corClasses {ape} | R Documentation |
Phylogenetic Correlation Structures
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 dutheil@evolbio.mpg.de, Emmanuel Paradis
See Also
corClasses
and gls
in the
nlme librarie, corBrownian
,
corMartins
, corGrafen
,
corPagel
, corBlomberg
,
vcv
, vcv2phylo
Examples
library(nlme)
txt <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
tree.primates <- read.tree(text = txt)
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
dat <- data.frame(Species = Species, X = X, Y = Y)
m1 <- gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form = ~Species))
summary(m1)
m2 <- gls(Y ~ X, dat, correlation=corMartins(1, tree.primates, form = ~Species))
summary(m2)
corMatrix(m2$modelStruct$corStruct)
m3 <- gls(Y ~ X, dat, correlation=corGrafen(1, tree.primates, form = ~Species))
summary(m3)
corMatrix(m3$modelStruct$corStruct)
[Package ape version 5.7-1 Index]