ape (version 1.8-4)

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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