bd.time: Time-Dependent Birth-Death Models

In ape: Analyses of Phylogenetics and Evolution

Time-Dependent Birth-Death Models

Description

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

Usage

bd.time(phy, birth, death, BIRTH = NULL, DEATH = NULL,
        ip, lower, upper, fast = FALSE, boot = 0, trace = 0)

Arguments

phy	an object of class "phylo".
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 birth.
DEATH	id. for death.
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 trace steps. This can be helpful if convergence is particularly slow.

Details

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.

Value

A list with the following components:

• par: a vector of estimates with names taken from the parameters in the specified functions.

• SS: the minimized sum of squares.

• convergence: output convergence criterion from nlminb.

• message: id.

• iterations: id.

• evaluations: id.

Author(s)

Emmanuel Paradis

References

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

See Also

ltt.plot, birthdeath, yule.time, LTT

Examples

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)

ape documentation built on May 29, 2024, 10:50 a.m.