Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/CDF.birth.death.R

This function fits a used-defined time-dependent birth-death model.

1 2 |

`phy` |
an object of class |

`birth` |
either a numeric (if speciation rate is assumed constant), or a (vectorized) function specifying how the birth (speciation) probability changes through time (see details). |

`death` |
id. for extinction probability. |

`BIRTH` |
(optional) a vectorized function giving the primitive
of |

`DEATH` |
id. for |

`ip` |
a numeric vector used as initial values for the estimation procedure. If missing, these values are guessed. |

`lower, upper` |
the lower and upper bounds of the parameters. If missing, these values are guessed too. |

`fast` |
a logical value specifying whether to use faster integration (see details). |

`boot` |
the number of bootstrap replicates to assess the confidence intervals of the parameters. Not run by default. |

`trace` |
an integer value. If non-zero, the fitting procedure is
printed every |

Details on how to specify the birth and death functions and their
primitives can be found in the help page of `yule.time`

.

The model is fitted by minimizing the least squares deviation between
the observed and the predicted distributions of branching times. These
computations rely heavily on numerical integrations. If ```
fast =
FALSE
```

, integrations are done with R's `integrate`

function. If `fast = TRUE`

, a faster but less accurate function
provided in ape is used. If fitting a complex model to a large
phylogeny, a strategy might be to first use the latter option, and
then to use the estimates as starting values with `fast = FALSE`

.

A list with the following components:

para vector of estimates with names taken from the parameters in the specified functions.

SSthe minimized sum of squares.

convergenceoutput convergence criterion from

`nlminb`

.messageid.

iterationsid.

evaluationsid.

Emmanuel Paradis

Paradis, E. (2011) Time-dependent speciation and extinction from
phylogenies: a least squares approach. *Evolution*, **65**,
661–672.

`ltt.plot`

, `birthdeath`

,
`yule.time`

, `LTT`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
set.seed(3)
tr <- rbdtree(0.1, 0.02)
bd.time(tr, 0, 0) # fits a simple BD model
bd.time(tr, 0, 0, ip = c(.1, .01)) # 'ip' is useful here
## the classic logistic:
birth.logis <- function(a, b) 1/(1 + exp(-a*t - b))
## Not run:
bd.time(tr, birth.logis, 0, ip = c(0, -2, 0.01))
## slow to get:
## $par
## a b death
## -0.003486961 -1.995983179 0.016496454
##
## $SS
## [1] 20.73023
## End(Not run)
``` |

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