https://github.com/cran/ape
Tip revision: 8e1bbb098540840e05975fc46ab4a39ffa3add40 authored by Emmanuel Paradis on 23 February 2003, 00:00:00 UTC
version 1.0
version 1.0
Tip revision: 8e1bbb0
compar.lynch.Rd
\name{compar.lynch}
\alias{compar.lynch}
\title{Lynch's Comparative Method}
\usage{
compar.lynch(x, G, eps = 1e-4)
}
\arguments{
\item{x}{eiher a matrix, a vector, or a data.frame containing the data
with species as rows and variables as columns.}
\item{G}{a matrix that can be interpreted as an among-species correlation
matrix.}
\item{eps}{a numeric value to detect convergence of the EM algorithm.}
}
\description{
This function computes the heritable additive value and the residual
deviation for continous characters, taking into account the
phylogenetic relationships among species, following the comparative
method described in Lynch (1991).
}
\details{
The parameter estimates are computed following the EM
(expectation-maximization) algorithm. This algorithm usually leads to
convergence but may lead to local optima of the likelihood
function. It is recommended to run several times the function in order
to detect these potential local optima. The `optimal' value for
\code{eps} depends actually on the range of the data and may be
changed by the user in order to check the stability of the parameter
estimates. Convergence occurs when the differences between two
successive iterations of the EM algorithm leads to differences between
both residual and additive values less than or equal to \code{eps}.
}
\note{
The present function does not perform the estimation of ancestral
phentoypes as proposed by Lynch (1991). This will be implemented in
a future version.
}
\value{
A list with the following components:
\item{vare}{estimated residual variance-covariance matrix.}
\item{vara}{estimated additive effect variance covariance matrix.}
\item{u}{estimates of the phylogeny-wide means.}
\item{A}{addtitive value estimates.}
\item{E}{residual values estimates.}
\item{lik}{logarithm of the likelihood for the entire set of observed
taxon-specific mean.}
}
\references{
Lynch, M. (1991) Methods for the analysis of comparative data in
evolutionary biology. \emph{Evolution}, \bold{45}, 1065--1080.
}
\author{Julien Claude \email{claude@isem.univ-montp2.fr}}
\seealso{
\code{\link{pic}}, \code{\link{compar.gee}}
}
\examples{
### The example in Lynch (1991)
cat("((((Homo:0.21,Pongo:0.21):0.28,",
"Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
file = "ex.tre", sep = "\n")
tree.primates <- read.tree("ex.tre")
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
compar.lynch(cbind(X, Y),
G = vcv.phylo(tree.primates, cor = TRUE))
}
\keyword{regression}