plotPerDbMcmcTrace: Plot MCMC trace for individual databases

Description

Plot MCMC trace for individual databases

Usage

plotPerDbMcmcTrace(
  estimate,
  showEstimate = TRUE,
  dataCutoff = 0.01,
  fileName = NULL
)

Value

A Ggplot object. Use the ggplot2::ggsave function to save to file.

Arguments

estimate: An object as generated using the computeBayesianMetaAnalysis() function.
showEstimate: Show the parameter estimates (mode) and 95 percent confidence intervals?
dataCutoff: This fraction of the data at both tails will be removed.
fileName: Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave in the ggplot2 package for supported file formats.

Details

Plot the samples of the posterior distribution of the theta parameter (the estimated log hazard ratio) at each site. Samples are taken using Markov-chain Monte Carlo (MCMC).

Examples

Run this code

# Simulate some data for this example:
populations <- simulatePopulations()

# Fit a Cox regression at each data site, and approximate likelihood function:
fitModelInDatabase <- function(population) {
  cyclopsData <- Cyclops::createCyclopsData(Surv(time, y) ~ x + strata(stratumId),
    data = population,
    modelType = "cox"
  )
  cyclopsFit <- Cyclops::fitCyclopsModel(cyclopsData)
  approximation <- approximateLikelihood(cyclopsFit,
                                         parameter = "x",
                                         approximation = "grid with gradients")
  return(approximation)
}
approximations <- lapply(populations, fitModelInDatabase)

# At study coordinating center, perform meta-analysis using per-site approximations:
estimate <- computeBayesianMetaAnalysis(approximations)
plotPerDbMcmcTrace(estimate)