R: Building Lists of Trees

c.phylo {ape} | R Documentation

## Building Lists of Trees

### Description

These functions help to build lists of trees of class `"multiPhylo"`.

### Usage

    ## S3 method for class 'phylo'
    c(..., recursive = TRUE)
    ## S3 method for class 'multiPhylo'
    c(..., recursive = TRUE)
    .compressTipLabel(x, ref = NULL)
    .uncompressTipLabel(x)

### Arguments

`...` | one or several objects of class `"phylo"` and/or `"multiPhylo"`.
`recursive` | see details.
`x` | an object of class `"phylo"` or `"multiPhylo"`.
`ref` | an optional vector of mode character to constrain the order of the tips. By default, the order from the first tree is used.

### Details

These `c` methods check all the arguments, and return by default a list of single trees unless some objects are not trees or lists of trees, in which case `recursive` is switched to FALSE and a warning message is given. If `recursive = FALSE`, the objects are simply concatenated into a list. Before ape 4.0, `recursive` was always set to FALSE.

`.compressTipLabel` transforms an object of class `"multiPhylo"` by checking that all trees have the same tip labels and renumbering the tips in the `edge` matrix so that the tip numbers are also the same taking the first tree as the reference (duplicated labels are not allowed). The returned object has a unique vector of tip labels (`attr(x, "TipLabel")`).

`.uncompressTipLabel` does the reverse operation.

### Value

An object of class `"multiPhylo"`.

### Author(s)

Emmanuel Paradis

### See Also

`summary.phylo`, `multiphylo`

### Examples

    x <- c(rtree(4), rtree(2))
    x
    y <- c(rtree(4), rtree(4))
    z <- c(x, y)
    z
    print(z, TRUE)
    try(.compressTipLabel(x)) # error
    a <- .compressTipLabel(y)
    .uncompressTipLabel(a) # back to y
    ## eventually compare str(a) and str(y)

[Package ape version 5.1 Index]