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