tests/testthat/test-simpleBayesianModel.R

In OHDSI/EvidenceSynthesis: Synthesizing Causal Evidence in a Distributed Research Network

library(survival)
library(testthat)

test_that("Simple Bayesian profile-normal model", {
  skip_if_not(supportsJava8())

  set.seed(666)
  population <- simulatePopulations(createSimulationSettings(nSites = 1))[[1]]
  cyclopsData <- Cyclops::createCyclopsData(Surv(time, y) ~ x + strata(stratumId),
    data = population,
    modelType = "cox"
  )
  cyclopsFit <- Cyclops::fitCyclopsModel(cyclopsData)
  likelihoodProfile <- approximateLikelihood(cyclopsFit, parameter = "x", approximation = "grid")

  traces <- approximateSimplePosterior(likelihoodProfile = likelihoodProfile, priorMean = 0, priorSd = 100, seed = 666)
  expect_equivalent(mean(traces$theta1), coef(cyclopsFit)[1], tolerance = 0.1)
})