write.tree {ape} | R Documentation |
Write Tree File in Parenthetic Format
Description
This function writes in a file a tree in parenthetic format using the Newick (also known as New Hampshire) format.
Usage
write.tree(phy, file = "", append = FALSE,
digits = 10, tree.names = FALSE)
Arguments
phy |
an object of class |
file |
a file name specified by either a variable of mode character,
or a double-quoted string; if |
append |
a logical, if |
digits |
a numeric giving the number of (significant) digits used for printing branch lengths (see details). For negative numbers no branch lengths are printed. |
tree.names |
either a logical or a vector of mode character. If
|
Details
The node labels and the root edge length, if available, are written in the file.
If tree.names == TRUE
then a variant of the Newick format is
written for which the name of a tree precedes the Newick format tree
(parentheses are eventually deleted beforehand). The tree names are
taken from the names
attribute if present (they are ignored if
tree.names
is a character vector).
The tip labels (and the node labels if present) are checked before being printed: the leading and trailing spaces, and the leading left and trailing right parentheses are deleted; the other spaces are replaced by underscores; the commas, colons, semicolons, and the other parentheses are replaced with dashes.
The argument digits
gives the number of significant
digits (not rounding). For instance, if digits = 2
the branch
length 1.234e-7 is printed as 1.23e-7 (not 0).
Value
a vector of mode character if file = ""
, none (invisible
NULL
) otherwise.
Author(s)
Emmanuel Paradis, Daniel Lawson dan.lawson@bristol.ac.uk, and Klaus Schliep klaus.schliep@gmail.com
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
read.tree
, read.nexus
,
write.nexus
, write.phyloXML