BEDASSLE-package        Disentangling the contributions of geographic
                        and ecological isolation to genetic
                        differentiation
Covariance              The parametric covariance matrix
HGDP.bedassle.data      The Eurasian subset of the HGDP dataset used in
                        example BEDASSLE analyses
MCMC                    Runs the Markov chain Monte Carlo with the
                        standard (Binomial) model
MCMC_BB                 Runs the Markov chain Monte Carlo with the
                        overdispersion (Beta-Binomial) model
a0_gibbs_rate           Internal BEDASSLE Functions
calculate.all.pairwise.Fst
                        Calculates unbiased pairwise Fst between all
                        sampled populations
calculate.pairwise.Fst
                        Calculates unbiased pairwise Fst between a pair
                        of populations
link.up.posteriors      Links up multiple MCMC output objects
make.continuing.params
                        Generates an R object containing the last
                        parameter values of an MCMC run (to be used for
                        a subsequent run)
mcmc.operators          Operator parameters that control the operation
                        of the MCMC
plot_acceptance_rate    Plots the acceptance rate of a parameter across
                        MCMC generations
plot_all_acceptance_rates
                        Plots the acceptance rates of all parameters
                        across MCMC generations
plot_all_joint_marginals
                        Plots the joint marginals for all parameter
                        pairs
plot_all_marginals      Plots the marginal densities for all parameters
plot_all_phi_marginals
                        Plot all the marginals for the phi parameters
                        for all populations
plot_all_phi_trace      Plots all the trace plots for the phi
                        parameters for all populations
plot_all_trace          Plots all the trace plots for all parameters
plot_joint_marginal     Plots the joint marginal for a pair of
                        parameters
plot_marginal           Plots the marginal density of a parameter
plot_phi_marginal       Plots the marginal for the phi parameter
                        estimated in a single population
plot_phi_trace          Plots the trace plot for the phi parameter
                        estimated in a single population
plot_posterior_predictive_samples
                        Plots posterior predictive sampling
plot_trace              Plot the trace plot for a parameter
posterior.predictive.sample
                        Generates posterior predictive samples
