R: Continuous trait simulation

rTrait {phylolm} | R Documentation

## 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. Ané

### 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))

[Package phylolm version 2.6.2 Index]