tests/testthat/test_adjusted_rmst.r

In RobinDenz1/adjustedCurves: Confounder-Adjusted Survival Curves and Cumulative Incidence Functions

suppressMessages(requireNamespace("survival"))

set.seed(42)
sim_dat <- sim_confounded_surv(n=50, max_t=1.5)
sim_dat$group <- factor(sim_dat$group)

adj <- adjustedsurv(data=sim_dat,
                    variable="group",
                    ev_time="time",
                    event="event",
                    method="km",
                    conf_int=TRUE,
                    bootstrap=TRUE,
                    n_boot=10)

adj_no_boot <- adj
adj_no_boot$boot_data <- NULL
adj_no_boot$boot_adj <- NULL

test_that("rmst 2 treatments, no boot", {
  adj_rmst <- adjusted_rmst(adj, to=1.1)
  expect_equal(round(adj_rmst$rmst, 4), c(0.5211, 0.6721))
})

test_that("rmst 2 treatments, multiple to, no boot", {
  adj_rmst <- adjusted_rmst(adj, to=c(1, 1.1))
  expect_equal(round(adj_rmst$rmst, 4), c(0.5115, 0.6566, 0.5211, 0.6721))
})

test_that("rmst 2 treatments, no boot, diff", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, contrast="diff")
  expect_equal(round(adj_rmst$diff, 4), -0.1510)
})

test_that("rmst 2 treatments, no boot, diff, multiple to", {
  adj_rmst <- adjusted_rmst(adj, to=c(1, 1.1), contrast="diff")
  expect_equal(round(adj_rmst$diff, 4), c(-0.1451, -0.1510))
})

test_that("rmst 2 treatments, no boot, diff, groups", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, contrast="diff",
                            group_1="1", group_2="0")
  expect_equal(round(adj_rmst$diff, 4), 0.1510)
})

test_that("rmst 2 treatments, no boot, linear", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, interpolation="linear")
  expect_equal(round(adj_rmst$rmst, 4), c(0.50430, 0.6599))
})

test_that("rmst 2 treatments, no boot, linear, multiple to", {
  adj_rmst <- adjusted_rmst(adj, to=c(1, 1.1), interpolation="linear")
  expect_equal(round(adj_rmst$rmst, 4), c(0.4958, 0.6462, 0.50430, 0.6599))
})

test_that("rmst 2 treatments, no boot but conf_int=TRUE", {
  adj_rmst <- suppressWarnings(adjusted_rmst(adj_no_boot, to=1.1,
                                             conf_int=TRUE))
  expect_equal(round(adj_rmst$rmst, 4), c(0.5211, 0.6721))
})

test_that("rmst 2 treatments, with boot", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, conf_int=TRUE)
  expect_equal(round(adj_rmst$rmst, 4), c(0.5211, 0.6721))
  expect_equal(round(adj_rmst$se, 4), c(0.0783, 0.0679))
  expect_equal(adj_rmst$n_boot, c(10, 7))
})

test_that("rmst 2 treatments, with boot, multiple to", {
  adj_rmst <- adjusted_rmst(adj, to=c(1, 1.1), conf_int=TRUE)
  expect_equal(round(adj_rmst$rmst, 4), c(0.5115, 0.6566, 0.5211, 0.6721))
  expect_equal(round(adj_rmst$se, 4), c(0.0744, 0.0512, 0.0783, 0.0679))
  expect_equal(adj_rmst$n_boot, c(10, 10, 10, 7))
})

test_that("rmst 2 treatments, with boot, ratio", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, conf_int=TRUE, contrast="ratio")
  expect_equal(round(adj_rmst$ratio, 4), 0.7753)
  expect_equal(round(adj_rmst$ci_lower, 4), 0.5245)
  expect_equal(round(adj_rmst$ci_upper, 4), 1.0894)
  expect_equal(round(adj_rmst$p_value, 4), 0.145)
})

