corClasses

0th

Percentile

Phylogenetic Correlation Structures

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)}

Keywords
models
See Also

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

Aliases
  • corClasses
  • corPhyl
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 = "")
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)
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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