tests/testthat/test-coxph.R

In javifar/ggeffects: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs

if (require("testthat") && require("ggeffects") && require("emmeans") && require("survival") && packageVersion("survival") >= "3.2.9") {

  data("lung2")
  m1 <- survival::coxph(survival::Surv(time, status) ~ sex + age + ph.ecog, data = lung2)

  test_that("ggpredict", {
    p <- ggpredict(m1, "sex")
    expect_equal(p$predicted[1], 1, tolerance = 1e-2)
    ggpredict(m1, c("sex", "age"))
  })

  test_that("ggemmeans", {
    if (packageVersion("emmeans") > "1.4.5") {
      p <- ggemmeans(m1, "sex")
      expect_equal(p$predicted[1], 0.7521603, tolerance = 1e-2)
      ggemmeans(m1, c("sex", "age"))
    }
  })

  test_that("ggpredict", {
    p <- ggpredict(m1, "sex", type = "surv")
    expect_equal(p$predicted[1], 0.9966796, tolerance = 1e-2)
    p <- ggpredict(m1, "sex", type = "cumhaz")
    expect_equal(p$predicted[1], 0.003325958, tolerance = 1e-2)
  })

  # test start of time
  df1 <- data.frame(
    production = c(15, 12, 10, 9, 6, 8, 9, 5, 3, 3, 2, 1, 0, 0, 0, 0),
    Treatment_Num = c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4),
    Genotype = c(1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2),
    Source_Salinity = c("Fresh", "Fresh", "Brackish", "Brackish", "Fresh", "Fresh",
                        "Brackish", "Brackish", "Fresh", "Fresh", "Brackish", "Brackish",
                        "Fresh", "Fresh", "Brackish", "Brackish"),
    Days_to_death = c(500, 500, 500, 500, 400, 350, 300, 500, 200, 202, 260,
                      280, 150, 150, 160, 140),
    censored = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0)
  )
  m <- coxph(Surv(time = Days_to_death, event = censored) ~ Treatment_Num + Source_Salinity, data = df1)

  test_that("ggpredict", {
    p <- ggpredict(m, c("Treatment_Num [all]", "Source_Salinity [all]"),type = "survival")
    expect_equal(head(p$x, 10), c(1, 1, 1, 1, 1, 1, 1, 1, 140, 140), tolerance = 1e-2)
    expect_equal(head(p$predicted, 10), c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), tolerance = 1e-2)

    p <- ggpredict(m, c("Treatment_Num [all]", "Source_Salinity [all]"),type = "cumulative_hazard")
    expect_equal(head(p$x, 10), c(1, 1, 1, 1, 1, 1, 1, 1, 140, 140), tolerance = 1e-2)
    expect_equal(head(p$predicted, 10), c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), tolerance = 1e-2)
  })
}