test_that("rmst 2 treatments, with boot, diff", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, conf_int=TRUE, contrast="diff")
  expect_equal(round(adj_rmst$diff, 4), -0.1510)
  expect_equal(round(adj_rmst$se, 4), 0.1036)
  expect_equal(round(adj_rmst$ci_lower, 4), -0.3541)
  expect_equal(round(adj_rmst$ci_upper, 4), 0.0521)
  expect_equal(round(adj_rmst$p_value, 4), 0.145)
})

test_that("rmst 2 treatments, with boot, linear", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, conf_int=TRUE,
                            interpolation="linear")
  expect_equal(round(adj_rmst$rmst, 4), c(0.5043, 0.6599))
  expect_equal(round(adj_rmst$se, 4), c(0.0774, 0.0683))
  expect_equal(adj_rmst$n_boot, c(10, 7))
})

test_that("rmst 2 treatments, no boot, using from", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, from=0.3)
  expect_equal(round(adj_rmst$rmst, 4), c(0.2565, 0.3809))
})

test_that("rmst 2 treatments, with boot, using from", {
  adj_rmst <- adjusted_rmst(adj, to=1.1, from=0.3, conf_int=TRUE)
  expect_equal(round(adj_rmst$rmst, 4), c(0.2565, 0.3809))
  expect_equal(round(adj_rmst$se, 4), c(0.0663, 0.0580))
  expect_equal(adj_rmst$n_boot, c(10, 7))
})

sim_dat$group <- as.character(sim_dat$group)
sim_dat$group[sim_dat$group==1] <- sample(c(1, 2),
                                          size=sum(sim_dat$group==1),
                                          replace=TRUE)
sim_dat$group <- factor(sim_dat$group)

adj <- adjustedsurv(data=sim_dat,
                    variable="group",
                    ev_time="time",
                    event="event",
                    method="km",
                    conf_int=TRUE,
                    bootstrap=TRUE,
                    n_boot=10)

test_that("rmst 3 treatments, no boot", {
  adj_rmst <- adjusted_rmst(adj, to=1)
  expect_equal(round(adj_rmst$rmst, 3), c(0.511, 0.702, 0.629))
})

test_that("rmst 3 treatments, no boot, diff", {
  adj_rmst <- adjusted_rmst(adj, to=1, contrast="diff")
  expect_equal(round(adj_rmst$diff, 4), -0.1906)
})

test_that("rmst 3 treatments, no boot, ratio", {
  adj_rmst <- adjusted_rmst(adj, to=1, contrast="ratio")
  expect_equal(round(adj_rmst$ratio, 4), 0.7286)
})

test_that("rmst 3 treatments, no boot, linear", {
  adj_rmst <- adjusted_rmst(adj, to=1, interpolation="linear")
  expect_equal(round(adj_rmst$rmst, 4), c(0.4958, 0.6867, 0.6221))
})

test_that("rmst 3 treatments, with boot, linear", {
  adj_rmst <- adjusted_rmst(adj, to=1, conf_int=TRUE, interpolation="linear")
  expect_equal(round(adj_rmst$rmst, 3), c(0.496, 0.687, 0.622))
  expect_equal(round(adj_rmst$se, 3), c(0.069, 0.066, 0.064))
  expect_equal(adj_rmst$n_boot, c(10, 10, 10))
})

test_that("rmst 3 treatments, no boot, using from", {
  adj_rmst <- adjusted_rmst(adj, to=1, from=0.3)
  expect_equal(round(adj_rmst$rmst, 4), c(0.2470, 0.4021, 0.3441))
})

test_that("rmst 3 treatments, with boot, using from", {
  adj_rmst <- adjusted_rmst(adj, to=1, from=0.3, conf_int=TRUE)
  expect_equal(round(adj_rmst$rmst, 4), c(0.2470, 0.4021, 0.3441))
  expect_equal(round(adj_rmst$se, 3), c(0.058, 0.067, 0.056))
  expect_equal(adj_rmst$n_boot, c(10, 10, 10))
})