https://github.com/cran/ape
Tip revision: 1330e272d62c723b8073c95b066950b294f59697 authored by Emmanuel Paradis on 20 October 2012, 00:00:00 UTC
version 3.0-6
version 3.0-6
Tip revision: 1330e27
varCompPhylip.Rd
\name{varCompPhylip}
\alias{varCompPhylip}
\title{Variance Components with Orthonormal Contrasts}
\description{
This function calls Phylip's contrast program and returns the
phylogenetic and phenotypic variance-covariance components for one or
several traits. There can be several observations per species.
}
\usage{
varCompPhylip(x, phy, exec = NULL)
}
\arguments{
\item{x}{a numeric vector, a matrix (or data frame), or a list.}
\item{phy}{an object of class \code{"phylo"}.}
\item{exec}{a character string giving the name of the executable
contrast program (see details).}
}
\details{
The data \code{x} can be in several forms: (i) a numeric vector if
there is single trait and one observation per species; (ii) a
matrix or data frame if there are several traits (as columns) and a
single observation of each trait for each species; (iii) a list of
vectors if there is a single trait and several observations per
species; (iv) a list of matrices or data frames: same than (ii) but
with several traits and the rows are individuals.
If \code{x} has names, its values are matched to the tip labels of
\code{phy}, otherwise its values are taken to be in the same order
than the tip labels of \code{phy}.
Phylip (version 3.68 or higher) must be accessible on your computer. If
you have a Unix-like operating system, the executable name is assumed
to be \code{"phylip contrast"} (as in Debian); otherwise it is set
to \code{"contrast"}. If this doesn't suit your system, use the
option \code{exec} accordingly. If the executable is not in the path, you
may need to specify it, e.g., \code{exec = "C:/Program Files/Phylip/contrast"}.
}
\value{
a list with elements \code{varA} and \code{varE} with the phylogenetic
(additive) and phenotypic (environmental) variance-covariance
matrices. If a single trait is analyzed, these contains its variances.
}
\references{
Felsenstein, J. (2004) Phylip (Phylogeny Inference Package) version
3.68. Department of Genetics, University of Washington, Seattle, USA.
\url{http://evolution.genetics.washington.edu/phylip/phylip.html}.
Felsenstein, J. (2008) Comparative methods with sampling error and
within-species variation: Contrasts revisited and revised.
\emph{American Naturalist}, \bold{171}, 713--725.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{pic}}, \code{\link{pic.ortho}}, \code{\link{compar.lynch}}
}
\examples{
\dontrun{
tr <- rcoal(30)
### Five traits, one observation per species:
x <- replicate(5, rTraitCont(tr, sigma = 1))
varCompPhylip(x, tr) # varE is small
x <- replicate(5, rnorm(30))
varCompPhylip(x, tr) # varE is large
### Five traits, ten observations per species:
x <- replicate(30, replicate(5, rnorm(10)), simplify = FALSE)
varCompPhylip(x, tr)
}}
\keyword{regression}