Read a newick formatted phylogenetic tree.

A phylogenetic tree is required for computing UniFrac distance matrices. You can load a tree from a file or by providing the tree string directly. This tree must be in Newick format, also known as parenthetic format and New Hampshire format.

Usage

read_tree(src, underscores = FALSE)

Arguments

src

Input data as either a file path, URL, or Newick string. Compressed (gzip or bzip2) files are also supported.

underscores

When parsing the tree, should underscores be kept as is? By default they will be converted to spaces (unless the entire ID is quoted). Default FALSE

Value

A phylo class object representing the tree.

Details

Labels may be enclosed in single quotes, following the Newick standard: inside quotes every character is literal (including ( ) [ ] : ; , and whitespace), and '' stands for one apostrophe. Quoted labels are never altered by underscores. Outside quotes, [...] is a comment and is ignored. [write_tree()] quotes labels the same way, so trees round-trip exactly.

[ ]: R:%20 [...]: R:... [write_tree()]: R:write_tree()

See also

Other phylogeny: tree_subset()

Examples

    library(rbiom)

    infile <- system.file("extdata", "newick.tre", package = "rbiom")
    tree <- read_tree(infile)
    print(tree)
#> 
#> Phylogenetic tree with 20 tips and 19 internal nodes.
#> 
#> Tip labels:
#>   Pa5Bac29, AtlPorci, AciSp313, MxlBact8, MxlBacte, PseS1107, ...
#> 
#> Rooted; includes branch length(s).

    tree <- read_tree("
        (A:0.99,((B:0.87,C:0.89):0.51,(((D:0.16,(E:0.83,F:0.96)
        :0.94):0.69,(G:0.92,(H:0.62,I:0.85):0.54):0.23):0.74,J:0.1
        2):0.43):0.67);")

    # Plotting a tree requires the 'ape' package.
    if (requireNamespace("ape", quietly = TRUE))
      ape::plot.phylo(tree)