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# Proposed list of checks all "vetted" models should pass.
# When adding a new "vetted model", copy paste the below list and
# add appropriate section of unit tests to cover the below.
# 1. Runs as expected with standard use
# - without errors, warnings, messages
# - numbers in table are correct
# - labels are correct
# 2. If applicable, runs as expected with logit and log link
# - without errors, warnings, messages
# - numbers in table are correct
# 3. Interaction terms are correctly printed in output table
# - without errors, warnings, messages
# - numbers in table are correct
# - interaction labels are correct
# 4. Other gtsummary functions work with model: add_global_p(), combine_terms(), add_nevent()
# - without errors, warnings, messages
# - numbers in table are correct
# 5. tbl_uvregression() works as expected
# - without errors, warnings, messages
# - works with add_global_p(), add_nevent(), add_q()
skip_on_cran()
# vetted models checks take a long time--only perform on CI checks
skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
library(dplyr)
library(survival)
# coxph() ----------------------------------------------------------------------
test_that("vetted_models coxph()", {
# building models to check
mod_coxph_lin <- coxph(Surv(ttdeath, death) ~ age + trt + grade, data = trial)
mod_coxph_int <- coxph(Surv(ttdeath, death) ~ age + trt * grade, data = trial)
# 1. Runs as expected with standard use
# - without errors, warnings, messages
expect_error(
tbl_coxph_lin <- tbl_regression(mod_coxph_lin), NA
)
expect_warning(
tbl_coxph_lin, NA
)
expect_error(
tbl_coxph_int <- tbl_regression(mod_coxph_int), NA
)
expect_warning(
tbl_coxph_int, NA
)
# - numbers in table are correct
expect_equal(
coef(mod_coxph_lin),
coefs_in_gt(tbl_coxph_lin),
ignore_attr = TRUE
)
expect_equal(
coef(mod_coxph_int),
coefs_in_gt(tbl_coxph_int),
ignore_attr = TRUE
)
# - labels are correct
expect_equal(
tbl_coxph_lin$table_body %>%
filter(row_type == "label") %>%
pull(label),
c("Age", "Chemotherapy Treatment", "Grade"),
ignore_attr = TRUE
)
expect_equal(
tbl_coxph_int$table_body %>%
filter(row_type == "label") %>%
pull(label),
c("Age", "Chemotherapy Treatment", "Grade", "Chemotherapy Treatment * Grade"),
ignore_attr = TRUE
)
# 2. If applicable, runs as expected with logit and log link
expect_equal(
coef(mod_coxph_lin) %>% exp(),
coefs_in_gt(mod_coxph_lin %>% tbl_regression(exponentiate = TRUE)),
ignore_attr = TRUE
)
# 3. Interaction terms are correctly printed in output table
# - interaction labels are correct
expect_equal(
tbl_coxph_int$table_body %>%
filter(var_type == "interaction") %>%
pull(label),
c("Chemotherapy Treatment * Grade", "Drug B * II", "Drug B * III"),
ignore_attr = TRUE
)
# 4. Other gtsummary functions work with model: add_global_p(), combine_terms(), add_nevent()
# - without errors, warnings, messages
expect_error(
tbl_coxph_lin2 <- tbl_coxph_lin %>% add_global_p(include = everything()), NA
)
expect_error(
tbl_coxph_int2 <- tbl_coxph_int %>% add_global_p(include = everything()), NA
)
expect_warning(
tbl_coxph_lin2, NA
)
expect_warning(
tbl_coxph_int2, NA
)
expect_error(
tbl_coxph_lin3 <- tbl_coxph_lin %>% combine_terms(. ~ . - trt), NA
)
expect_warning(
tbl_coxph_lin3, NA
)
expect_error(
tbl_coxph_lin4 <- tbl_coxph_lin %>% add_nevent(), NA
)
expect_warning(
tbl_coxph_lin4, NA
)
# - numbers in table are correct
expect_equal(
tbl_coxph_lin2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_coxph_lin, type = "III") %>%
as.data.frame() %>%
pull(`Pr(>Chisq)`),
ignore_attr = TRUE
)
expect_equal(
tbl_coxph_int2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_coxph_int, type = "III") %>%
as.data.frame() %>%
pull(`Pr(>Chisq)`),
ignore_attr = TRUE
)
expect_equal(
tbl_coxph_lin3$table_body %>% filter(variable == "trt") %>% pull(p.value),
car::Anova(mod_coxph_lin, type = "III") %>%
as.data.frame() %>%
tibble::rownames_to_column() %>%
filter(rowname == "trt") %>%
pull(`Pr(>Chisq)`),
ignore_attr = TRUE
)
expect_equal(
trial %>% select(death, age, trt, grade) %>% na.omit() %>% pull(death) %>% sum(),
tbl_coxph_lin4$table_body %>% slice(1) %>% pull(nevent),
ignore_attr = TRUE
)
# 5. tbl_uvregression() works as expected
# - without errors, warnings, messages
# - works with add_global_p(), add_nevent()
expect_error(
trial %>%
tbl_uvregression(
y = Surv(ttdeath, death),
method = coxph
) %>%
add_global_p() %>%
add_q(),
NA
)
expect_warning(
trial %>%
tbl_uvregression(
y = Surv(ttdeath, death),
method = coxph
) %>%
add_nevent() %>%
add_global_p() %>%
add_q(),
NA
)
})
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