4 \title{Phylogenetic Correlation Structures}
6 Classes of phylogenetic correlation structures (\code{"corPhyl"})
7 available in \pkg{ape}.
9 \item{corBrownian}{Brownian motion model (Felsenstein 1985)}
10 \item{corMartins}{The covariance matrix defined in Martins and Hansen
12 \item{corGrafen}{The covariance matrix defined in Grafen (1989)}
13 \item{corPagel}{The covariance matrix defined in Freckelton et al. (2002)}
14 \item{corBlomberg}{The covariance matrix defined in Blomberg et al. (2003)}
16 See the help page of each class for references and detailed
20 \code{\link[nlme]{corClasses}} and \code{\link[nlme]{gls}} in the
21 \pkg{nlme} librarie, \code{\link{corBrownian}},
22 \code{\link{corMartins}}, \code{\link{corGrafen}},
23 \code{\link{corPagel}}, \code{\link{corBlomberg}}
25 \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}, Emmanuel
29 cat("((((Homo:0.21,Pongo:0.21):0.28,",
30 "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
31 file = "ex.tre", sep = "\n")
32 tree.primates <- read.tree("ex.tre")
33 X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
34 Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
35 unlink("ex.tre") # delete the file "ex.tre"
36 m1 <- gls(Y~X, correlation=corBrownian(1, tree.primates))
38 m2 <- gls(Y~X, correlation=corMartins(1, tree.primates))
40 corMatrix(m2$modelStruct$corStruct)
41 m3 <- gls(Y~X, correlation=corGrafen(1, tree.primates))
43 corMatrix(m3$modelStruct$corStruct)