test_that("Log likelihood components work correctly", {
  
  # Create a simple model with known parameters
  modelParameters <- LinearAbxModel(nstates = 2)
  
  # Override with simpler values that shouldn't cause -inf
  modelParameters$Insitu$probs <- c(0.9, 0.0, 0.1)
  modelParameters$Insitu$priors <- c(0.9, 0.0, 0.1)
  modelParameters$Insitu$doit <- c(TRUE, FALSE, TRUE)
  
  # Create a minimal test with just a few events
  minimal_data <- data.frame(
    facility = c(1, 1, 1),
    unit = c(1, 1, 1),
    time = c(0.0, 0.1, 1.0),
    patient = c(1, 1, 1),
    type = c(0, 1, 3)  # admission, pos test, discharge
  )
  
  # Try to create a model
  model_result <- tryCatch({
    newModelExport(modelParameters, verbose = FALSE)
  }, error = function(e) {
    list(error = e$message)
  })
  
  if (!is.null(model_result$error)) {
    skip(paste("Model creation failed:", model_result$error))
  }
  
  expect_true(!is.null(model_result))
})

test_that("InsituParams probabilities are valid", {
  # Test that insitu parameters don't produce -inf
  modelParameters <- LinearAbxModel(nstates = 2)
  
  # Check R-side values
  expect_true(all(modelParameters$Insitu$probs >= 0))
  expect_true(all(modelParameters$Insitu$probs <= 1))
  expect_equal(sum(modelParameters$Insitu$probs), 1.0, tolerance = 1e-10)
  
  # For 2-state model, latent should be 0
  expect_equal(modelParameters$Insitu$probs[2], 0.0)
})

test_that("Acquisition parameters don't produce NaN", {
  modelParameters <- LinearAbxModel(nstates = 2)
  
  acq <- modelParameters$InCol$acquisition
  
  # Check that init values are in valid ranges
  expect_true(acq$base$init > 0, info = "base should be positive")
  
  # Mass and freq are probabilities (logit-transformed)
  expect_true(acq$mass$init >= 0 && acq$mass$init <= 1, 
              info = sprintf("mass init = %f should be in [0,1]", acq$mass$init))
  expect_true(acq$freq$init >= 0 && acq$freq$init <= 1,
              info = sprintf("freq init = %f should be in [0,1]", acq$freq$init))
  
  # Check priors are also valid
  expect_true(acq$mass$prior >= 0 && acq$mass$prior <= 1,
              info = sprintf("mass prior = %f should be in [0,1]", acq$mass$prior))
  expect_true(acq$freq$prior >= 0 && acq$freq$prior <= 1,
              info = sprintf("freq prior = %f should be in [0,1]", acq$freq$prior))
})

test_that("Test with original model defaults", {
  # Try to replicate the original C++ defaults
  modelParameters <- LinearAbxModel(nstates = 2)
  
  # Set to values from original simulated.Model (all commented, so defaults used)
  # Original defaults from C++ code for 2-state:
  modelParameters$Insitu$probs <- c(0.9, 0.0, 0.1)
  modelParameters$Insitu$priors <- c(1, 1, 1)
  modelParameters$Insitu$doit <- c(TRUE, FALSE, TRUE)
  
  # Updated to match original C++ model file values:
  # - mass = 1.0 (to avoid logit issues at 0.5)
  # - freq = 1.0 (to avoid logit issues at 0.5)
  # - base = 0.001 (must be > 0)
  
  expect_equal(modelParameters$InCol$acquisition$mass$init, 1.0)
  expect_equal(modelParameters$InCol$acquisition$freq$init, 1.0)
  expect_equal(modelParameters$InCol$acquisition$base$init, 0.001)
})

test_that("Simple MCMC with minimal iterations", {
  skip_if_not(interactive(), "Skipping interactive MCMC test")
  
  modelParameters <- LinearAbxModel(nstates = 2)
  
  # Use original-style parameters
  modelParameters$Insitu$probs <- c(0.9, 0.0, 0.1)
  
  # Try with just 1 burn-in and 1 simulation
  results <- tryCatch({
    runMCMC(
      data = simulated.data,
      nburn = 0,  # No burn-in
      nsims = 1,   # Just 1 iteration
      outputparam = TRUE,
      outputfinal = FALSE,
      modelParameters = modelParameters,
      verbose = FALSE
    )
  }, error = function(e) {
    list(error = e$message, trace = capture.output(traceback()))
  })
  
  # Quiet: don't print errors; assertion below includes details on failure
  
  expect_true(is.null(results$error), 
              info = paste("MCMC failed:", results$error,
                            if (!is.null(results$trace)) paste0("\nTraceback:\n", paste(results$trace, collapse = "\n")) else ""))
})