RPANDA (version 2.3)

likelihood_t_MC_geog: Likelihood of a dataset under the matching competition model with biogeography.

Description

Computes the likelihood of a dataset under the matching competition model with specified sigma2 and S values and with a geography.object formed using CreateGeoObject.

Usage

likelihood_t_MC_geog(phylo, data, par,geo.object)

Value

the negative log-likelihood value of the dataset (accordingly, the negative of the output should be recorded as the likelihood), given the phylogeny, sig2 and S values, and geography.object.

Arguments

phylo

an object of type 'phylo' (see ape documentation)

data

a named vector of continuous data with names corresponding to phylo$tip.label

par

a vector listing a value for log(sig2) (see Note) and S (parameters of the matching competition model), in that order

geo.object

a geography object indicating sympatry through time, created using CreateGeoObject

Author

Jonathan Drury

Julien Clavel

Details

When specifying par, log(sig2) must be listed before S.

References

Drury, J., Clavel, J., Manceau, M., and Morlon, H. 2016. Estimating the effect of competition on trait evolution using maximum likelihood inference. Systematic Biology doi 10.1093/sysbio/syw020

Nuismer, S. & Harmon, L. 2015. Predicting rates of interspecific interaction from phylogenetic trees. Ecology Letters 18:17-27.

See Also

fit_t_comp CreateGeoObject likelihood_t_MC

Examples

data(Anolis.data)
phylo <- Anolis.data$phylo
pPC1 <- Anolis.data$data
geography.object <-  Anolis.data$geography.object

# Compute the likelihood with geography using ML parameters for fit without geography
par <- c(0.0003139751, -0.06387258)
lh <- -likelihood_t_MC_geog(phylo,pPC1,par,geography.object)