ape (version 5.5)

corClasses: 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.

See Also

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

Examples

# NOT RUN {
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)
# }