ade4: PI2newick – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

PI2newick

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)

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release