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 |