| ccvt-package | A short title line describing what the package does |
| bevimed | Perform inference under model gamma = 1 |
| call_cpp | R interface to BeviMed c++ MCMC procedure |
| ccvt | A short title line describing what the package does |
| CI_gamma1_evidence | Estimate confidence interval for estimated marginal likelihood by simulation |
| 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 |
| summary.BeviMed | Create summary of 'BeviMed' classed-object |
| sum_ML_over_PP | Calculate the Marginal Likelihood by summation over power posterior likelihood exptectances |
| 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 |