R: Discrete Character Simulation

rTraitDisc {ape} | R Documentation

## Discrete Character Simulation

### Description

This function simulates the evolution of a discrete character along a phylogeny. If `model` is a character or a matrix, evolution is simulated with a Markovian model; the transition probabilities are calculated for each branch with P = e^{Qt} where Q is the rate matrix given by `model` and t is the branch length. The calculation is done recursively from the root. See Paradis (2006, p. 101) for a general introduction applied to evolution.

### Usage

    rTraitDisc(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
               rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k),
               ancestor = FALSE, root.value = 1, ...)

### Arguments

`phy` | an object of class `"phylo"`.
`model` | a character, a square numeric matrix, or a function specifying the model (see details).
`k` | the number of states of the character.
`rate` | the rate of change used if `model` is a character; it is not recycled if `model = "ARD"` of `model = "SYM"`.
`states` | the labels used for the states; by default “A”, “B”, ...
`freq` | a numeric vector giving the equilibrium relative frequencies of each state; by default the frequencies are equal.
`ancestor` | a logical value specifying whether to return the values at the nodes as well (by default, only the values at the tips are returned).
`root.value` | an integer giving the value at the root (by default, it's the first state). To have a random value, use `root.value = sample(k)`.
`...` | further arguments passed to `model` if it is a function.

### Details

There are three possibilities to specify `model`:

- A matrix:it must be a numeric square matrix; the diagonal is always ignored. The arguments `k` and `rate` are ignored.

- A character:these are the same short-cuts than in the function `ace`: `"ER"` is an equal-rates model, `"ARD"` is an all-rates-different model, and `"SYM"` is a symmetrical model. Note that the argument `rate` must be of the appropriate length, i.e., 1, k(k - 1), or k(k - 1)/2 for the three models, respectively. The rate matrix Q is then filled column-wise.

- A function:it must be of the form `foo(x, l)` where `x` is the trait of the ancestor and `l` is the branch length. It must return the value of the descendant as an integer.

### Value

A factor with names taken from the tip labels of `phy`. If `ancestor = TRUE`, the node labels are used if present, otherwise, “Node1”, “Node2”, etc.

### Author(s)

Emmanuel Paradis

### References

Paradis, E. (2006) Analyses of Phylogenetics and Evolution with R. New York: Springer.

### See Also

`rTraitCont`, `rTraitMult`, `ace`

### Examples

    data(bird.orders)
    ### the two followings are the same:
    rTraitDisc(bird.orders)
    rTraitDisc(bird.orders, model = matrix(c(0, 0.1, 0.1, 0), 2))

    ### two-state model with irreversibility:
    rTraitDisc(bird.orders, model = matrix(c(0, 0, 0.1, 0), 2))

    ### simple two-state model:
    tr <- rcoal(n <- 40, br = runif)
    x <- rTraitDisc(tr, ancestor = TRUE)
    plot(tr, show.tip.label = FALSE)
    nodelabels(pch = 19, col = x[-(1:n)])
    tiplabels(pch = 19, col = x[1:n])

    ### an imaginary model with stasis 0.5 time unit after a node, then
    ### random evolution:
    foo <- function(x, l) {
        if (l < 0.5) return(x)
        sample(2, size = 1)
    }
    tr <- rcoal(20, br = runif)
    x <- rTraitDisc(tr, foo, ancestor = TRUE)
    plot(tr, show.tip.label = FALSE)
    co <- c("blue", "yellow")
    cot <- c("white", "black")
    Y <- x[1:20]
    A <- x[-(1:20)]
    nodelabels(A, bg = co[A], col = cot[A])
    tiplabels(Y, bg = co[Y], col = cot[Y])

[Package ape version 5.6 Index]