R: Read a Newick tree

readTree {treeman} | R Documentation

## Read a Newick tree

### Description

Return a `TreeMan` or `TreeMen` object from a Newick treefile

### Usage

    readTree(
      file = NULL,
      text = NULL,
      spcl_slt_nm = "Unknown",
      wndmtrx = FALSE,
      parallel = FALSE,
      progress = "none"
    )

### Arguments

`file` | file path
`text` | Newick character string
`spcl_slt_nm` | name of special slot for internal node labels, default 'Unknown'.
`wndmtrx` | T/F add node matrix? Default FALSE.
`parallel` | logical, make parallel?
`progress` | name of the progress bar to use, see `create_progress_bar`

### Details

Read a single or multiple trees from a file, or a text string. Parallelizable when reading multiple trees. The function will add any internal node labels in the Newick tree as a user-defined data slots. The name of this slot is defined with the `spcl_slt_nm`. These data can be accessed/manipulated with the ``getNdsSlt()`` function. Trees are always read as rooted. (Unrooted trees have polytomous root nodes.)

### See Also

https://en.wikipedia.org/wiki/Newick_format, `addNdmtrx`, `writeTree`, `randTree`, `readTrmn`, `writeTrmn`, `saveTreeMan`, `loadTreeMan`

### Examples

    library(treeman)
    # tree string with internal node labels as bootstrap results
    tree <- readTree(text="((A:1.0,B:1.0)0.9:1.0,(C:1.0,D:1.0)0.8:1.0)0.7:1.0;",
    spcl_slt_nm='bootstrap')
    # retrieve bootstrap values by node
    tree['bootstrap']

[Package treeman version 1.1.4 Index]