corClasses {ape} | R Documentation |
Standard classes of phylogenetic correlation structures (corPhyl
) available in ape.
Available standard classes:
corBrownian |
Brownian model (Felsenstein 1985), |
corMartins |
The covariance matrix defined in Martins and Hansen (1997), |
corGrafen |
The covariance matrix defined in Grafen (1989). |
See classes documentation for reference and detailed description.
Julien Dutheil julien.dutheil@univ-montp2.fr
corClasses
and gls
in the nlme librarie,
corBrownian
, corMartins
, corGrafen
.
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 = "\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)