\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
+ 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"}, \code{"logratio"}, 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}}.}
+ \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.
+ the signed difference is used (Sargent 2004). If \code{method = "logratio"},
+ then this is Wiegmann et al.'s (1993) version. These
+ four tests are essentially different versions of the same test (Vamosi
+ and Vamosi 2005, Vamosi 2007). See Paradis (2012) for a comparison of
+ their statistical performance with other tests.
If \code{nrep = 0}, a Wilcoxon test is done on the species diversity
contrasts with the null hypothesis is that they are distributed around
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.
+ of London. Series B. Biological Sciences}, \bold{263}, 589--591.
+
+ Paradis, E. (2012) Shift in diversification in sister-clade
+ comparisons: a more powerful test. \emph{Evolution}, \bold{66},
+ 288--295.
+
+ Sargent, R. D. (2004) Floral symmetry affects speciation rates in
+ angiosperms. \emph{Proceedings of the Royal Society of London. Series
+ B. Biological Sciences}, \bold{271}, 603--608.
+
+ Vamosi, S. M. (2007) Endless tests: guidelines for analysing non-nested
+ sister-group comparisons. An addendum. \emph{Evolutionary Ecology
+ Research}, \bold{9}, 717.
Vamosi, S. M. and Vamosi, J. C. (2005) Endless tests: guidelines for
analysing non-nested sister-group comparisons. \emph{Evolutionary