read_tree: Load a tree from a string or file in Newick (parenthetic) format.

Description

Load a phylogenetic tree from a file or a string, in Newick (parenthetic) format. Any valid Newick format is acceptable.

Usage

read_tree(  string  = "", 
            file    = "", 
            include_edge_lengths    = TRUE, 
            include_node_labels     = TRUE, 
            underscores_as_blanks   = FALSE, 
            check_label_uniqueness  = FALSE)

Arguments

string

A string containing a single tree in Newick format. Can be used alternatively to file.

file

A path to an input text file containing a single tree in Newick format. Can be used alternatively to string.

include_edge_lengths

Logical, specifying whether edge lengths (if available) should be included in the generated tree.

include_node_labels

Logical, specifying whether node labels (if available) should be included in the generated tree.

underscores_as_blanks

Logical, specifying whether underscores ("_") in tip and node labels should be replaced by spaces (" "). This is common behavior in other tree parsers. In any case, tip and node labels are also allowed to contain explicit whitespace (other than newlines).

check_label_uniqueness

Logical, specifying whether to check if all tip labels are unique.

Value

A single rooted phylogenetic tree in ``phylo'' format.

Details

This function is comparable to (but typically much faster than) the ape function read.tree. The function supports trees with monofurcations and multifurcations, trees with or without tip/node labels, and trees with or without edge lengths. The time complexity is linear in the number of edges in the tree.

Either file or string must be specified, but not both. The tree may be arbitrarily split across multiple lines, but no other non-whitespace text is permitted in string or in the input file. Flanking whitespace (space, tab, newlines) is ignored.

Examples

Run this code

# NOT RUN {
# 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)

# re-parse tree from string
parsed_tree = read_tree(Newick_string)
# }