corClasses: Phylogenetic Correlation Structures

In gjuggler/ape: Analyses of Phylogenetics and Evolution

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 [e-mail], 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)

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.