tests/testthat/testExacerbations.R

In epicR: Evaluation Platform in Chronic Obstructive Pulmonary Disease

test_that("In untreated patients:
           (1) The number of severe exacerbations per year is close to 100,000 (CIHI data),
           (2) The annual rate of all exacerbations is higher in diagnosed than undiagnosed patients, and
           (3) The rate of all exacerbations and severe exacerbations increases by GOLD stage", {


  library(dplyr)
  init_session()
  input <- get_input()
  input$values$medication$medication_ln_hr_exac <- rep(0, length(input$values$medication$medication_ln_hr_exac))
  run(input = input$values)

  inputs <- get_inputs()
  output_ex <- get_output_ex()
  
  # Get test values from config
  config <- get_input()$config
  population_over_40 <- config$test_values$population_over_40_2015
  expected_severe_exac <- config$test_values$expected_severe_exacerbations_per_year
  tolerance_value <- config$test_values$expected_severe_exac_tolerance

  #(1) Number of severe exacerbations per year close to expected value from config:
  n_exac <- data.frame(year= 1:inputs$global_parameters$time_horizon,
                      Severe_Exacerbations = output_ex$n_exac_by_ctime_severity_diagnosed[,3]* (population_over_40/rowSums(output_ex$n_alive_by_ctime_sex)))

  averagen_severeexac <- mean(n_exac$Severe_Exacerbations[round(nrow(n_exac)/2,0):nrow(n_exac)])

  expect_equal(averagen_severeexac, expected_severe_exac, tolerance= tolerance_value)

  terminate_session()

  # (2) Annual rate of all exacerbations is higher in diagnosed than undiagnosed patients
  diag_exacrate <- mean(rowSums(output_ex$n_exac_by_ctime_severity_diagnosed)/rowSums(output_ex$n_Diagnosed_by_ctime_sex))

  undiag_exacrate <- mean(rowSums(output_ex$n_exac_by_ctime_severity - output_ex$n_exac_by_ctime_severity_diagnosed)/
                             rowSums(output_ex$n_COPD_by_ctime_sex - output_ex$n_Diagnosed_by_ctime_sex))

  expect_lt(undiag_exacrate, diag_exacrate)

  # (3a) The overall rate of exacerbations increases by GOLD stage
  diag_exacrate_gold <- rowSums(output_ex$n_exac_by_gold_severity_diagnosed)/
                            colSums(output_ex$n_Diagnosed_by_ctime_severity[,2:5])

  diag_exacrategoldTest <- data.frame(mean=diag_exacrate_gold)

  diag_exacrategoldTest$difference <- diag_exacrategoldTest$mean - lag(diag_exacrategoldTest$mean)

  expect_gt(diag_exacrategoldTest$difference[2], 0)
  expect_gt(diag_exacrategoldTest$difference[3], 0)
  expect_gt(diag_exacrategoldTest$difference[4], 0)

  # (3b) The rate of severe exacerbations increases by Gold stage
  diag_sevexacrate_gold <- output_ex$n_exac_by_gold_severity_diagnosed[,3]/colSums(output_ex$n_Diagnosed_by_ctime_severity[,2:5])
  diag_sevexacrategoldTest <- data.frame(mean=diag_sevexacrate_gold)
  diag_sevexacrategoldTest$difference <- diag_sevexacrategoldTest$mean - lag(diag_sevexacrategoldTest$mean)

  expect_gt(diag_sevexacrategoldTest$difference[2], 0)
  expect_gt(diag_sevexacrategoldTest$difference[3], 0)
  expect_gt(diag_sevexacrategoldTest$difference[4], 0)

  terminate_session()

})