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)

S├ębastien Ollier ollier@biomserv.univ-lyon1.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)

Worked out examples


> library(ade4)
> ### Name: PI2newick
> ### Title: Import data files from Phylogenetic Independance Package
> ### Aliases: PI2newick
> ### Keywords: manip
> 
> ### ** 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 Index]