diversi.gof.Rd
\name{diversi.gof}
\alias{diversi.gof}
\title{Tests of Constant Diversification Rates}
\usage{
diversi.gof(x, null = "exponential", z = NULL)
}
\arguments{
\item{x}{a numeric vector with the branching times.}
\item{null}{a character string specifying the null distribution for
the branching times. Only two choices are possible: either
\code{"exponential"}, or \code{"user"}.}
\item{z}{used if \code{null = "user"}; gives the expected distribution
under the model.}
}
\description{
This function computes two tests of the distribution of branching
times using the Cramťr-von Mises and Anderson-Darling goodness-of-fit
tests. By default, it is assumed that the diversification rate is
constant, and an exponential distribution is assumed for the branching
times. In this case, the expected distribution under this model is
computed with a rate estimated from the data. Alternatively, the user
may specify an expected cumulative density function (\code{z}): in this
case, \code{x} and \code{z} must be of the same length.
}
\details{
The Cramťr-von Mises and Anderson-Darling tests compare the empirical
density function (EDF) of the observations to an expected cumulative
density function. By contrast to the Kolmogorov--Smirnov test where
the greatest difference between these two functions is used, in both
tests all differences are taken into account.
The distributions of both test statistics depend on the null
hypothesis, and on whether or not some parameters were estimated from
the data. However, these distributions are not known precisely and
critical values were determined by Stephens (1974) using
simulations. These critical values were used for the present function.
}
\value{
A NULL value is returned, the results are simply printed.
}
\references{
Paradis, E. (1998) Testing for constant diversification rates using
molecular phylogenies: a general approach based on statistical tests
for goodness of fit. \emph{Molecular Biology and Evolution},
\bold{15}, 476--479.
Stephens, M. A. (1974) EDF statistics for goodness of fit and some
comparisons. \emph{Journal of American Statistical Association},
\bold{69}, 730--737.
}
\author{Emmanuel Paradis \email{paradis@isem.univ-montp2.fr}}
\seealso{
\code{\link{branching.times}}, \code{\link{diversi.time}}
\code{\link{ltt.plot}}, \code{\link{birthdeath}}
}
\keyword{univar}