ape (version 1.8-3)

corClasses: Phylogenetic Correlation Structures

Description

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

Arguments

Value

  • Available standard classes:
  • corBrownianBrownian model (Felsenstein 1985),
  • corMartinsThe covariance matrix defined in Martins and Hansen (1997),
  • corGrafenThe covariance matrix defined in Grafen (1989).
  • See classes documentation for reference and detailed description.

See Also

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

Examples

Run this code
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 = "")
	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)

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