Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure

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Documentation for package ‘GUILDS’ version 1.4.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

GUILDS-package	Package implementing the Guilds sampling formula for the Neutral Theory of Biodiversity
expected.SAD	Calculate the expected species abundance distribution of the standard neutral model, given theta, m and J
expected.SAD.Guilds	Estimate the expected species abundance distribution of both guilds using the guilds model, provided theta, alpha_x, alpha_y and J.
expected.SAD.Guilds.Conditional	Estimate the expected species abundance distribution of both guilds using the guilds model, provided theta, alpha_x, alpha_y, conditional on the size of guild X, Jx and the size of guild Y, Jy.
generate.ESF	Generate community data under the standard neutral model of biodiversity, using the urn scheme as described in Etienne 2005
generate.Guilds	Generate Artificial data under the GUILDS model
generate.Guilds.Cond	Generate Artificial data under the GUILDS model, conditioned on Guild size
GUILDS	Package implementing the Guilds sampling formula for the Neutral Theory of Biodiversity
logLikelihood.ESF	Likelihood of the Etienne sampling formula
logLikelihood.Guilds	Likelihood of the Guilds sampling formula
logLikelihood.Guilds.Conditional	Likelihood of the Guilds sampling formula, conditional on guild size
maxLikelihood.ESF	Maximization of the loglikelihood given the standard Neutral Model, using the Etienne Sampling Formula
maxLikelihood.Guilds	Maximization of the loglikelihood under the Guilds Model.
maxLikelihood.Guilds.Conditional	Maximization of the loglikelihood under the Guilds Model, conditioned on guild size.
preston_plot	Barplot in Preston style of an abundance dataset