| rTrait {phylolm} | R Documentation |
Simulates a continuous trait along a tree from various phylogenetic models.
rTrait(n=1, phy, model=c("BM","OU","lambda","kappa","delta","EB","trend"),
parameters = NULL, plot.tree=FALSE)
n |
number of independent replicates |
phy |
a phylogenetic tree of type phylo with branch lengths. |
model |
a phylogenetic model. Default is "BM", for Brownian motion. Alternatives are "OU", "lambda", "kappa", "delta", "EB" and "trend". |
parameters |
List of parameters for the model (see Note). |
plot.tree |
If TRUE, the tree with transformed branch lengths will be shown, except for the OU model. |
Possible phylogenetic models are the Brownian motion model (BM), the Ornstein-Uhlenbeck model (OU), Pagel's lambda model (lambda), Pagel's kappa model (kappa), Pagel's delta model (delta), the early burst model (EB), and the Brownian motion model with a trend (trend).
If n=1, a numeric vector with names from the tip labels in
the tree. For more than 1 replicate, a matrix with the tip labels as
row names, and one column per replicate.
The default choice for the parameters are as follows:
ancestral.state=0,
sigma2=1, optimal.value=0 for the OU model,
alpha=0 for the selection strength in the OU model,
lambda=1, kappa=1, delta=1, rate=0 for the
EB model, trend=0. These default choices correspond to the BM model.
Lam Si Tung Ho and C. Ané
tre = rtree(50)
y = rTrait(n=1, phy=tre, model="OU",
parameters=list(optimal.value=2,sigma2=1,alpha=0.1))