1 \name{slowinskiguyer.test}
2 \alias{slowinskiguyer.test}
3 \title{Slowinski-Guyer Test of Homogeneous Diversification}
5 This function performs the Slowinski--Guyer test that a trait or
6 variable does not increase diversification rate.
9 slowinskiguyer.test(x, detail = FALSE)
12 \item{x}{a matrix or a data frame with at least two columns: the first
13 one gives the number of species in clades with a trait supposed to
14 increase diversification rate, and the second one the number of
15 species in the corresponding sister-clade without the trait. Each
16 row represents a pair of sister-clades.}
17 \item{detail}{if \code{TRUE}, the individual P-values are appended.}
20 The Slowinski--Guyer test compares a series of sister-clades where one
21 of the two is characterized by a trait supposed to increase
22 diversification rate. The null hypothesis is that the trait does not
23 affect diversification. If the trait decreased diversification rate,
24 then the null hypothesis cannot be rejected.
26 The present function has mainly a historical interest. The
27 Slowinski--Guyer test generally performs poorly: see McConway and Sims
28 (2004) for an alternative and the functions cited below.
31 a data frame with the \eqn{\chi^2}{chi2}, the number of degrees of
32 freedom, and the \emph{P}-value. If \code{detail = TRUE}, a list is
33 returned with the data frame and a vector of individual
34 \emph{P}-values for each pair of sister-clades.
37 McConway, K. J. and Sims, H. J. (2004) A likelihood-based method for
38 testing for nonstochastic variation of diversification rates in
39 phylogenies. \emph{Evolution}, \bold{58}, 12--23.
41 Slowinski, J. B. and Guyer, C. (1993) Testing whether certain traits
42 have caused amplified diversification: an improved method based on a
43 model of random speciation and extinction. \emph{American Naturalist},
44 \bold{142}, 1019--1024.
46 \author{Emmanuel Paradis}
48 \code{\link{balance}}, \code{\link{mcconwaysims.test}},
49 \code{\link{diversity.contrast.test}},
50 \code{\link{richness.yule.test}},
51 \code{\link[geiger]{rc}} in \pkg{geiger},
52 \code{\link[apTreeshape]{shift.test}} in \pkg{apTreeshape}
55 ### from Table 1 in Slowinski and Guyer(1993):
56 viviparous <- c(98, 8, 193, 36, 7, 128, 2, 3, 23, 70)
57 oviparous <- c(234, 17, 100, 4, 1, 12, 6, 1, 481, 11)
58 x <- data.frame(viviparous, oviparous)
59 slowinskiguyer.test(x, TRUE) # 'P ~ 0.32' in the paper
62 slowinskiguyer.test(xalt)