corClasses {ape}R Documentation

Phylogenetic Correlation Structures

Description

Standard classes of phylogenetic correlation structures (corPhyl) available in ape.

Value

Available standard classes:

corBrownian Brownian model (Felsenstein 1985),
corMartins The covariance matrix defined in Martins and Hansen (1997),
corGrafen The covariance matrix defined in Grafen (1989).

See classes documentation for reference and detailed description.

Author(s)

Julien Dutheil julien.dutheil@univ-montp2.fr

See Also

corClasses and gls in the nlme librarie, corBrownian, corMartins, corGrafen.

Examples

        library(ape)
        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 1.7 Index]