R: Binary trait simulation

rbinTrait {phylolm} | R Documentation

## Binary trait simulation

### Description

Simulates a binary trait along a phylogeny, according to the model in Ives and Garland (2010).

### Usage

    rbinTrait(n=1, phy, beta, alpha, X = NULL, model = c("LogReg"))

### Arguments

`n` | number of independent replicates.
`phy` | a phylogenetic tree of type phylo with brach lengths.
`beta` | a vector of coefficients for the logistic regression model.
`alpha` | the phylogenetic correlation parameter.
`X` | a design matrix with one row for each tip in the phylogenetic tree.
`model` | Currently, only phylogenetic logistic regression is implemented.

### Value

If `n=1`, a numeric vector of 0-1 values 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

In the absence of a design matrix `X`, a single intercept is used. In this case `beta` should be a vector of length one and the model reduces to a 2-state Markov process on the tree with stationary mean exp(beta)/(1+exp(beta)). If a design matrix `X` is provided, the length of `beta` should be equal to the number of columns in `X`.

### Author(s)

Lam Si Tung Ho and C. An?

### References

Ives, A. R. and T. Garland, Jr. 2010. "Phylogenetic logistic regression for binary dependent variables". Systematic Biology 59:9-26.

### See Also

`rTrait`.

### Examples

    tre = rtree(50)
    x = rTrait(n=1,phy=tre)
    X = cbind(rep(1,50),x)
    y = rbinTrait(n=1, phy=tre, beta=c(-1,0.5), alpha=1, X=X)

[Package phylolm version 2.6.2 Index]