This function computes the maximum likelihood estimates of the parameters of the DAMOCLES model for a given phylogeny and presence-absence data. It also outputs the corresponding loglikelihood that can be used in model comparisons.
This function computes the maximum likelihood estimates of colonisation and local extinction rate for a given phylogeny and presence-absence data under the DAMOCLES model. These rate estimates are used to simulate null communities under the DAMOCLES model. Standardized effect size of mean nearest taxon distance (mntd), mean phylogentic distance (mpd) and loglikelihood are calculated For comparison, standardised effect sizes are also calculated relative to a "Random-Draw" null model i.e. presence absence randomised across tips
providing 
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