corClasses {ape}R Documentation

Phylogenetic Correlation Structures

Description

Classes of phylogenetic correlation structures ("corPhyl") available in ape.

corBrownian
Brownian motion model (Felsenstein 1985)
corMartins
The covariance matrix defined in Martins and Hansen (1997)
corGrafen
The covariance matrix defined in Grafen (1989)
corPagel
The covariance matrix defined in Freckelton et al. (2002)
corBlomberg
The covariance matrix defined in Blomberg et al. (2003)

See the help page of each class for references and detailed description.

Author(s)

Julien Dutheil julien.dutheil@univ-montp2.fr, Emmanuel Paradis

See Also

corClasses and gls in the nlme librarie, corBrownian, corMartins, corGrafen, corPagel, corBlomberg

Examples

library(nlme)
cat("((((Homo:0.21,Pongo:0.21):0.28,",
"Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
file = "ex.tre", sep = "\n")
tree.primates <- read.tree("ex.tre")
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
unlink("ex.tre") # delete the file "ex.tre"
m1 <- gls(Y~X, correlation=corBrownian(1, tree.primates))
summary(m1)
m2 <- gls(Y~X, correlation=corMartins(1, tree.primates))
summary(m2)
corMatrix(m2$modelStruct$corStruct)
m3 <- gls(Y~X, correlation=corGrafen(1, tree.primates))
summary(m3)
corMatrix(m3$modelStruct$corStruct)

[Package ape version 2.2 Index]