R: Conversion from Taxonomy Variables to Phylogenetic Trees

as.phylo.formula {ape} | R Documentation

## Conversion from Taxonomy Variables to Phylogenetic Trees

### Description

The function `as.phylo.formula` (short form `as.phylo`) builds a phylogenetic tree (an object of class `phylo`) from a set of nested taxonomic variables.

### Usage

    ## S3 method for class 'formula'
    as.phylo(x, data = parent.frame(), collapse = TRUE, ...)

### Arguments

`x` | a right-side formula describing the taxonomic relationship: `~C1/C2/.../Cn`.
`data` | the data.frame where to look for the variables (default to user's workspace).
`collapse` | a logical value specifying whether to collapse single nodes in the returned tree (see details).
`...` | further arguments to be passed from other methods.

### Details

Taxonomic variables must be nested and passed in the correct order: the higher clade must be on the left of the formula, for instance `~Order/Family/Genus/Species`. In most cases, the resulting tree will be unresolved and will contain polytomies.

The option `collapse = FALSE` has for effect to add single nodes in the tree when a given higher level has only one element in the level below (e.g., a monospecific genus); see the example below.

### Value

an object of class `"phylo"`.

### Author(s)

Julien Dutheil dutheil@evolbio.mpg.de, Eric Marcon and Klaus Schliep

### See Also

`as.phylo`, `read.tree` for a description of `"phylo"` objects, `multi2di`

### Examples

    data(carnivora)
    frm <- ~SuperFamily/Family/Genus/Species
    tr <- as.phylo(frm, data = carnivora, collapse=FALSE)
    tr$edge.length <- rep(1, nrow(tr$edge))
    plot(tr, show.node.label=TRUE)
    Nnode(tr)
    ## compare with:
    Nnode(as.phylo(frm, data = carnivora, collapse = FALSE))

[Package ape version 5.6-2 Index]