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v2.0 additional tests for tbl uvregression() #1730

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Jun 28, 2024
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v2.0 additional tests for tbl uvregression() #1730

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5566b51
there's preexisting add_global_p() tests?
zdz2101 Jun 11, 2024
8aed270
add basic plot test
zdz2101 Jun 11, 2024
9028fc0
remove purrr dependencies
zdz2101 Jun 12, 2024
d0b81ec
swap in tests for each argument
zdz2101 Jun 18, 2024
f19d1e1
styler and fix errors
zdz2101 Jun 18, 2024
dc20c6e
Merge branch 'v2.0' of https://github.com/ddsjoberg/gtsummary into v2…
ddsjoberg Jun 25, 2024
e41c357
Merge branch 'v2.0' of https://github.com/ddsjoberg/gtsummary into v2…
ddsjoberg Jun 26, 2024
b7b661f
adopt feedback
zdz2101 Jun 27, 2024
91401b6
accidentally pushed one
zdz2101 Jun 27, 2024
2e3ecd4
add geepack
zdz2101 Jun 27, 2024
8c395f9
new snap
zdz2101 Jun 27, 2024
bf1c408
make sure p-values match properly
zdz2101 Jun 27, 2024
3261c4a
avoid using example geepack uses
zdz2101 Jun 28, 2024
5a38625
adopt feedback
zdz2101 Jun 28, 2024
0832039
forgot to push new snap
zdz2101 Jun 28, 2024
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107 changes: 107 additions & 0 deletions tests/testthat/_snaps/add_gloabl_p.tbl_uvregression.md
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# add_n.tbl_regression() works

Code
as.data.frame(res)
Output
**Characteristic** **N** **OR** **95% CI** **p-value**
1 Chemotherapy Treatment 193 <NA> <NA> 0.5
2 Drug A <NA> <NA> <NA> <NA>
3 Drug B <NA> 1.21 0.66, 2.24 <NA>
4 Grade 193 <NA> <NA> >0.9
5 I <NA> <NA> <NA> <NA>
6 II <NA> 0.95 0.45, 2.00 <NA>
7 III <NA> 1.10 0.52, 2.29 <NA>
8 Age 183 1.02 1.00, 1.04 0.091

# no errors/warnings with standard use after tbl_uvregression

Code
res %>% as.data.frame()
Output
**Characteristic** **N** **Beta** **95% CI** **p-value**
1 Chemotherapy Treatment 189 <NA> <NA> 0.8
2 Drug A <NA> <NA> <NA> <NA>
3 Drug B <NA> 0.44 -3.7, 4.6 <NA>
4 Marker Level (ng/mL) 179 -0.05 -2.5, 2.4 >0.9
5 T Stage 189 <NA> <NA> 0.5
6 T1 <NA> <NA> <NA> <NA>
7 T2 <NA> 1.3 -4.2, 6.9 <NA>
8 T3 <NA> 2.6 -3.3, 8.6 <NA>
9 T4 <NA> -2.0 -7.8, 3.8 <NA>
10 Grade 189 <NA> <NA> 0.7
11 I <NA> <NA> <NA> <NA>
12 II <NA> 1.4 -3.6, 6.4 <NA>
13 III <NA> 2.0 -3.1, 7.0 <NA>
14 Tumor Response 183 3.8 -0.66, 8.3 0.094
15 Patient Died 189 2.2 -2.0, 6.3 0.3
16 Months to Death/Censor 189 -0.14 -0.54, 0.26 0.5

---

Code
res %>% as.data.frame()
Output
**Characteristic** **N** **Beta** **95% CI** **p-value**
1 Chemotherapy Treatment 189 <NA> <NA> 0.8
2 Drug A <NA> <NA> <NA> <NA>
3 Drug B <NA> 0.44 -3.7, 4.6 0.8
4 Marker Level (ng/mL) 179 -0.05 -2.5, 2.4 >0.9
5 T Stage 189 <NA> <NA> 0.5
6 T1 <NA> <NA> <NA> <NA>
7 T2 <NA> 1.3 -4.2, 6.9 0.6
8 T3 <NA> 2.6 -3.3, 8.6 0.4
9 T4 <NA> -2.0 -7.8, 3.8 0.5
10 Grade 189 <NA> <NA> 0.7
11 I <NA> <NA> <NA> <NA>
12 II <NA> 1.4 -3.6, 6.4 0.6
13 III <NA> 2.0 -3.1, 7.0 0.4
14 Tumor Response 183 3.8 -0.66, 8.3 0.094
15 Patient Died 189 2.2 -2.0, 6.3 0.3
16 Months to Death/Censor 189 -0.14 -0.54, 0.26 0.5

