Nothing
# 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
testthat::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)
# lm() ------------------------------------------------------------------------
test_that("vetted_models lm()", {
# building models to check
mod_lm_lin <- lm(marker ~ age + trt + grade,
data = trial
)
mod_lm_int <- lm(marker ~ age + trt * grade,
data = trial
)
# 1. Runs as expected with standard use
# - without errors, warnings, messages
expect_error(
tbl_lm_lin <- tbl_regression(mod_lm_lin,
label = list(
age ~ "Age",
trt ~ "Chemotherapy Treatment",
grade ~ "Grade"
)
), NA
)
expect_warning(
tbl_lm_lin, NA
)
expect_error(
tbl_lm_int <- tbl_regression(mod_lm_int,
label = list(
age ~ "Age",
trt ~ "Chemotherapy Treatment",
grade ~ "Grade"
)
), NA
)
expect_warning(
tbl_lm_int, NA
)
# - numbers in table are correct
expect_equal(
coef(mod_lm_lin)[-1],
coefs_in_gt(tbl_lm_lin),
ignore_attr = TRUE
)
expect_equal(
coef(mod_lm_int)[-1],
coefs_in_gt(tbl_lm_int),
ignore_attr = TRUE
)
# - labels are correct
expect_equal(
tbl_lm_lin$table_body %>%
filter(row_type == "label") %>%
pull(label),
c("Age", "Chemotherapy Treatment", "Grade"),
ignore_attr = TRUE
)
expect_equal(
tbl_lm_int$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
# 3. Interaction terms are correctly printed in output table
# - interaction labels are correct
expect_equal(
tbl_lm_int$table_body %>%
filter(var_type == "interaction") %>%
pull(label),
c("Chemotherapy Treatment * Grade", "Drug B * II", "Drug B * III"),
ignore_attr = TRUE
)
# 4. Other gtsummary functions work with model: add_global_p(), combine_terms(), add_nevent()
# - without errors, warnings, messages
# lm() does not work with car::Anova()! update this after #409 issue complete?
expect_error(
tbl_lm_lin2 <- tbl_lm_lin %>% add_global_p(include = everything()), NA
)
expect_error(
tbl_lm_int2 <- tbl_lm_int %>% add_global_p(include = everything()), NA
)
expect_warning(
tbl_lm_lin2, NA
)
expect_warning(
tbl_lm_int2, NA
)
# - numbers in table are correct
expect_equal(
tbl_lm_lin2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_lm_lin, type = "III") %>%
as.data.frame() %>%
filter(!rownames(.) %in% c("Residuals", "(Intercept)")) %>%
pull(`Pr(>F)`)
)
expect_equal(
tbl_lm_int2$table_body %>%
pull(p.value) %>%
na.omit() %>%
as.vector(),
car::Anova(mod_lm_int, type = "III") %>%
as.data.frame() %>%
filter(!rownames(.) %in% c("Residuals", "(Intercept)")) %>%
pull(`Pr(>F)`)
)
# 5. tbl_uvregression() works as expected
# - without errors, warnings, messages
# - works with add_global_p(), add_nevent()
expect_error(
na.omit(trial) %>%
tbl_uvregression(
y = response,
method = lm
),
NA
)
expect_warning(
na.omit(trial) %>%
tbl_uvregression(
y = response,
method = lm
),
NA
)
})
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