tests/testthat/test_cif_aiptw.r

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

library(survival)

set.seed(42)

sim_dat <- readRDS(system.file("testdata",
                               "d_sim_crisk_n_100.Rds",
                               package="adjustedCurves"))
sim_dat$group <- as.factor(sim_dat$group)

# outcome model
outc_mod <- riskRegression::CSC(Hist(time, event) ~ x1 + x2 + x3 + x4 + x5 + x6,
                                data=sim_dat)

# treatment model
treat_mod <- glm(group ~ x1 + x2 + x3 + x4 + x5 + x6, data=sim_dat,
                 family="binomial")

## Just check if function throws any errors
test_that("2 treatments, no conf_int, no boot", {
  adj <- adjustedcif(data=sim_dat,
                     variable="group",
                     ev_time="time",
                     event="event",
                     method="aiptw",
                     conf_int=FALSE,
                     outcome_model=outc_mod,
                     treatment_model=treat_mod,
                     cause=1)
  expect_s3_class(adj, "adjustedcif")
  expect_true(is.numeric(adj$adj$cif))
  expect_equal(levels(adj$adj$group), levels(sim_dat$group))
})

test_that("2 treatments, with conf_int, no boot", {
  adj <- adjustedcif(data=sim_dat,
                     variable="group",
                     ev_time="time",
                     event="event",
                     method="aiptw",
                     conf_int=TRUE,
                     outcome_model=outc_mod,
                     treatment_model=treat_mod,
                     cause=1)
  expect_s3_class(adj, "adjustedcif")
  expect_true(is.numeric(adj$adj$cif))
  expect_equal(levels(adj$adj$group), levels(sim_dat$group))
})

test_that("2 treatments, no conf_int, with boot", {
  adj <- adjustedcif(data=sim_dat,
                     variable="group",
                     ev_time="time",
                     event="event",
                     method="aiptw",
                     conf_int=FALSE,
                     bootstrap=TRUE,
                     n_boot=2,
                     outcome_model=outc_mod,
                     treatment_model=treat_mod,
                     cause=1)
  expect_s3_class(adj, "adjustedcif")
  expect_true(is.numeric(adj$adj$cif))
  expect_equal(levels(adj$adj$group), levels(sim_dat$group))
})

test_that("2 treatments, no conf_int, no boot, with times", {
  adj <- adjustedcif(data=sim_dat,
                     variable="group",
                     ev_time="time",
                     event="event",
                     method="aiptw",
                     conf_int=FALSE,
                     bootstrap=FALSE,
                     n_boot=2,
                     outcome_model=outc_mod,
                     treatment_model=treat_mod,
                     times=c(0.5, 1),
                     cause=1)
  expect_s3_class(adj, "adjustedcif")
  expect_true(is.numeric(adj$adj$cif))
  expect_equal(levels(adj$adj$group), levels(sim_dat$group))
})

cens_mod <- survival::coxph(Surv(time, event==0) ~ x2, data=sim_dat, x=TRUE)

test_that("2 treatments, no conf_int, no boot, with times, with cens_mod", {
  adj <- adjustedcif(data=sim_dat,
                     variable="group",
                     ev_time="time",
                     event="event",
                     method="aiptw",
                     conf_int=FALSE,
                     bootstrap=FALSE,
                     n_boot=2,
                     outcome_model=outc_mod,
                     treatment_model=treat_mod,
                     censoring_model=cens_mod,
                     times=c(0.5, 1),
                     cause=1)
  expect_s3_class(adj, "adjustedcif")
  expect_true(is.numeric(adj$adj$cif))
  expect_equal(levels(adj$adj$group), levels(sim_dat$group))
})