Nothing
skip_on_cran()
t1 <- trial %>% tbl_summary()
t2 <- trial %>% tbl_summary(by = trt)
test_that("no errors/warnings with standard use", {
expect_error(res <- t1 %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_error(res <- t2 %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(), NA)
expect_warning(t2 %>% add_n(), NA)
expect_error(res <- t1 %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_error(res <- t2 %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(last = TRUE), NA)
expect_warning(t2 %>% add_n(last = TRUE), NA)
expect_error(
res <-
t1 %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
t2 %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
expect_warning(t2 %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
# check that the Ns are the same when add overall is run before/after add_n()
tbl1 <- tbl_summary(trial, by = trt, include = c(age, stage))
expect_equal(
tbl1 %>% add_n() %>% add_overall() %>% purrr::pluck("table_body", "n"),
tbl1 %>% add_overall() %>% add_n() %>% purrr::pluck("table_body", "n")
)
})
t1 <- trial %>% tbl_summary(type = all_continuous() ~ "continuous2")
t2 <- trial %>% tbl_summary(by = trt, type = all_continuous() ~ "continuous2")
test_that("no errors/warnings with standard use with continuous2", {
expect_error(res <- t1 %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_error(res <- t2 %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(), NA)
expect_warning(t2 %>% add_n(), NA)
expect_error(res <- t1 %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_error(res <- t2 %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(last = TRUE), NA)
expect_warning(t2 %>% add_n(last = TRUE), NA)
expect_error(
res <- t1 %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
res <- t2 %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(t1 %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
expect_warning(t2 %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
expect_equal(
data.frame(
x = c(1, 2, NA, NA, NA, 1, 2, 1),
y = c(rep(0, 4), rep(1, 4))
) %>%
tbl_summary(by = y) %>%
add_n(statistic = "{n_miss}/{N} = {p_miss}%") %>%
as_tibble(col_labels = FALSE) %>%
purrr::pluck("n", 1),
"3/8 = 38%"
)
expect_equal(
data.frame(
x = c(1, 2, NA, NA, NA, 1, 2, 1),
y = c(rep(0, 4), rep(1, 4))
) %>%
select(x) %>%
tbl_summary() %>%
add_n(statistic = "{n_miss}/{N} = {p_miss}%") %>%
as_tibble(col_labels = FALSE) %>%
purrr::pluck("n", 1),
"3/8 = 38%"
)
})
test_that("no errors/warnings with standard use for tbl_svysummary", {
skip_if_not(broom.helpers::.assert_package("survey", pkg_search = "gtsummary", boolean = TRUE))
t <- trial %>%
survey::svydesign(data = ., ids = ~1, weights = ~1) %>%
tbl_svysummary(by = trt)
expect_error(res <- t %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(), NA)
expect_error(res <- t %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(last = TRUE), NA)
t <- Titanic %>%
as.data.frame() %>%
survey::svydesign(data = ., ids = ~1, weights = ~Freq) %>%
tbl_svysummary(by = Survived)
expect_error(
res <-
t %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
})
test_that("no errors/warnings with standard use for tbl_svysummary with continuous2", {
skip_if_not(broom.helpers::.assert_package("survey", pkg_search = "gtsummary", boolean = TRUE))
t <- trial %>%
survey::svydesign(data = ., ids = ~1, weights = ~1) %>%
tbl_svysummary(by = trt, type = all_continuous() ~ "continuous2")
expect_error(res <- t %>% add_n(), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(), NA)
expect_error(res <- t %>% add_n(last = TRUE), NA)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(last = TRUE), NA)
t <- Titanic %>%
as.data.frame() %>%
survey::svydesign(data = ., ids = ~1, weights = ~Freq) %>%
tbl_svysummary(by = Survived, type = all_continuous() ~ "continuous2")
expect_error(
res <- t %>%
add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
),
NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(t %>% add_n(
statistic = "{N}{n}{n_miss}{p}{p_miss}",
footnote = TRUE
), NA)
})
# add_n.tbl_survfit --------------------------------------------------------
test_that("add_n.tbl_survfit", {
skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
tbl_survfit <-
list(
survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial),
survival::survfit(survival::Surv(ttdeath, death) ~ trt, trial)
) %>%
tbl_survfit(times = c(12, 24))
expect_error(
res <- add_n(tbl_survfit),
NA
)
expect_snapshot(res %>% as.data.frame())
})
# add_n.tbl_regression ---------------------------------------------------------
test_that("add_n.tbl_regression", {
tbl <-
glm(response ~ grade + age, trial, family = binomial) %>%
tbl_regression()
expect_error(
res <- tbl %>% add_n(), NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
res <- tbl %>% add_n(location = "level"), NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
res <- tbl %>% add_n(location = c("label", "level")), NA
)
expect_snapshot(res %>% as.data.frame())
})
# add_n.tbl_uvregression ---------------------------------------------------------
test_that("add_n.tbl_regression", {
tbl <-
trial %>%
select(response, age, grade) %>%
tbl_uvregression(
y = response,
method = glm,
method.args = list(family = binomial)
)
expect_error(
res <- tbl %>% add_n(), NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
res <- tbl %>% add_n(location = "level"), NA
)
expect_snapshot(res %>% as.data.frame())
expect_error(
res <- tbl %>% add_n(location = c("label", "level")), NA
)
expect_snapshot(res %>% as.data.frame())
})
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