PI2newick {ade4} | R Documentation |
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.
PI2newick(x)
x |
is a data frame that contains information on phylogeny topology and trait values |
Returns a list containing :
tre |
: a character string giving the phylogenetic tree in Newick format |
trait |
: a vector containing values of the trait |
Sébastien Ollier sebastien.ollier@u-psud.fr
Daniel Chessel
Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1, 895–909.
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)