# yule.time

##### Fits the Time-Dependent Yule Model

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

) to the
present.

- Keywords
- models

##### 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.

##### See Also

`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
yule.time(bird.families, birth.step) # fails
yule.time(bird.families, birth.step, BIRTH.step,
opti = "nlminb", start = c(.01, .01, 100))
```

*Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)*