R: Bias Correction with Inference

biasCorrectionInference {EvidenceSynthesis}

R Documentation

Bias Correction with Inference

Description

Perform Bayesian posterior inference regarding an outcome of interest with bias correction using negative control analysis. There is an option to not perform bias correction so that un-corrected results can be obtained.

Usage

biasCorrectionInference(
  likelihoodProfiles,
  ncLikelihoodProfiles = NULL,
  biasDistributions = NULL,
  priorMean = 0,
  priorSd = 1,
  numsamps = 10000,
  thin = 10,
  doCorrection = TRUE,
  seed = 1,
  ...
)

Arguments

`likelihoodProfiles`	A list of grid profile likelihoods for the outcome of interest.
`ncLikelihoodProfiles`	Likelihood profiles for the negative control outcomes. Must be a list of lists of profile likelihoods; if there is only one analysis period, then this must be a length-1 list, with the first item as a list all outcome-wise profile likelihoods.
`biasDistributions`	Pre-saved bias distribution(s), formatted as the output from `fitBiasDistribution()` or `sequentialFitBiasDistribution()`. If NULL, then `ncLikelihoodProfiles` must be provided.
`priorMean`	Prior mean for the effect size (log rate ratio).
`priorSd`	Prior standard deviation for the effect size (log rate ratio).
`numsamps`	Total number of MCMC samples needed.
`thin`	Thinning frequency: how many iterations before another sample is obtained?
`doCorrection`	Whether or not to perform bias correction; default: TRUE.
`seed`	Seed for the random number generator.
`...`	Arguments to be passed to `sequentialFitBiasDistribution()` to fit bias distributions if `biasDistributions` is NULL.

Value

A dataframe with five columns, including posterior median and mean of log RR effect size estimates, 95% credible intervals (ci95Lb and ci95Ub), posterior probability that log RR > 0 (p1), and the period or group ID (Id).

It is accompanied by the following attributes:

samplesCorrected: all MCMC samples for the bias corrected log RR effect size estimate.
samplesRaw: all MCMC samples for log RR effect size estimate, without bias correction.
biasDistributions: the learned empirical bias distribution from negative control analysis.
summaryRaw: a summary dataframe (same format as in the main result) without bias correction.
corrected: a logical flag indicating if bias correction has been performed; = TRUE if doCorrection = TRUE.

Examples

# load example data
data("ncLikelihoods")
data("ooiLikelihoods")

# perform sequential analysis with bias correction, using the t model
# NOT RUN
# bbcResults = biasCorrectionInference(ooiLikelihoods,
#                                      ncLikelihoodProfiles = ncLikelihoods,
#                                      robust = TRUE,
#                                      seed = 42)

# check out analysis summary
# bbcResults