corClasses: Phylogenetic Correlation Structures

In ape: Analyses of Phylogenetics and Evolution

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 [e-mail], Emmanuel Paradis

See Also

corClasses and gls in the nlme librarie, corBrownian, corMartins, corGrafen, corPagel, corBlomberg, vcv, vcv2phylo

Examples

library(nlme)
txt <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
tree.primates <- read.tree(text = txt)
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
dat <- data.frame(Species = Species, X = X, Y = Y)

m1 <- gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form = ~Species))
summary(m1)
m2 <- gls(Y ~ X, dat, correlation=corMartins(1, tree.primates, form = ~Species))
summary(m2)
corMatrix(m2$modelStruct$corStruct)
m3 <- gls(Y ~ X, dat, correlation=corGrafen(1, tree.primates, form = ~Species))
summary(m3)
corMatrix(m3$modelStruct$corStruct)

ape documentation built on May 29, 2024, 10:50 a.m.