https://github.com/cran/ape
Tip revision: b8e44dd55faa64ef893b1da841b999c0b0b396f6 authored by Emmanuel Paradis on 13 March 2023, 11:20:09 UTC
version 5.7-1
version 5.7-1
Tip revision: b8e44dd
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{dutheil@evolbio.mpg.de}}
\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}