tests/testthat/test-plot.bcrosspred.R

In bdlnm: Bayesian Distributed Lag Non-Linear Models (B-DLNM)

test_that("does an overall plot (crossbasis)", {
  skip_on_cran()
  skip_if_not(check_inla(), "INLA not available")

  expect_no_error(plot(
    cpred,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    main = "Overall",
    log = "y"
  ))
  expect_no_error(plot(
    cpred,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    main = "Overall",
    log = "y",
    ci.level = 0.99
  ))
  expect_no_error(plot(
    cpred,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    main = "Overall",
    log = "y",
    ci = "sampling"
  ))
})


test_that("does a 3d plot", {
  skip_on_cran()
  skip_if_not(check_inla(), "INLA not available")

  expect_no_error(plot(
    cpred,
    "3d",
    zlab = "Relative risk",
    col = 4,
    lphi = 60,
    cex.axis = 0.6,
    xlab = "Temperature (ºC)",
    main = "3D graph of temperature effect"
  ))
})

test_that("does a contour plot", {
  skip_on_cran()
  skip_if_not(check_inla(), "INLA not available")

  expect_no_error(plot(
    cpred,
    "contour",
    xlab = "Temperature (ºC)",
    ylab = "Lag",
    main = "Contour plot"
  ))
})

test_that("does a slice plot", {
  skip_on_cran()
  skip_if_not(check_inla(), "INLA not available")

  htemp <- 23
  expect_no_error(plot(
    cpred,
    "slices",
    exp_at = htemp,
    col = 3,
    ylab = "RR",
    main = paste0("Association for a high temperature (", htemp, "ºC)")
  ))

  expect_no_error(plot(
    cpred,
    "slices",
    lag_at = 0,
    col = 4,
    ylab = "RR",
    main = paste0("Association at Lag 0")
  ))
})

test_that("onebasis plots", {
  skip_on_cran()
  skip_if_not(check_inla(), "INLA not available")

  ob <- dlnm::onebasis(slondon$tmean, "strata", breaks = c(5, 10, 20))
  mod_2 <- suppressWarnings(bdlnm(
    mort_75plus ~ ob + factor(dow) + seas,
    data = slondon,
    family = "poisson",
    sample.arg = list(n = n_sim, seed = 1L)
  ))
  cpred_2 <- bcrosspred(mod_2, "ob", exp_at = temp)

  # overall
  expect_no_error(plot(
    cpred_2,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    log = "y"
  ))
  expect_no_error(plot(
    cpred_2,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    log = "y",
    ci.level = 0.99
  ))
  expect_no_error(plot(
    cpred_2,
    "overall",
    xlab = "Temperature (ºC)",
    ylab = "Relative Risk",
    col = 4,
    log = "y",
    ci = "sampling"
  ))

  # 3d plot
  expect_error(plot(
    cpred_2,
    "3d",
    zlab = "Relative risk",
    col = 4,
    lphi = 60,
    cex.axis = 0.6,
    xlab = "Temperature (ºC)",
    main = "3D graph of temperature effect"
  ))

  # contour plot
  expect_error(plot(
    cpred_2,
    "contour",
    xlab = "Temperature (ºC)",
    ylab = "Lag",
    main = "Contour plot"
  ))

  # slices
  htemp <- 23
  expect_error(plot(
    cpred_2,
    "slices",
    exp_at = htemp,
    col = 3,
    ylab = "RR",
    main = paste0("Association for a high temperature (", htemp, "ºC)")
  ))
  expect_error(plot(
    cpred_2,
    "slices",
    lag_at = 0,
    col = 4,
    ylab = "RR",
    main = paste0("Association at Lag 0")
  ))
})