+\name{diversity.contrast.test}
+\alias{diversity.contrast.test}
+\title{Diversity Contrast Test}
+\description{
+ This function performs the diversity contrast test comparing pairs of
+ sister-clades.
+}
+\usage{
+diversity.contrast.test(x, method = "ratiolog",
+ alternative = "two.sided", nrep = 0, ...)
+}
+\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 or decrease diversification rate, and the second one the number of
+ species in the sister-clades without the trait. Each
+ row represents a pair of sister-clades.}
+ \item{method}{a character string specifying the kind of test: \code{"ratiolog"} (default),
+ \code{"proportion"}, \code{"difference"}, or any unambiguous
+ abbreviation of these.}
+ \item{alternative}{a character string defining the alternative
+ hypothesis: \code{"two.sided"} (default), \code{"less"},
+ \code{"greater"}, or any unambiguous abbreviation of these.}
+ \item{nrep}{the number of replications of the randomization test; by
+ default, a Wilcoxon test is done.}
+ \item{\dots}{arguments passed to the function \code{\link[stats]{wilcox.test}}.}
+}
+\details{
+ If \code{method = "ratiolog"}, the test described in Barraclough et
+ al. (1996) is performed. If \code{method = "proportion"}, the version
+ in Barraclough et al. (1995) is used. If \code{method = "difference"},
+ then this is Wiegmann et al.'s (1993) version. Vamosi and Vamosi (2005)
+ gave a detailed account of these three tests which are essentially
+ different versions of the same test.
+
+ If \code{nrep = 0}, a Wilcoxon test is done on the species diversity
+ contrasts with the null hypothesis is that they are distributed around
+ zero. If \code{nrep > 0}, a randomization procedure is done where the
+ signs of the diversity contrasts are randomly chosen. This is used to
+ create a distribution of the test statistic which is compared with the
+ observed value (the sum of the diversity contrasts).
+}
+\value{
+ a single numeric value with the \emph{P}-value.
+}
+\references{
+ Barraclough, T. G., Harvey, P. H. and Nee, S. (1995) Sexual
+ selection and taxonomic diversity in passerine birds.
+ \emph{Proceedings of the Royal Society of London. Series B. Biological
+ Sciences}, \bold{259}, 211--215.
+
+ Barraclough, T. G., Harvey, P. H., and Nee, S. (1996) Rate of
+ \emph{rbc}L gene sequence evolution and species diversification in
+ flowering plants (angiosperms). \emph{Proceedings of the Royal Society
+ of London. Series B. Biological Sciences}, \bold{263}, 589--591.
+
+ Vamosi, S. M. and Vamosi, J. C. (2005) Endless tests: guidelines for
+ analysing non-nested sister-group comparisons. \emph{Evolutionary
+ Ecology Research}, \bold{7}, 567--579.
+
+ Wiegmann, B., Mitter, C. and Farrell, B. 1993. Diversification of
+ carnivorous parasitic insects: extraordinary radiation or specialized
+ dead end? \emph{American Naturalist}, \bold{142}, 737--754.
+}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link{slowinskiguyer.test}}, \code{\link{mcconwaysims.test}}
+ \code{\link{richness.yule.test}}
+}
+\examples{
+### data from Vamosi & Vamosi (2005):
+fleshy <- c(1, 1, 1, 1, 1, 3, 3, 5, 9, 16, 33, 40, 50, 100, 216, 393, 850, 947,1700)
+dry <- c(2, 64, 300, 89, 67, 4, 34, 10, 150, 35, 2, 60, 81, 1, 3, 1, 11, 1, 18)
+x <- cbind(fleshy, dry)
+diversity.contrast.test(x)
+diversity.contrast.test(x, alt = "g")
+diversity.contrast.test(x, alt = "g", nrep = 1e4)
+slowinskiguyer.test(x)
+mcconwaysims.test(x)
+}
+\keyword{htest}