R: Import data files from Phylogenetic Independance Package

PI2newick {ade4} | R Documentation

## Import data files from Phylogenetic Independance Package

### Description

This function ensures to transform a data set written for the Phylogenetic Independance package of Abouheif (1999) in a data set formatting for the functions of ade4.

### Usage

    PI2newick(x)

### Arguments

`x` | is a data frame that contains information on phylogeny topology and trait values

### Value

Returns a list containing :

`tre` | : a character string giving the phylogenetic tree in Newick format
`trait` | : a vector containing values of the trait

### Author(s)

Sébastien Ollier sebastien.ollier@u-psud.fr
Daniel Chessel

### References

Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1, 895–909.

### Examples

    x <- c(2.0266, 0.5832, 0.2460, 1.2963, 0.2460, 0.1565, -99.0000,
            -99.0000, 10.1000, -99.0000,  20.2000,  28.2000, -99.0000,
            14.1000, 11.2000, -99.0000, 21.3000, 27.5000, 1.0000, 2.0000,
            -1.0000, 4.0000, -1.0000, -1.0000, 3.0000, -1.0000, -1.0000,
            5.0000, -1.0000, -1.0000, 0.0000, 0.0000, 0.0000, 0.0000,
            0.0000, 0.0000)
    x <- matrix(x, nrow = 6)
    x <- as.data.frame(x)
    res <- PI2newick(x)
    dotchart.phylog(newick2phylog(res$tre), res$trait)

[Package ade4 version 1.7-8 Index]