Fits the equilibrium diversity model with potentially time-varying turnover rate and potentially missing extant species to a phylogeny, by maximum likelihood. The implementation allows only exponential time variation of the turnover rate, although this could be modified using expressions in Morlon et al. PloSB 2010. Notations follow Morlon et al. PLoSB 2010.
fit_coal_cst(phylo, tau0 = 1e-2, gamma = 1, cst.rate = FALSE,
meth = "Nelder-Mead", N0 = 0)a list with the following components
the name of the fitted model
the maximum log-likelihood value
the second order Akaike's Information Criterion
the estimated turnover rate at present
the estimated parameter controlling the exponential variation in turnover rate (if cst.rate is FALSE)
an object of type 'phylo' (see ape documentation)
initial value of the turnover rate at present (used by the optimization algorithm)
initial value of the parameter controlling the exponential variation in turnover rate (used by the optimization algorithm)
logical: should be set to TRUE to fit an equilibrium diversity model with time-constant turnover rate (know as the Hey model, model 1 in Morlon et al. PloSB 2010). By default, a model with expontential time-varying rate exponential is fitted (model 2 in Morlon et al. PloSB 2010).
optimization to use to maximize the likelihood function, see optim for more details.
Number of extant species. With default value(0), N0 is set to the number of tips in the phylogeny. That is, the phylogeny is assumed to be 100% complete.
H Morlon
This function fits models 1 (when cst.rate=TRUE) and 2 (when cst.rate=FALSE) from the PloSB 2010 paper. Likelihoods arising from these models are directly comparable to likelihoods from the fit_coal_var function, thus allowing to test support for equilibrium versus expanding diversity scenarios. Time runs from the present to the past. Hence, if gamma is estimated to be positive (for example), this means that the speciation rate decreases from past to present.
Hey, J. (1992) Using phylogenetic trees to study speciation and extinction, Evolution, 46: 627-640
Morlon, H., Potts, M.D., Plotkin, J.B. (2010) Inferring the dynamics of diversification: a coalescent approach, PLoS B, 8(9): e1000493
Morlon, H., Kemps, B., Plotkin, J.B., Brisson, D. (2012) Explosive radiation of a bacterial species group, Evolution, 66: 2577-2586
Morlon, H. (2014) Phylogenetic approaches for studying diversification, Eco Lett, 17:508-525
likelihood_coal_cst, fit_coal_var
data(Cetacea)
test <- FALSE
if(test){
result <- fit_coal_cst(Cetacea, tau0=1.e-3, gamma=-1, cst.rate=FALSE, N0=89)
print(result)
}
Run the code above in your browser using DataLab