PI2newick: Import data files from Phylogenetic Independance Package

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

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 [e-mail]
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)

ade4 documentation built on May 2, 2019, 5:50 p.m.