write_tree: Write a tree in Newick (parenthetic) format.

In castor: Efficient Phylogenetics on Large Trees

Write a tree in Newick (parenthetic) format.

Description

Write a phylogenetic tree to a file or a string, in Newick (parenthetic) format. If the tree is unrooted, it is first rooted internally at the first node.

Usage

write_tree (tree, 
            file                 = "",
            append               = FALSE,
            digits               = 10,
            quoting              = 0,
            include_edge_labels  = FALSE,
            include_edge_numbers = FALSE)

Arguments

tree	A tree of class "phylo".
file	An optional path to a file, to which the tree should be written. The file may be overwritten without warning. If left empty (default), then a string is returned representing the tree.
append	Logical, specifying whether the tree should be appended at the end of the file, rather than replacing the entire file (if it exists).
digits	Integer, number of significant digits for writing edge lengths.
quoting	Integer, specifying whether and how to quote tip/node/edge names, as follows: 0:no quoting at all, 1:always use single quotes, 2:always use double quotes, -1:only quote when needed and prefer single quotes if possible, -2:only quote when needed and prefer double quotes if possible.
include_edge_labels	Logical, specifying whether to include edge labels (if available) in the output tree, inside square brackets. Note that this is an extension (Matsen et al. 2012) to the standard Newick format, as, and edge labels in square brackets may not be supported by all Newick readers.
include_edge_numbers	Logical, specifying whether to include edge numbers (if available) in the output tree, inside curly braces. Note that this is an extension (Matsen et al. 2012) to the standard Newick format, and edge numbers in curly braces may not be supported by all Newick readers.

Details

If your tip and/or node and/or edge labels contain special characters (round brackets, commas, colons or quotes) then you should set quoting to non-zero, as appropriate.

If the tree contains edge labels (as a character vector named edge.label) and include_edge_labels==TRUE, then edge labels are written in square brackets (Matsen et al. 2012). If tree contains edge numbers (as an integer vector named edge.number) and include_edge_numbers==TRUE, then edge numbers are written in curly braces (Matsen et al. 2012).

This function is comparable to (but typically much faster than) the ape function write.tree.

Value

If file=="", then a string is returned containing the Newick representation of the tree. Otherwise, the tree is directly written to the file and no value is returned.

Author(s)

Stilianos Louca

References

Frederick A. Matsen et al. (2012). A format for phylogenetic placements. PLOS One. 7:e31009

See Also

read_tree

Examples

# generate a random tree
tree = generate_random_tree(list(birth_rate_intercept=1),max_tips=100)$tree

# obtain a string representation of the tree in Newick format
Newick_string = write_tree(tree)

castor documentation built on Aug. 18, 2023, 1:07 a.m.