent correctly trees with a badly represented root edge (i.e. with an extra pair of parentheses). For instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;" but a warning message will be issued in the former case as this is apparently not a valid Newick format. If there are two root edges (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error message is issued.

References

Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html

Olsen, G. Interpretation of the "Newick's 8:45" tree format standard. http://evolution.genetics.washington.edu/phylip/newick_doc.html

See Also

write.tree, read.nexus, write.nexus, scan for the basic R function to read data in a file

Examples

### 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