3 \title{Phylogenetically Independent Contrasts}
5 pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
8 \item{x}{a numeric vector.}
9 \item{phy}{an object of class \code{"phylo"}.}
10 \item{scaled}{logical, indicates whether the contrasts should be
11 scaled with their expected variances (default to \code{TRUE}).}
12 \item{var.contrasts}{logical, indicates whether the expected
13 variances of the contrasts should be returned (default to \code{FALSE}).}
16 Compute the phylogenetically independent contrasts using the method
17 described by Felsenstein (1985).
20 If \code{x} has names, its values are matched to the tip labels of
21 \code{phy}, otherwise its values are taken to be in the same order
22 than the tip labels of \code{phy}.
24 The user must be careful here since the function requires that both
25 series of names perfectly match, so this operation may fail if there
26 is a typing or syntax error. If both series of names do not match, the
27 values in the \code{x} are taken to be in the same order than the tip
28 labels of \code{phy}, and a warning message is issued.
31 either a vector of phylogenetically independent contrasts (if
32 \code{var.contrasts = FALSE}), or a two-column matrix with the
33 phylogenetically independent contrasts in the first column and their
34 expected variance in the second column (if \code{var.contrasts =
35 TRUE}). If the tree has node labels, these are used as labels of the
39 Felsenstein, J. (1985) Phylogenies and the comparative method.
40 \emph{American Naturalist}, \bold{125}, 1--15.
42 \author{Emmanuel Paradis}
44 \code{\link{read.tree}}, \code{\link{compar.gee}},
45 \code{\link{compar.lynch}}, \code{\link{pic.ortho}},
46 \code{\link{varCompPhylip}}
49 ### The example in Phylip 3.5c (originally from Lynch 1991)
50 cat("((((Homo:0.21,Pongo:0.21):0.28,",
51 "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
52 file = "ex.tre", sep = "\n")
53 tree.primates <- read.tree("ex.tre")
54 X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
55 Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
56 names(X) <- names(Y) <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
57 pic.X <- pic(X, tree.primates)
58 pic.Y <- pic(Y, tree.primates)
59 cor.test(pic.X, pic.Y)
60 lm(pic.Y ~ pic.X - 1) # both regressions
61 lm(pic.X ~ pic.Y - 1) # through the origin
62 unlink("ex.tre") # delete the file "ex.tre"