1 \name{mcconwaysims.test}
2 \alias{mcconwaysims.test}
3 \title{McConway-Sims Test of Homogeneous Diversification}
5 This function performs the McConway--Sims test that a trait or
6 variable does not affect diversification rate.
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 or decrease diversification rate, and the second one the number of
15 species in the sister-clades without the trait. Each
16 row represents a pair of sister-clades.}
19 The McConway--Sims test compares a series of sister-clades where one
20 of the two is characterized by a trait supposed to affect
21 diversification rate. The null hypothesis is that the trait does not
22 affect diversification. The alternative hypothesis is that
23 diversification rate is increased or decreased by the trait (by
24 contrast to the Slowinski--Guyer test). The test is a likelihood-ratio
25 of a null Yule model and an alternative model with two parameters.
28 a data frame with the \eqn{\chi^2}{chi2}, the number of degrees of
29 freedom, and the \emph{P}-value.
32 McConway, K. J. and Sims, H. J. (2004) A likelihood-based method for
33 testing for nonstochastic variation of diversification rates in
34 phylogenies. \emph{Evolution}, \bold{58}, 12--23.
36 \author{Emmanuel Paradis}
38 \code{\link{balance}}, \code{\link{slowinskiguyer.test}},
39 \code{\link[geiger]{rc}} in \pkg{geiger},
40 \code{\link[apTreeshape]{shift.test}} in \pkg{apTreeshape}
43 ### simulate 10 clades with lambda = 0.1 and mu = 0.09:
44 n0 <- replicate(10, balance(rbdtree(.1, .09, Tmax = 35))[1])
45 ### simulate 10 clades with lambda = 0.15 and mu = 0.1:
46 n1 <- replicate(10, balance(rbdtree(.15, .1, Tmax = 35))[1])
49 slowinskiguyer.test(x)
50 richness.yule.test(x, 35)