1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
\name{PI2newick}
\alias{PI2newick}
\title{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{
\item{x}{is a data frame that contains information on phylogeny topology and trait values}
}
\value{
Returns a list containing :
\item{tre}{: a character string giving the phylogenetic tree in Newick format}
\item{trait}{: a vector containing values of the trait}
}
\references{
Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. \emph{Evolutionary Ecology Research}, \bold{1}, 895--909.
}
\author{Sébastien Ollier \email{sebastien.ollier@u-psud.fr} \cr
Daniel Chessel
}
\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)
}
\keyword{manip}
|
