tests/testthat/test_hier.R

In disbayes: Bayesian Multi-State Modelling of Chronic Disease Burden Data

source("data.r")

test_that("hierarchical model", {
  db <- disbayes_hier(ihdmale, age="age", group="area", 
                             inc_num = "inc_num", inc_denom = "inc_denom",
                           prev_num = "prev_num", prev_denom = "prev_denom",
                           mort_num = "mort_num", mort_denom = "mort_denom",
                    iter=10, chains=1, method="mcmc", algorithm="Fixed_param")
  expect_s3_class(db, "disbayes_hier")
})

test_that("errors in specifying hierarchical model", {
  expect_error(disbayes_hier(ihdengland, age="age", group="area", 
                             inc_num = "inc_num", inc_denom = "inc_denom",
                             prev_num = "prev_num", prev_denom = "prev_denom",
                             mort_num = "mort_num", mort_denom = "mort_denom"),
               "rows in data, expected")
  
  ## call nonhier model by mistake 
  expect_error(
    disbayes(ihdmale, age="age", 
             inc_num = "inc_num", inc_denom = "inc_denom",
             prev_num = "prev_num", prev_denom = "prev_denom",
             mort_num = "mort_num", mort_denom = "mort_denom"),
    "rows in data")
  ihdmale$badage <- ihdmale$age
  ihdmale$badage[20:30] <- 92
  
  expect_error(disbayes_hier(ihdmale, age="nonexistent", group="area", 
                             inc_num = "inc_num", inc_denom = "inc_denom",
                             prev_num = "prev_num", prev_denom = "prev_denom",
                             mort_num = "mort_num", mort_denom = "mort_denom"),
               "age variable")
  
  expect_error(disbayes_hier(ihdmale, age = "badage",
                             inc_num = "inc_num", inc_denom = "inc_denom",
                             prev_num = "prev_num", prev_denom = "prev_denom",
                             mort_num = "mort_num", mort_denom = "mort_denom"
  ),
  "`group` variable not supplied")
  
  expect_error(disbayes_hier(ihdmale, age = "badage", group="area",
                             inc_num = "inc_num", inc_denom = "inc_denom",
                             prev_num = "prev_num", prev_denom = "prev_denom",
                             mort_num = "mort_num", mort_denom = "mort_denom"
  ),
  "value per year of age")
  
  ihdmale$badage <- ihdmale$age
  ihdmale$badage[20:21] <- 20:19
  expect_error(disbayes_hier(data = ihdmale, age = "badage", group="area",
                             inc_num = "inc_num", inc_denom = "inc_denom",
                             prev_num = "prev_num", prev_denom = "prev_denom",
                             mort_num = "mort_num", mort_denom = "mort_denom"
  ),
  "one value per year of age")
})



test_that("fixed hyperparameters",{
  
  db <- disbayes_hier(ihdmale, age="age", group="area", 
                      inc_num = "inc_num", inc_denom = "inc_denom",
                      prev_num = "prev_num", prev_denom = "prev_denom",
                      mort_num = "mort_num", mort_denom = "mort_denom",
                      hp_fixed = list(scf = 1), 
                      iter=10, chains=1, method="mcmc", algorithm="Fixed_param")
  expect_equivalent(db$hp_fixed["scf"], 1)

  db <- disbayes_hier(ihdmale, age="age", group="area", 
                      inc_num = "inc_num", inc_denom = "inc_denom",
                      prev_num = "prev_num", prev_denom = "prev_denom",
                      mort_num = "mort_num", mort_denom = "mort_denom",
                      hp_fixed = list(scf = 1, sd_int = 1), 
                      iter=10, chains=1, method="mcmc", algorithm="Fixed_param")
  expect_equivalent(db$hp_fixed["sd_int"], 1)

  db <- disbayes_hier(ihdmale, age="age", group="area", 
                      inc_num = "inc_num", inc_denom = "inc_denom",
                      prev_num = "prev_num", prev_denom = "prev_denom",
                      mort_num = "mort_num", mort_denom = "mort_denom",
                      hp_fixed = list(scf = TRUE, sinc = 1.234, sd_int = TRUE), 
                      iter=10, chains=1, method="mcmc", algorithm="Fixed_param")
  expect_equivalent(db$hp_fixed["sinc"], 1.234)
  expect_type(db$hp_fixed["scf"], "double")
  
  expect_warning(
    disbayes_hier(ihdmale, age="age", group="area", 
                  inc_num = "inc_num", inc_denom = "inc_denom",
                  prev_num = "prev_num", prev_denom = "prev_denom",
                  mort_num = "mort_num", mort_denom = "mort_denom",
                  cf_model = "interceptonly",
                  hp_fixed = list(sd_slope = 1), 
                  chains=1, iter=10, method="mcmc", algorithm="Fixed_param"),
    "Ignoring hp_fixed")
  
})