R: Fit model with continuous-time varying speciation/extinction...

fitSPVAR

R Documentation

Fit model with continuous-time varying speciation/extinction rates to phylogeny

Description

Functions that fit time-varying speciation and extinction models to branching times
derived from phylogenetic data. fitSPVAR fits a model with an exponentially
declining speciation rate through time and constant extinction. fitEXVAR fits a model
with exponentially increasing extinction and constant speciation. fitBOTHVAR fits
a model where both speciation and extinction rates can vary through time.

a vector of starting parameter values for the optimization algorithm. Note that there are 3 parameters in SPVAR and EXVAR models, but 4 parameters in BOTHVAR

Details

These functions are described in Rabosky & Lovette (2008, Evolution).
There is a high likelihood that the optimization will fail across a large span of parameter
space, so you should not expect the default parameters to work. I recommend varying the first parameter (e.g., init[1])
before changing anything else.

The three models return the log-likelihood, the AIC, and the parameter estimates. Parameters correspond exactly to those
described in Rabosky and Lovette (2008), equations 7-11. The speciation rate is specified by parameters lam0 and k, and extinction
through time is described by mu0 and z. lam0 and mu0 are the initial speciation and final extinction rates, respectively.
k and z control the rate of decrease / increase in speciation and extinction, respectively.

Because the underlying mathematical model of speciation and extinction requires that the extinction rate not exceed
the speciation rate, the models have been reparameterized as follows: for the SPVAR model, optimization is performed on
the parameter set c(X, k, mu0), where k and mu0 are defined as above and X corresponds the net diversification rate. This provides for a
fixed minimum bound for the optimization interval (because X must always be greater than 0).
This should be irrelevant to the useage of the function. However, if you are having a difficult time getting optimization
to work without an error, bear in mind that the initial parameters you are suppling correspond to:
SPVAR: X, k, mu0;
EXVAR: X, mu0, z;
and BOTHVAR, X, k, mu0, z.
A good solution might be to start with initial parameter values under the pure birth or constant rate birth death model. You will
need to estimate these in light of equations 7-11 in Rabosky & Lovette (2008).

Optimization uses the L-BFGS-B algorithm as implemented in the function optimize. Numerical integration uses integrate.

You can use the equations from Rabosky & Lovette (2008) with your parameter estimates to generate a plot of the speciation and extinction
through time curves, or you can use the function plotRate

Value

model

The name of the model

LH

Maximum log-likelihood of the fitted model

aic

AIC

lam0

The initial speciation rate

k

Parameter of the exponential change in speciation rate

mu0

the final extinction rate

z

Parameter of the exponential change in extinction rate

Rabosky, D. L. and I. J. Lovette. 2008. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution, doi:10.1111/j.1558-5646.2008.00409.x