tests/testthat/test_plot_surv_at_t.r

In contsurvplot: Visualize the Effect of a Continuous Variable on a Time-to-Event Outcome

suppressMessages(requireNamespace("survival"))

sim_dat <- readRDS(system.file("testdata", "sim150.Rds",
                               package="contsurvplot"))
sim_dat$group <- factor(sim_dat$group)

model <- survival::coxph(survival::Surv(time, event) ~ x3 + group,
                         data=sim_dat, x=TRUE)

set.seed(34)

test_that("plot, defaults", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, t=20)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, defaults", fig=plt)
})

test_that("plot, with ci, one t", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, t=20, conf_int=TRUE,
                        n_boot=3)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, with ci, one t", fig=plt)
})

test_that("plot, with ci, multiple t", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, t=c(20, 25), conf_int=TRUE,
                        n_boot=3)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, with ci, multiple t", fig=plt)
})

test_that("plot, cif", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, cif=TRUE, t=20,
                        na.action=na.omit)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, cif", fig=plt)
})

test_that("plot, change horizon", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model,  horizon=seq(30, 60, 1),
                        t=20)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, change horizon", fig=plt)
})

test_that("plot, custom colors", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, t=c(7, 20, 45),
                        custom_colors=c("black", "red", "green"))
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, custom colors", fig=plt)
})

test_that("plot, with group", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        group="group", data=sim_dat, model=model, t=20)
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, with group", fig=plt)
})

test_that("plot, lots of stuff", {
  plt <- plot_surv_at_t(time="time", status="event", variable="x3",
                        data=sim_dat, model=model, cif=TRUE, t=35,
                        linetype="dashed", alpha=0.8, title="Title",
                        subtitle="Subtitle", xlab="x", ylab="y",
                        gg_theme=ggplot2::theme_classic())
  expect_s3_class(plt, "ggplot")
  vdiffr::expect_doppelganger("plot, lots of stuff", fig=plt)
})