Simulation and likelihood methods for a dynamical community assembly that accounts for phylogenetic history New in version 1.1: - Function added to do bootstrap
| Package: | DAMOCLES |
| Type: | Package |
| Version: | 1.1 |
| Date: | 2015-03-05 |
| License: | GPL 2.0 |
DAMOCLES_loglik computes the likelihood of presence-absence data in a local community given a set of parameters and a phylogeny under an immigration-extinction model
DAMOCLES_ML finds the parameters that maximizes the likelihood computed by DAMOCLES_loglik.
DAMOCLES_sim simulates presence-absence data for a given phylogeny
DAMOCLES_bootstrap 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.
Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.