read.caic {ape} | R Documentation

## Read Tree File in CAIC Format

### Description

This function reads one tree from a CAIC file. A second file containing branch lengths values may also be passed (experimental).

### Usage

    read.caic(file, brlen = NULL, skip = 0, comment.char = "#", ...)

### Arguments

`file` | a file name specified by either a variable of mode character, or a double-quoted string.
`brlen` | a file name for the branch lengths file.
`skip` | the number of lines of the input file to skip before beginning to read data (this is passed directly to scan()).
`comment.char` | a single character, the remaining of the line after this character is ignored (this is passed directly to scan()).
`...` | Further arguments to be passed to scan().

### Details

Read a tree from a file in the format used by the CAIC and MacroCAIc program.

### Value

an object of class `"phylo"`.

### Warning

The branch length support is still experimental and was not fully tested.

### Author(s)

Julien Dutheil julien.dutheil@univ-montp2.fr

### References

Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. CABIOS, 11 :241–251.

### See Also

`read.tree`, `read.nexus`

### Examples

    ### The same example than in read.tree, without branch lengths.
    ### An extract from Sibley and Ahlquist (1990)
    cat("AAA","Strix_aluco","AAB","Asio_otus",
       "AB","Athene_noctua","B","Tyto_alba",
       file = "ex.tre", sep = "\n")
    tree.owls <- read.caic("ex.tre")
    plot(tree.owls)
    tree.owls
    unlink("ex.tre") # delete the file "ex.tre"

[Package ape version 5.0 Index]