Likelihood of a dataset under the matching competition model.

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Description

Computes the likelihood of a dataset under the matching competition model with specified sigma2 and S values.

Usage

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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 sig2 and S (parameters of the matching competition model), in that order

Details

When specifying par, sig2 must be listed before S.

Value

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

Author(s)

Jonathan Drury drury@biologie.ens.fr

Julien Clavel

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 likelihood_t_MC_geog

Examples

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

# Compute the likelihood that the S value is twice the ML estimate
par <- c(0.0003139751, (2*-0.06387258))
lh <- -likelihood_t_MC(phylo,pPC1,par)

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