---

Code
res %>% as.data.frame()
Output
**Characteristic** **N** **Beta** **95% CI** **p-value**
1 Chemotherapy Treatment 189 <NA> <NA> 0.8
2 Drug A <NA> <NA> <NA> <NA>
3 Drug B <NA> 0.44 -3.7, 4.6 <NA>
4 Marker Level (ng/mL) 179 -0.05 -2.5, 2.4 >0.9
5 T Stage 189 <NA> <NA> 0.5
6 T1 <NA> <NA> <NA> <NA>
7 T2 <NA> 1.3 -4.2, 6.9 <NA>
8 T3 <NA> 2.6 -3.3, 8.6 <NA>
9 T4 <NA> -2.0 -7.8, 3.8 <NA>
10 Grade 189 <NA> <NA> 0.7
11 I <NA> <NA> <NA> <NA>
12 II <NA> 1.4 -3.6, 6.4 <NA>
13 III <NA> 2.0 -3.1, 7.0 <NA>
14 Tumor Response 183 3.8 -0.66, 8.3 0.094
15 Patient Died 189 2.2 -2.0, 6.3 0.3
16 Months to Death/Censor 189 -0.14 -0.54, 0.26 0.5

---

Code
res %>% as.data.frame()
Output
**Characteristic** **N** **Beta** **95% CI** **p-value**
1 Chemotherapy Treatment 189 <NA> <NA> 0.8
2 Drug A <NA> <NA> <NA> <NA>
3 Drug B <NA> 0.44 -3.7, 4.6 0.8
4 Marker Level (ng/mL) 179 -0.05 -2.5, 2.4 >0.9
5 T Stage 189 <NA> <NA> 0.5
6 T1 <NA> <NA> <NA> <NA>
7 T2 <NA> 1.3 -4.2, 6.9 0.6
8 T3 <NA> 2.6 -3.3, 8.6 0.4
9 T4 <NA> -2.0 -7.8, 3.8 0.5
10 Grade 189 <NA> <NA> 0.7
11 I <NA> <NA> <NA> <NA>
12 II <NA> 1.4 -3.6, 6.4 0.6
13 III <NA> 2.0 -3.1, 7.0 0.4
14 Tumor Response 183 3.8 -0.66, 8.3 0.094
15 Patient Died 189 2.2 -2.0, 6.3 0.3
16 Months to Death/Censor 189 -0.14 -0.54, 0.26 0.5

76 changes: 76 additions & 0 deletions tests/testthat/test-add_gloabl_p.tbl_uvregression.R
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test_that("add_n.tbl_regression() works", {
tbl <- tbl_uvregression(
trial,
method = glm,
include = c(trt, grade, age),
y = response,
method.args = list(family = binomial),
exponentiate = TRUE
)

# total N added to table is accurate
expect_error(
res <- tbl |> add_global_p(),
NA
)

expect_snapshot(
res |> as.data.frame()
)
})


test_that("no errors/warnings with standard use after tbl_uvregression", {
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tbl2 <- trial %>% tbl_uvregression(method = lm, y = age)
expect_error(
res <- tbl2 %>% add_global_p(), NA
)
expect_warning(
tbl2 %>% add_global_p(), NA
)
expect_snapshot(res %>% as.data.frame())

expect_error(
res <- tbl2 %>% add_global_p(type = 2, keep = TRUE), NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(
tbl2 %>% add_global_p(type = "II"), NA
)
expect_equal(
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lm(age ~ trt, trial) %>% car::Anova(type = "II") %>% select(last_col()) %>%
dplyr::pull() %>% purrr::discard(is.na),
tbl2 %>% add_global_p(type = "II", include = trt) %>% purrr::pluck("table_body", "p.value", 1)
)

expect_message(tbl2 %>% add_global_p(), NA)
})

skip_on_cran()
skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))

test_that("no errors/warnings with standard use after tbl_uvregression", {
tbl2 <- trial %>% tbl_uvregression(method = lm, y = age)
expect_error(
res <- tbl2 %>% add_global_p(), NA
)
expect_warning(
tbl2 %>% add_global_p(), NA
)
expect_snapshot(res %>% as.data.frame())

expect_error(
res <- tbl2 %>% add_global_p(type = 2, keep = TRUE), NA
)
expect_snapshot(res %>% as.data.frame())
expect_warning(
tbl2 %>% add_global_p(type = "II"), NA
)
expect_equal(
lm(age ~ trt, trial) %>% car::Anova(type = "II") %>% dplyr::select(last_col()) %>%
dplyr::pull() %>% purrr::discard(is.na),
tbl2 %>% add_global_p(type = "II", include = trt) %>% purrr::pluck("table_body", "p.value", 1)
)

expect_message(tbl2 %>% add_global_p(), NA)
})
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