| read.tree {ape} | R Documentation |
This function reads a file which contains one or several trees in parenthetic format known as the Newick or New Hampshire format.
read.tree(file = "", text = NULL, tree.names = NULL,
skip = 0, comment.char = "#", ...)
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. |
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 NULL, then the argument
file is ignored. |
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 to scan()). |
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(). |
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.
an object of class "phylo" with the following components:
edge |
a two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numbered 1, 2, ..., and the nodes are numbered after the tips. For each row, the first column gives the ancestor. |
edge.length |
(optional) a numeric vector giving the lengths of the
branches given by edge. |
tip.label |
a 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. |
Nnode |
the number of (internal) nodes. |
node.label |
(optional) a vector of mode character giving the names of the nodes. |
root.edge |
(optional) a numeric value giving the length of the branch at the root if it exists. |
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".
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
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
Paradis, E. (2006) Definition of Formats for Coding Phylogenetic Trees in R. http://pbil.univ-lyon1.fr/R/ape/misc/FormatTreeR_4Dec2006.pdf
write.tree, read.nexus,
write.nexus, scan for the basic R
function to read data in a file
### 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 = "\n")
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