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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()
# stats::lm() DONE
# stats::glm() DONE
# survival::survreg() DONE
# survival::coxph() DONE
# lme4::lmer() DONE
# lme4::glmer() DONE
# geepack::geeglm() DONE
# survival::clogit() DONE
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("lme4", pkg_search = "gtsummary", boolean = TRUE))
skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
library(dplyr)
library(survival)
# survreg() --------------------------------------------------------------------
test_that("vetted_models survreg()", {
# building models to check
mod_survreg_lin <- survreg(Surv(ttdeath, death) ~ age + trt + grade, data = trial)
mod_survreg_int <- survreg(Surv(ttdeath, death) ~ age + trt * grade, data = trial)
# 1. Runs as expected with standard use
# - without errors, warnings, messages
expect_error(
tbl_survreg_lin <- tbl_regression(mod_survreg_lin), NA
)
expect_warning(
tbl_survreg_lin, NA
)
expect_error(
tbl_survreg_int <- tbl_regression(mod_survreg_int), NA
)
expect_warning(
tbl_survreg_int, NA
)
# - numbers in table are correct
expect_equal(
coef(mod_survreg_lin)[-1],
coefs_in_gt(tbl_survreg_lin),
ignore_attr = TRUE
)
expect_equal(
coef(mod_survreg_int)[-1],
coefs_in_gt(tbl_survreg_int),
ignore_attr = TRUE
)
expect_equal(
coef(mod_survreg_lin),
coefs_in_gt(tbl_regression(mod_survreg_lin, intercept = TRUE)),
ignore_attr = TRUE
)
expect_equal(
coef(mod_survreg_int),
coefs_in_gt(tbl_regression(mod_survreg_int, intercept = TRUE)),
ignore_attr = TRUE
)
# - labels are correct
expect_equal(
tbl_survreg_lin$table_body %>%
filter(row_type == "label") %>%
pull(label),
c("Age", "Chemotherapy Treatment", "Grade"),
ignore_attr = TRUE
)
expect_equal(
tbl_survreg_int$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 (NOT APPLICABLE)
# 3. Interaction terms are correctly printed in output table
# - interaction labels are correct
expect_equal(
tbl_survreg_int$table_body %>%
filter(var_type == "interaction") %>%
pull(label),
c("Chemotherapy Treatment * Grade", "Drug B * II", "Drug B * III"),
ignore_attr = TRUE
)
# 4. Other gtsummary functions work with model: add_global_p(), combine_terms()
# - without errors, warnings, messages
expect_error(
tbl_survreg_lin2 <- tbl_survreg_lin %>% add_global_p(include = everything()), NA
)
expect_error(
tbl_survreg_int2 <- tbl_survreg_int %>% add_global_p(include = everything()), NA
)
expect_warning(
tbl_survreg_lin2, NA
)
expect_warning(
tbl_survreg_int2, NA
)
expect_error(
tbl_survreg_lin3 <- tbl_survreg_lin %>% combine_terms(. ~ . - trt), NA
)
expect_warning(
tbl_survreg_lin3, NA
)
# - numbers in table are correct
expect_equal(
tbl_survreg_lin2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_survreg_lin, type = "III") %>%
as.data.frame() %>%
pull(`Pr(>Chisq)`),
ignore_attr = TRUE
)
expect_equal(
tbl_survreg_int2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_survreg_int, type = "III") %>%
as.data.frame() %>%
pull(`Pr(>Chisq)`),
ignore_attr = TRUE
)
expect_equal(
tbl_survreg_lin3$table_body %>% filter(variable == "trt") %>% pull(p.value),
car::Anova(mod_survreg_lin, type = "III") %>%
as.data.frame() %>%
tibble::rownames_to_column() %>%
filter(rowname == "trt") %>%
pull(`Pr(>Chisq)`),
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 = survreg
) %>%
add_global_p() %>%
add_q(),
NA
)
})
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