yule.time {ape} R Documentation

Fits the Time-Dependent Yule Model

Description

This function fits by maximum likelihood the time-dependent Yule model. The time is measured from the past (`root.time`) to the present.

Usage

```yule.time(phy, birth, BIRTH = NULL, root.time = 0, opti = "nlm", start = 0.01)
```

Arguments

 `phy` an object of class `"phylo"`. `birth` a (vectorized) function specifying how the birth (speciation) probability changes through time (see details). `BIRTH` a (vectorized) function giving the primitive of `birth`. `root.time` a numeric value giving the time of the root node (time is measured from the past towards the present). `opti` a character string giving the function used for optimisation of the likelihood function. Three choices are possible: `"nlm"`, `"nlminb"`, or `"optim"`, or any unambiguous abbreviation of these. `start` the initial values used in the optimisation.

Details

The model fitted is a straightforward extension of the Yule model with covariates (see `yule.cov`). Rather than having heterogeneity among lineages, the speciation probability is the same for all lineages at a given time, but can change through time.

The function `birth` must meet these two requirements: (i) the parameters to be estimated are the formal arguments; (ii) time is named `t` in the body of the function. However, this is the opposite for the primitive `BIRTH`: `t` is the formal argument, and the parameters are used in its body. See the examples.

It is recommended to use `BIRTH` if possible, and required if speciation probability is constant on some time interval. If this primitive cannot be provided, a numerical integration is done with `integrate`.

The standard-errors of the parameters are computed with the Hessian of the log-likelihood function.

Value

An object of class `"yule"` (see `yule`).

References

Hubert, N., Paradis, E., Bruggemann, H. and Planes, S. (2011) Community assembly and diversification in Indo-Pacific coral reef fishes. Ecology and Evolution, 1, 229–277.

`branching.times`, `ltt.plot`, `birthdeath`, `yule`, `yule.cov`, `bd.time`

Examples

```### define two models...
birth.logis <- function(a, b) 1/(1 + exp(-a*t - b)) # logistic
birth.step <- function(l1, l2, Tcl) { # 2 rates with one break-point
ans <- rep(l1, length(t))
ans[t > Tcl] <- l2
ans
}
### ... and their primitives:
BIRTH.logis <- function(t) log(exp(-a*t) + exp(b))/a + t
BIRTH.step <- function(t)
{
out <- numeric(length(t))
sel <- t <= Tcl
if (any(sel)) out[sel] <- t[sel] * l1
if (any(!sel)) out[!sel] <- Tcl * l1 + (t[!sel] - Tcl) * l2
out
}
data(bird.families)
### fit both models:
yule.time(bird.families, birth.logis)
yule.time(bird.families, birth.logis, BIRTH.logis) # same but faster
## Not run: yule.time(bird.families, birth.step)  # fails
yule.time(bird.families, birth.step, BIRTH.step,
opti = "nlminb", start = c(.01, .01, 100))
```

[Package ape version 5.5 Index]