Nothing
cuminc1 <- tidycmprsk::cuminc(Surv(ttdeath, death_cr) ~ 1, data = tidycmprsk::trial)
cuminc2 <- tidycmprsk::cuminc(Surv(ttdeath, death_cr) ~ trt, data = tidycmprsk::trial)
cuminc3 <- tidycmprsk::cuminc(Surv(ttdeath, death_cr) ~ trt + grade, data = tidycmprsk::trial)
sf_cuminc1 <- survfit2(Surv(ttdeath, death_cr) ~ 1, data = tidycmprsk::trial)
sf_cuminc2 <- survfit2(Surv(ttdeath, death_cr) ~ trt, data = tidycmprsk::trial)
sf_cuminc3 <- survfit2(Surv(ttdeath, death_cr) ~ trt + grade, data = tidycmprsk::trial)
test_that("ggcuminc() works", {
expect_error(
lst_ggcuminc_sf <- list(sf_cuminc1, sf_cuminc2, sf_cuminc3) %>% lapply(ggcuminc),
NA
)
expect_error(
lst_ggcuminc <- list(cuminc1, cuminc2, cuminc3) %>% lapply(ggcuminc),
NA
)
expect_error(ggcuminc(mtcars))
expect_error(ggcuminc(cuminc1, outcome = "not an outcome"))
# the linetype_aes argument is silently ignored here
expect_error(
ggcuminc(cuminc1,
outcome = c("death from cancer", "death other causes"),
linetype_aes = TRUE),
NA
)
expect_error(
ggcuminc(cuminc1, outcome = c("death from cancer", "death other causes")),
NA
)
skip_on_ci()
vdiffr::expect_doppelganger("sf_cuminc1-ggcuminc", lst_ggcuminc_sf[[1]])
vdiffr::expect_doppelganger("sf_cuminc2-ggcuminc", lst_ggcuminc_sf[[2]])
vdiffr::expect_doppelganger("sf_cuminc3-ggcuminc", lst_ggcuminc_sf[[3]])
vdiffr::expect_doppelganger("cuminc1-ggcuminc", lst_ggcuminc[[1]])
vdiffr::expect_doppelganger("cuminc2-ggcuminc", lst_ggcuminc[[2]])
vdiffr::expect_doppelganger("cuminc3-ggcuminc", lst_ggcuminc[[3]])
})
test_that("ggcuminc() works with multiple outcomes", {
expect_error(
lst_ggcuminc_outcomes <-
list(cuminc1, cuminc2, cuminc3) %>%
lapply(ggcuminc, outcome = c("death from cancer", "death other causes")),
NA
)
expect_error(
lst_ggcuminc_outcomes_sf <-
list(sf_cuminc1, sf_cuminc2, sf_cuminc3) %>%
lapply(ggcuminc, outcome = c("death from cancer", "death other causes")),
NA
)
skip_on_ci()
vdiffr::expect_doppelganger("cuminc1-ggcuminc-all-outcomes", lst_ggcuminc_outcomes[[1]])
vdiffr::expect_doppelganger("cuminc2-ggcuminc-all-outcomes", lst_ggcuminc_outcomes[[2]])
vdiffr::expect_doppelganger("cuminc3-ggcuminc-all-outcomes", lst_ggcuminc_outcomes[[3]])
vdiffr::expect_doppelganger("cuminc1-ggcuminc_sf-all-outcomes", lst_ggcuminc_outcomes_sf[[1]])
vdiffr::expect_doppelganger("cuminc2-ggcuminc_sf-all-outcomes", lst_ggcuminc_outcomes_sf[[2]])
vdiffr::expect_doppelganger("cuminc3-ggcuminc_sf-all-outcomes", lst_ggcuminc_outcomes_sf[[3]])
})
test_that("ggcuminc() axis label correct with multi-state model ", {
d1 <- subset(survival::colon, etype==1)
d2 <- subset(survival::colon, etype==2)
cdata <- survival::tmerge(subset(d1,,c(id, rx, extent, node4)), d2, id = id,
death = event(time, status))
cdata <- survival::tmerge(cdata, d1, id = id, recur=event(time, status))
# a death and recurrence on the same day is counted as a recurrence
cdata$state <- with(cdata, factor(ifelse(recur==1,1, 2*death), 0:2,
c("censor", "recur", "death")))
cdata$trt <- 1*(cdata$rx=="Lev+5FU") # lump the Obs and Lev arms together
cfit <- survfit(Surv(tstart, tstop, state) ~ trt, cdata, id=id)
expect_equal(
tidy_survfit(cfit, times = 1000)$estimate_type_label %>% unique(),
"Probability in State"
)
})
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