scaleBranchingtimes: Scale Branching Times

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

Description

Scales a vector of branching times by a known basal divergence time.

Usage

scaleBranchingtimes(x, basal = 100)

Arguments

x	a numeric vector of branching times
basal	estimated time of the basal divergence for the clade

Details

This function can be used when analyzing branching times for which it is possible to estimate the basal divergence time. If branch lengths in a specified phylogenetic tree are given in units of genetic distance, but the basal divergence is estimated at Z mya, call res <- scaleBranchingtimes(x, basal = Z). Rate parameters estimated by fitting variants of birth-death models will then be in units of lineage births or deaths per million years.

Value

a vector of scaled branching times

Author(s)

Dan Rabosky [e-mail]

Examples

  data(plethodon)
  # suppose plethodon basal divergence occurred 23 mya:
  svec <- scaleBranchingtimes(plethodon, basal = 23)
  plotLtt(svec)
  # plots lineages through time in units of time, rather than genetic
  # distance
  
  pureBirth(svec)
  # returns speciation rate in units of lineages/million years

Example output

Loading required package: ape
Loading required package: geiger
 [1] 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101 2.0794415
 [8] 2.1972246 2.3025851 2.3978953 2.4849066 2.5649494 2.6390573 2.7080502
[15] 2.7725887 2.8332133 2.8903718 2.9444390 2.9957323 3.0445224 3.0910425
[22] 3.1354942 3.1780538 3.2188758 3.2580965 3.2958369
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

$LH
       LH 
-13.06009 

$aic
      LH 
28.12019 

$r1
     smax 
0.1407194 

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