Last chance! 50% off unlimited learning
Sale ends in
This function simulates the evolution of a multivariate set of traits along a phylogeny. The calculation is done recursively from the root.
rTraitMult(phy, model, p = 1, root.value = rep(0, p), ancestor = FALSE,
asFactor = NULL, trait.labels = paste("x", 1:p, sep = ""), ...)A data frame with p columns whose names are given by
trait.labels and row names taken from the labels of the tree.
an object of class "phylo".
a function specifying the model (see details).
an integer giving the number of traits.
a numeric vector giving the values at the root.
a logical value specifying whether to return the values at the nodes as well (by default, only the values at the tips are returned).
the indices of the traits that are returned as factors (discrete traits).
a vector of mode character giving the names of the traits.
further arguments passed to model if it is a
function.
Emmanuel Paradis
The model is specified with an R function of the form foo(x,
l) where x is a vector of the traits of the ancestor and
l is the branch length. Other arguments may be added. The
function must return a vector of length p.
rTraitCont, rTraitDisc, ace
## correlated evolution of 2 continuous traits:
mod <- function(x, l) {
y1 <- rnorm(1, x[1] + 0.5*x[2], 0.1)
y2 <- rnorm(1, 0.5*x[1] + x[2], 0.1)
c(y1, y2)
}
set.seed(11)
tr <- makeNodeLabel(rcoal(20))
x <- rTraitMult(tr, mod, 2, ancestor = TRUE)
op <- par(mfcol = c(2, 1))
plot(x, type = "n")
text(x, labels = rownames(x), cex = 0.7)
oq <- par(mar = c(0, 1, 0, 1), xpd = TRUE)
plot(tr, font = 1, cex = 0.7)
nodelabels(tr$node.label, cex = 0.7, adj = 1)
par(c(op, oq))
Run the code above in your browser using DataLab