readPhySim.tree {PhySim}R Documentation

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

readPhySim.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 to read trees in Nexus files).
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 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().

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.

Note

phylogenetic tree information in PhySim is stored in objects of class phylo compatible with old versions of APE (<=1.8-4) but in a format no longer usable by that program. In order to read in phylogenetic trees generated by APE into PhySim first write the tree using APE function write.tree and then read the tree into PhySim using readPhySim.tree.

readPhySim.tree and this help file are derived from read.tree and its helpfile obtained from old versions of the package APE (<=1.8-4) by Emmanuel Paradis.

Author(s)

Emmanuel Paradis wrote the original code

See Also

writePhySim.tree, to write a phylogenetic tree to a file


[Package PhySim version 1.0 Index]