pureBirth: pureBirth

In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Description

Fits pure birth (Yule) model to set of branching times

Usage

pureBirth(x)

Arguments

x	a numeric vector of branching times

Value

A list containing the following elements:

LH	the log-likelihood at the maximum
aic	the Akaike Information Criterion
r1	the speciation rate giving the maximum log-likelihood

Author(s)

Dan Rabosky [e-mail]

References

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

Yule, G. U. 1924. A mathematical theory of evolution based on the conclusions of Dr. J. C. Willis. Phil. Trans. R. Soc. Lond. B 213:21-87.

See Also

yule-n-rate, bd, yuleWindow

Examples

  data("plethodon")
  ### loads branching times for plethodontid salamander dataset
  pureBirth(plethodon)

Example output

Loading required package: ape
Loading required package: geiger
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

$LH
       LH 
-47.35259 

$aic
      LH 
96.70518 

$r1
      smax 
0.03371402 

laser documentation built on Jan. 15, 2017, 4:49 p.m.