Nothing
test_that("crr() works", {
cmprsk_crr1 <-
cmprsk::crr(
ftime = trial$ttdeath,
fstatus = as.numeric(trial$death_cr) - 1L,
cov1 = as.matrix(trial[["age"]]),
failcode = 1
)
expect_error(
crr1 <- crr(Surv(ttdeath, death_cr) ~ age, data = trial, conf.level = 0.90),
NA
)
expect_equal(
crr(Surv(ttdeath, death_cr) ~ age + trt,
data = trial %>% dplyr::mutate(trt = factor(trt, levels = paste("Drug", c("A", "B", "C"))))) %>%
utils::modifyList(val = list(data = NULL, blueprint = NULL, xlevels = NULL)),
crr(Surv(ttdeath, death_cr) ~ age + trt,
data = trial %>% dplyr::mutate(trt = factor(trt))) %>%
utils::modifyList(val = list(data = NULL, blueprint = NULL, xlevels = NULL))
)
expect_equal(
tidy(crr1, conf.int = TRUE) %>%
select(all_of(names(.) %>% sort())),
broom::tidy(crr1$cmprsk, conf.int = TRUE, conf.level = 0.90) %>%
select(all_of(names(.) %>% sort()))
)
expect_equal(
glance(crr1),
broom::glance(crr1$cmprsk)
)
expect_equal(
summary(crr1$cmprsk)$coef %>% unname(),
summary(cmprsk_crr1)$coef %>% unname()
)
expect_equal(
summary(crr1$cmprsk)$conf.int %>% unname(),
summary(cmprsk_crr1)$conf.int %>% unname()
)
expect_error(
as_numeric_failcode(Surv(NOT_A_VAR, death) ~ age, trial, NULL)
)
expect_error(
as_numeric_failcode(Surv(ttdeath, death) ~ age, trial, NULL)
)
expect_error(
as_numeric_failcode(Surv(ttdeath, death_cr) ~ age, trial, failcode = "NOT_A_LEVEL")
)
expect_error(
crr(letters)
)
# `crr()` works with no observed censoring
expect_error(
crr_no_censor<-
crr(
Surv(ttdeath, death_cr) ~ trt,
data = trial %>% dplyr::filter(!death_cr %in% "censor")
),
NA
)
expect_equal(
cmprsk::crr(
ftime = trial$ttdeath[!trial$death_cr %in% "censor"],
fstatus = as.numeric(trial$death_cr[!trial$death_cr %in% "censor"]) - 1L,
cov1 = model.matrix(~., data = trial[!trial$death_cr %in% "censor", "trt"])[, -1, drop = FALSE]
)[1:6],
crr_no_censor$cmprsk[1:6]
)
})
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