laser (version 2.1)

Rate-Variable Birth Death: Fit Rate-Variable Diversification Model With Extinction to Branching Times

Description

Fits a two-rate variant of the birth death model to branching times derived from phylogenetic data. The model assumes that a clade has diversified under a net diversification rate r1 until some time st, at which point the net diversification rate shifts to r2. The extinction fraction a is assumed constant and can take values from [0, 1). The shift time st giving the maximum log-likelihood is found by sequentially optimizing r1 and r2 across a large number of possible shift times.

Usage

rvbd(x, ai = c(0.1, 0.5, 0.95), ints = NULL, verbose = FALSE, file = "out_rvbd.txt")

Value

• a list with the following components:
• LH
  the log-likelihood at the maximum
• aic
  the Akaike Information Criterion
• r1
  the initial net diversification rate
• r2
  the final net diversification rate
• a
  the extinction fraction
• st
  the shift time giving the maximum log-likelihood

Details

Non-linear optimization can be notoriously difficult, and the functions used in fitting this model can be susceptible to the presence of multiple optima in the likelihood surface. To guard against the possibility, the model is fitted using 3 initial values of the extinction fraction, a. You should check results obtained against those obtained using the yule2rate model. If the maximum log-likelihood under rvbd is less than that obtained using yule2rate, your analysis has been fooled by a local (sub)optimum. Repeat the analysis using additional starting values for a, e.g., 'ai = seq(0, .99. length.out = 15)'. 'ints' is used in determining the number of shift points to consider. If 'ints = NULL' (the default), the model will consider only observed branching times as possible shift points. See yule-n-rate for additional discussion of the 'ints' option. 'verbose = TRUE' will write maximum log-likelihoods and parameter estimates for each shift time under consideration to . The file can then be loaded to examine the likelihood of a rate shift at different points in time.

References

Barraclough, T. G., and A. P. Vogler. 2002. Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree. Mol. Biol. Evol. 19:1706-1716.

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

Rabosky, D. L. 2006. Likelihood methods for inferring temporal shifts in diversification rates. Evolution 60:1152-1164.

See Also

yule-n-rate, fitdAICrc

Examples

data(plethodon)
  result <- rvbd(plethodon, ints = 100, verbose = TRUE, file = 'temp.txt')
  
  ### now to generate a plot of log-likelihoods against shift times:
  temp <- read.table(file = 'temp.txt', header = TRUE)
  
  ### Rescaling shift times to reflect time since basal divergence
  stvec <- plethodon[1] - temp$st
  plot(temp$LH~stvec, xlab = "Time From Basal Divergence", 
        ylab = "Log-likelihood")
  
  unlink('temp.txt')  #clean-up temp file.