read_tree {phyloseq} | R Documentation

## Somewhat flexible tree-import function

### Description

This function is a convenience wrapper around the `read.tree` (Newick-format) and `read.nexus` (Nexus-format) importers provided by the `ape-package`. This function attempts to return a valid tree if possible using either format importer. If it fails, it silently returns `NULL` by default, rather than throwing a show-stopping error.

### Usage

    read_tree(treefile, errorIfNULL=FALSE, ...)

### Arguments

`treefile` | (Required). A character string implying a file `connection` (like a path or URL), or an actual `connection`. Must be a Newick- or Nexus-formatted tree.
`errorIfNULL` | (Optional). Logical. Should an error be thrown if no tree can be extracted from the connection? Default is `FALSE`, indicating that `NULL` will be SILENTLY returned, rather than an error. Be cautious about this behavior. Useful for phyloseq internals, but might be hard to track in your own code if you're not aware of this “no error by default” setting. If this is a problem, change this value to `TRUE`, and you can still use the function.
`...` | (Optional). Additional parameter(s) passed to the relevant tree-importing function.

### Value

If successful, returns a `phylo`-class object as defined in the `ape-package`. Returns NULL if neither tree-reading function worked.

### See Also

`read_tree_greengenes`

`phylo`

`read.tree`

`read.nexus`

### Examples

    read_tree(system.file("extdata", "esophagus.tree.gz", package="phyloseq"))
    read_tree(system.file("extdata", "GP_tree_rand_short.newick.gz", package="phyloseq"))

[Package phyloseq version 1.28.0 Index]