pic {ape}R Documentation

Phylogenetically Independent Contrasts

Description

Compute the phylogenetically independent contrasts using the method described by Felsenstein (1985).

Usage

pic(x, phy, scaled = TRUE, var.contrasts = FALSE)

Arguments

x a numeric vector.
phy an object of class "phylo".
scaled logical, indicates whether the contrasts should be scaled with their expected variance (default to TRUE).
var.contrasts logical, indicates whether the expected variance of the contrasts should be returned (default to FALSE).

Details

If x has names, its values are matched to the tip labels of phy, otherwise its values are taken to be in the same order than the tip labels of phy.

Value

either a vector of phylogenetically independent contrasts (if var.contrasts = FALSE), or a two-column matrix with the phylogenetically independent contrasts in the first column and their expected variance in the second column (if var.contrasts = TRUE).

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

References

Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1–15.

See Also

read.tree, compar.gee, compar.lynch

Examples

### The example in Phylip 3.5c (originally from Lynch 1991)
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)
names(X) <- names(Y) <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
pic.X <- pic(X, tree.primates)
pic.Y <- pic(Y, tree.primates)
cor.test(pic.X, pic.Y)
lm(pic.Y ~ pic.X - 1) # both regressions
lm(pic.X ~ pic.Y - 1) # through the origin
unlink("ex.tre") # delete the file "ex.tre"

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