pic {ape} | R Documentation |
Compute the phylogenetically independent contrasts using the method described by Felsenstein (1985).
pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
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 ). |
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
.
The user must be careful here since the function requires that both
series of names perfectly match, so this operation may fail if there
is a typing or syntax error. If both series of names do not match, the
values in the x
are taken to be in the same order than the tip
labels of phy
, and a warning message is issued.
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
).
Emmanuel Paradis paradis@isem.univ-montp2.fr
Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1–15.
read.tree
, compar.gee
, compar.lynch
### 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"