rTrait: Continuous trait simulation

In phylolm: Phylogenetic Linear Regression

Continuous trait simulation

Description

Simulates a continuous trait along a tree from various phylogenetic models.

Usage

rTrait(n=1, phy, model=c("BM","OU","lambda","kappa","delta","EB","trend"),
       parameters = NULL, plot.tree=FALSE)

Arguments

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.

Details

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).

Value

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.

Note

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.

Author(s)

Lam Si Tung Ho and C. Ane

See Also

rTraitCont.

Examples

tre = rtree(50)
y = rTrait(n=1, phy=tre, model="OU",
           parameters=list(optimal.value=2,sigma2=1,alpha=0.1))

phylolm documentation built on Oct. 1, 2024, 1:09 a.m.