tests/testthat/test-predicts-0-at-mean.R

In OxWearables/epicoda: Supports epidemiological analyses using compositional exposure variables

comp_labels <-
  c("vigorous", "moderate", "light", "sedentary", "sleep")
m <- comp_model(
  type = "linear",
  data = simdata,
  outcome = "BMI",
  covariates = c("agegroup", "sex"),
  comp_labels = comp_labels,
  rounded_zeroes = TRUE,
  det_limit = 0.00119
)
m2 <- comp_model(
  type = "logistic",
  data = simdata,
  outcome = "disease",
  covariates = c("agegroup", "sex"),
  comp_labels = comp_labels,
  rounded_zeroes = TRUE,
  det_limit = 0.00119
)
m3 <- comp_model(
  type = "cox",
  data = simdata,
  outcome = survival::Surv(simdata$follow_up_time, simdata$event),
  covariates = c("agegroup", "sex"),
  comp_labels = comp_labels,
  rounded_zeroes = TRUE,
  det_limit = 0.00119
)
nd <- comp_mean(
  data = simdata,
  rounded_zeroes = TRUE,
  comp_labels = comp_labels,
  det_limit = 0.00119
)

test_that("prediction at the comp mean is 0", {
  expect_equal(
    0,
    predict_fit_and_ci(
      model = m,
      new_data = nd,
      comp_labels = comp_labels,
      terms = TRUE
    )[1, "fit"]
  )
})

test_that("prediction at the comp mean is 0", {
  expect_equal(0,
               as.numeric(
                 predict_fit_and_ci(
                   model = m,
                   new_data = nd,
                   comp_labels = comp_labels,
                   terms = TRUE
                 )[1, "upper_CI"]
               ))
})


test_that("prediction at the comp mean is 1 - logistic", {
  expect_equal(
    1,
    predict_fit_and_ci(
      model = m2,
      new_data = nd,
      comp_labels = comp_labels,
      terms = TRUE
    )[1, "fit"]
  )
})


test_that("prediction at the comp mean is 1 - logistic", {
  expect_equal(1,
               as.numeric(
                 predict_fit_and_ci(
                   model = m2,
                   new_data = nd,
                   comp_labels = comp_labels,
                   terms = TRUE
                 )[1, "lower_CI"]
               ))
})

test_that("prediction at the comp mean is 1 - cox", {
  expect_equal(
    1,
    predict_fit_and_ci(
      model = m3,
      new_data = nd,
      comp_labels = comp_labels,
      terms = TRUE
    )[1, "fit"]
  )
})

test_that("prediction at the comp mean is 1 - cox", {
  expect_equal(1,
               as.numeric(
                 predict_fit_and_ci(
                   model = m3,
                   new_data = nd,
                   comp_labels = comp_labels,
                   terms = TRUE
                 )[1, "upper_CI"]
               ))
})