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
slowinskiguyer.test.Rd
\name{slowinskiguyer.test}
\alias{slowinskiguyer.test}
\title{Slowinski-Guyer Test of Homogeneous Diversification}
\description{
This function performs the Slowinski--Guyer test that a trait or
variable does not increase diversification rate.
}
\usage{
slowinskiguyer.test(x, detail = FALSE)
}
\arguments{
\item{x}{a matrix or a data frame with at least two columns: the first
one gives the number of species in clades with a trait supposed to
increase diversification rate, and the second one the number of
species in the corresponding sister-clade without the trait. Each
row represents a pair of sister-clades.}
\item{detail}{if \code{TRUE}, the individual P-values are appended.}
}
\details{
The Slowinski--Guyer test compares a series of sister-clades where one
of the two is characterized by a trait supposed to increase
diversification rate. The null hypothesis is that the trait does not
affect diversification. If the trait decreased diversification rate,
then the null hypothesis cannot be rejected.
The present function has mainly a historical interest. The
Slowinski--Guyer test generally performs poorly: see Paradis (2012)
alternatives and the functions cited below.
}
\value{
a data frame with the \eqn{\chi^2}{chi2}, the number of degrees of
freedom, and the \emph{P}-value. If \code{detail = TRUE}, a list is
returned with the data frame and a vector of individual
\emph{P}-values for each pair of sister-clades.
}
\references{
Paradis, E. (2012) Shift in diversification in sister-clade
comparisons: a more powerful test. \emph{Evolution}, \bold{66},
288--295.
Slowinski, J. B. and Guyer, C. (1993) Testing whether certain traits
have caused amplified diversification: an improved method based on a
model of random speciation and extinction. \emph{American Naturalist},
\bold{142}, 1019--1024.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{balance}}, \code{\link{mcconwaysims.test}},
\code{\link{diversity.contrast.test}},
\code{\link{richness.yule.test}},
\code{\link[geiger]{rc}} in \pkg{geiger},
\code{\link[apTreeshape]{shift.test}} in \pkg{apTreeshape}
}
\examples{
### from Table 1 in Slowinski and Guyer(1993):
viviparous <- c(98, 8, 193, 36, 7, 128, 2, 3, 23, 70)
oviparous <- c(234, 17, 100, 4, 1, 12, 6, 1, 481, 11)
x <- data.frame(viviparous, oviparous)
slowinskiguyer.test(x, TRUE) # 'P ~ 0.32' in the paper
xalt <- x
xalt[3, 2] <- 1
slowinskiguyer.test(xalt)
}
\keyword{htest}