R: Phylogenetic Correlation Structures

corClasses {ape} | R Documentation

## Phylogenetic Correlation Structures

### Description

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

- corBrownianBrownian motion model (Felsenstein 1985)

- corMartinsThe covariance matrix defined in Martins and Hansen (1997)

- corGrafenThe covariance matrix defined in Grafen (1989)

- corPagelThe covariance matrix defined in Freckelton et al. (2002)

- corBlombergThe 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`, `vcv`, `vcv2phylo`

### 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 4.1 Index]