CI_gamma1_evidence      Estimate confidence interval for estimated
                        marginal likelihood by simulation
bevimed                 Perform inference under model gamma = 1
call_cpp                R interface to BeviMed c++ MCMC procedure
ccvt-package            A short title line describing what the package
                        does
conditional_prob_pathogenic
                        Calculate probability of pathogencity for
                        variants in region given an association between
                        case label and the region
exact_evidence          Calculate exact evidence for model gamma=1
gamma0_evidence         Calculate marginal probability of observed
                        case-control status y under model gamma = 0
gamma1_evidence         Calculate marginal probability of observed
                        case-control status under model gamma = 1
gamma1_prob             Calculate probability of an association
log_BF                  Calculate log Bayes factor between models
                        gamma=1 and gamma=0 given the data
lower_bound_gamma1_evidence
                        Calculate log lower bound for marginal
                        probability of observations under model gamma =
                        1 by summing likelihood over pathogenic variant
                        (Z) configurations, or probabilities that
                        individual variants are pathogenic.
print.BeviMed           Print readable summary of 'BeviMed' object.
print.BeviMed_summary   Print readable summary of 'BeviMed_summary'
                        object.
prob_association        Calculate probability of an association between
                        presence/absence of local genotype
                        configuration and case-control label
prob_pathogenic         Calculate probability of pathogencity for
                        variants in region given a prior probability of
                        association between case label and the region
region_association_evidence
                        Calculate marginal probability of observed
                        genotypes under 'pathogenic region' model
stack_BeviMeds          Concatenate objects of class 'BeviMed'
stop_chain              Apply the MCMC algorithm in blocks until
                        conditions are met
sum_ML_over_PP          Calculate the Marginal Likelihood by summation
                        over power posterior likelihood exptectances
summary.BeviMed         Create summary of 'BeviMed' classed-object
tune_proposal_sds       Tune the proposal standard deviations for the
                        Metropolis-Hastings updates of either phi or
                        omega
tune_temperatures       Tune temperatures using interval bisection to
                        minimimise Kullback-Liebler divergence between
                        adjacent power posteriors
