Bayesian General Mixed Yule-Coalescent Model for Species Delimitation

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Documentation for package ‘bGMYC4’ version 4.1.6

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

Help Pages

bGMYC	A Bayesian MCMC implementation of the general mixed Yule-coalescent model for species delimitation.
bgmyc.dataprep	Prepares a tree for analysis.
bgmyc.gibbs	MCMC sampler
bgmyc.lik	GMYC likelihood function
bgmyc.multiphylo	Multi-tree GMYC analysis
bgmyc.point	Returns a point estimate of species limits based on a posterior probability threshold input by the user.
bgmyc.prior	a function to return the prior probability of a model.
bgmyc.singlephy	Single tree GMYC analysis.
bgmyc.spec	bGMYC output processing.
checkrates	bGMYC output processing.
east10	10 trees sampled from a posterior distribution. based on simulated data.
gmyc.5parameter.lik	5 parameter likelihood function.
plot.bgmycprobmat	Plots the matrix of probability of conspecificity.
plot.bgmycrates	Plots relative coalescent and Yule rates for model fit evaluation.
plot.interactive.probmat	Interactive Probability Matrix Plot for bGMYC Results
plot.multibgmyc	Plot MCMC output.
plot.singlebgmyc	Plot MCMC output.
spec.probmat	Return matrix of probability of conspecificity.