https://github.com/cran/ape
Tip revision: cd23fe5fe5692cfe373ecf9400904eb07d5e7636 authored by Emmanuel Paradis on 18 September 2006, 00:00:00 UTC
version 1.8-5
version 1.8-5
Tip revision: cd23fe5
compar.cheverud.Rd
\name{compar.cheverud}
\alias{compar.cheverud}
\title{Cheverud's Comparative Method}
\description{
This function computes the phylogenetic variance component and the residual deviation for continous characters, taking into account the phylogenetic relationships among species, following the comparative method described in Cheverud et al. (1985).
The correction proposed by Rholf (2001) is used.
}
\usage{
compar.cheverud(y, W, tolerance = 1e-06, gold.tol = 1e-04)
}
\arguments{
\item{y}{A vector containing the data to analyse. }
\item{W}{The phylogenetic connectivity matrix.
All diagonal elements will be ignored.}
\item{tolerance}{Minimum difference allowed to consider eigenvalues as distinct.}
\item{gold.tol}{Precision to use in golden section search alogrithm.}
}
\details{
Model: \deqn{y = \rho W y + e}{y = rho.W.y + e}
where \eqn{e}{e} is the error term, assumed to be normally distributed.
\eqn{\rho}{rho} is estimated by the maximum likelihood procedure given in Rohlf (2001),
using a golden section search algorithm.
The code of this function is indeed adapted from a MatLab code given in appendix in Rohlf's article,
to correct a mistake in Cheverud's original paper.
}
\value{
A list with the following components:
\item{rhohat}{The maximum likelihood estimate of \eqn{\rho}{rho}}
\item{Wnorm}{The normalized version of \code{W}}
\item{residuals}{Error terms (\eqn{e}{e})}
}
\references{
Cheverud, J. M., Dow, M. M. and Leutenegger, W. (1985) The quantitative
assessment of phylogenetic constraints in comparative analyses: sexual
dimorphism in body weight among primates. \emph{Evolution},
\bold{39}, 1335--1351.
Rohlf, F. J. (2001) Comparative methods for the analysis of continuous
variables: geometric interpretations. \emph{Evolution}, \bold{55},
2143--2160.
Harvey, P. H. and Pagel, M. D. (1991) \emph{The comparative method in
evolutionary biology}. Oxford University Press.
}
\author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr} }
\seealso{ \code{\link{compar.lynch}}}
\examples{
### Example from Harvey and Pagel's book:
y<-c(10,8,3,4)
W <- matrix(c(1,1/6,1/6,1/6,1/6,1,1/2,1/2,1/6,1/2,1,1,1/6,1/2,1,1), 4)
compar.cheverud(y,W)
### Example from Rohlf's 2001 article:
W<- matrix(c(
0,1,1,2,0,0,0,0,
1,0,1,2,0,0,0,0,
1,1,0,2,0,0,0,0,
2,2,2,0,0,0,0,0,
0,0,0,0,0,1,1,2,
0,0,0,0,1,0,1,2,
0,0,0,0,1,1,0,2,
0,0,0,0,2,2,2,0
),8)
W <- 1/W
W[W == Inf] <- 0
y<-c(-0.12,0.36,-0.1,0.04,-0.15,0.29,-0.11,-0.06)
compar.cheverud(y,W)
}
\keyword{regression}