laser (version 2.4-1)

yuleWindow: Fit Yule Model (Pure Birth) to Temporal Window of Branching Times

Description

This function fits the Yule model to any temporal window that includes at least one branching time.

Usage

yuleWindow(x, st1 = x[1], st2 = 0)

Arguments

x

a numeric vector of branching times

st1

the start of the interval you wish to examine

st2

the end of the interval you wish to examine

Value

a list with the following components:

LH

the log-likelihood at the maximum

smax

the speciation rate giving the maximum log-likelihood

Details

'st1' and 'st2' are given in divergence units before present. If we had a set of branching times with an initial divergence 100 mya, yuleWindow(x, 75, 25) would fit the pure birth model to the portion of the tree between 75 and 25 mya. Calling yuleWindow(x, x[1], 0) will fit the model to the entire tree (identical to pureBirth(x)). Note that st1 must be greater than st2, because they are given in units of divergence before present.

References

Nee, S., R. M. May, and P. H. Harvey. 1994b. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344:305-311.

Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661-668.

See Also

fitdAICrc, pureBirth, bd

Examples

  data(agamids)
  agbtimes <- getBtimes(string = agamids)
  yuleWindow(agbtimes, 0.22, 0.10)
  # fits Yule model to temporal window between 0.22 and 0.10 divergence
  # units before present