4 \title{Phylogenetic Correlation Structures}
6 Standard classes of phylogenetic correlation structures (\code{corPhyl}) available in \pkg{ape}.
9 Available standard classes:
10 \item{corBrownian}{Brownian model (Felsenstein 1985),}
11 \item{corMartins}{The covariance matrix defined in Martins and Hansen (1997),}
12 \item{corGrafen}{The covariance matrix defined in Grafen (1989).}
13 See classes documentation for reference and detailed description.
16 \code{\link[nlme]{corClasses}} and \code{\link[nlme]{gls}} in the \pkg{nlme} librarie,
17 \code{\link{corBrownian}}, \code{\link{corMartins}}, \code{\link{corGrafen}}.
19 \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
22 cat("((((Homo:0.21,Pongo:0.21):0.28,",
23 "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
24 file = "ex.tre", sep = "\n")
25 tree.primates <- read.tree("ex.tre")
26 X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
27 Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
28 unlink("ex.tre") # delete the file "ex.tre"
29 m1 <- gls(Y~X, correlation=corBrownian(1, tree.primates))
31 m2 <- gls(Y~X, correlation=corMartins(1, tree.primates))
33 corMatrix(m2$modelStruct$corStruct)
34 m3 <- gls(Y~X, correlation=corGrafen(1, tree.primates))
36 corMatrix(m3$modelStruct$corStruct)