makeGeoHiSSELikelihood: Export likelihood function for the GeoHiSSE model

In thej022214/hisse: Hidden State Speciation and Extinction

Export likelihood function for the GeoHiSSE model

Description

Exports a likelihood function conditioned on the data and a named vector with the parameters for each of the models.

Usage

makeGeoHiSSELikelihood(phy, data, hidden.areas=0, f=c(1,1,1), assume.cladogenetic=TRUE, 
condition.on.survival=TRUE, root.type="madfitz", root.p=NULL, dt.threads=1, ode.eps = 0, 
bad.likelihood = exp(-300))

Arguments

phy	a phylogenetic tree, in ape “phylo” format and with internal nodes labeled denoting the ancestral selective regimes.
data	a data matrix containing species information (see Details).
hidden.areas	Number of hidden areas included in the model. When hidden.areas = 0, the model is equal to the GeoSSE model (i.e., no hidden states included).
f	vector of length 3 with the estimated proportion of extant species in areas 0, 1, and 2 (see fgeohisse function for more information) that are included in the phylogeny. By default all species are assumed to be sampled.
assume.cladogenetic	a logical indicating whether the likelihood should be conditioned on geographical speciation happening at the nodes. If set to FALSE then all range transitions are treated as anagenetic. The default is TRUE. See Caetano et al. (2018 - Evolution) for more information.
condition.on.survival	a logical indicating whether the likelihood should be conditioned on the survival of two lineages and the speciation event subtending them (Nee et al. 1994). The default is TRUE.
root.type	indicates whether root summarization follow the procedure described by FitzJohn et al. 2009, “madfitz” or Herrera-Alsina et al. 2018, “herr_als”.
root.p	a vector indicating fixed root state probabilities. The default is NULL.
dt.threads	Number of core threads to be used by the data.table function. Default is 1.
ode.eps	sets the tolerance for the integration at the end of a branch. Essentially if the sum of compD is less than this tolerance, then it assumes the results are unstable and discards them. The default is set to zero, but in testing a value of 1e-8 can sometimes produce stable solutions for both easy and very difficult optimization problems.
bad.likelihood	Value returned when there is a problem in the computation of the likelihood value for the function.

Details

This function sets up and returns the likelihood for the GeoHiSSE model together with a vector of parameters. The likelihood function is conditioned on the observed data and will return a value of loglikelihood given a vector of parameter values. The length of the parameter vector as well as the order of the parameter vector cannot be changed. Please pay special attention to the length of the parameter vector and the names of the parameters provided by the “pars” element of the list.

Note that when the likelihood computation fails the function will return the value set as “bad.likelihood”.

Value

makeGeoHiSSELikelihood returns a list with elements:

$loglik	the likelihood function for the model. This has a single parameter 'p'.
$pars	a named vector for the likelihood function pupulated with 0 values.

Author(s)

Jeremy M. Beaulieu and Daniel S. Caetano

References

Caetano, D.S., B.C. O'Meara, and J.M. Beaulieu. 2018. Hidden state models improve state-dependent diversification approaches, including biogeographic models. Evolution, 72:2308-2324.

Beaulieu, J.M, and B.C. O'Meara. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65:583-601.

FitzJohn R.G., Maddison W.P., and Otto S.P. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58:595-611.

Maddison W.P., Midford P.E., and Otto S.P. 2007. Estimating a binary characters effect on speciation and extinction. Syst. Biol. 56:701-710.

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

Examples

library(diversitree)
library(hisse)
## Generate data:
pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01)
set.seed(4) 
phy <- tree.bisse(pars, max.t=30, x0=0)
sim.dat <- data.frame(names(phy$tip.state), phy$tip.state)
## Get lik function:
lik.hisse <- makeHiSSELikelihood(phy = phy, data = sim.dat, hidden.states = FALSE)
likf <- lik.hisse$log.lik
pars <- lik.hisse$pars
## Set the parameter values. Note that we have turnover and eps, not speciation and extinction!
pars <- setNames(c(0.1+0.03,0.2+0.03,0.03/0.1,0.03/0.2,0.01,0.01), names(pars))
## Compute the log-likelihood for the model.
likf(pars)

thej022214/hisse documentation built on Sept. 20, 2023, 12:40 a.m.