Skip to content

Commit

Permalink
addin gnoew snapshot
Browse files Browse the repository at this point in the history
  • Loading branch information
@shajoezhu
shajoezhu committed Dec 5, 2024
1 parent 70be90e commit d21214f
Show file tree
Hide file tree
Showing 6 changed files with 234 additions and 6 deletions.
6 changes: 3 additions & 3 deletions tests/testthat/_snaps/filter_spec-verbose.md
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
# Listing print correctly

Code
full_spec %>% filter_spec(., program %in% c("t_ds_slide", "t_ds_trt_slide"),
verbose = TRUE)
full_spec %>% filter_spec(., program %in% c("t_ds_slide", "t_ds_trt_slide",
"i_am_wrong"), verbose = TRUE)
Output
v 2/47 outputs matched the filter condition `program %in% c("t_ds_slide", "t_ds_trt_slide")`.
v 2/47 outputs matched the filter condition `program %in% c("t_ds_slide", "t_ds_trt_slide", "i_am_wrong")`.
$t_ds_slide_FAS
$t_ds_slide_FAS$program
[1] "t_ds_slide"
Expand Down
96 changes: 96 additions & 0 deletions tests/testthat/_snaps/t_ds_slide.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
# Test table creation of t_ds_slide

Code
t_ds_slide(adsl = testdata$adsl)
Output
Discontinue table
————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X B: Placebo C: Combination All Patients
————————————————————————————————————————————————————————————————————————————————————————————————
Received Treatment 134 (100.00%) 134 (100.00%) 132 (100.00%) 400 (100.00%)
On-study Status 3 (2.2%) 2 (1.5%) 4 (3.0%) 9 (2.2%)
On Treatment 0 0 0 0
In Follow-up 3 (2.2%) 2 (1.5%) 4 (3%) 9 (2.2%)
Discontinued the study 42 (31.3%) 40 (29.9%) 38 (28.8%) 120 (30.0%)
Adverse Event 3 (2.2%) 6 (4.5%) 5 (3.8%) 14 (3.5%)
Death 25 (18.7%) 23 (17.2%) 22 (16.7%) 70 (17.5%)
Lack Of Efficacy 2 (1.5%) 2 (1.5%) 3 (2.3%) 7 (1.8%)
Physician Decision 2 (1.5%) 3 (2.2%) 2 (1.5%) 7 (1.8%)
Protocol Violation 5 (3.7%) 3 (2.2%) 4 (3%) 12 (3%)
Withdrawal By Parent/Guardian 4 (3%) 2 (1.5%) 1 (0.8%) 7 (1.8%)
Withdrawal By Subject 1 (0.7%) 1 (0.7%) 1 (0.8%) 3 (0.8%)

---

Code
t_ds_slide(adsl = testdata$adsl, side_by_side = TRUE)
Output
Discontinue table
————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X B: Placebo C: Combination All Patients
————————————————————————————————————————————————————————————————————————————————————————————————
Received Treatment 134 (100.00%) 134 (100.00%) 132 (100.00%) 400 (100.00%)
On-study Status 3 (2.2%) 2 (1.5%) 4 (3.0%) 9 (2.2%)
On Treatment 0 0 0 0
In Follow-up 3 (2.2%) 2 (1.5%) 4 (3%) 9 (2.2%)
Discontinued the study 42 (31.3%) 40 (29.9%) 38 (28.8%) 120 (30.0%)
Adverse Event 3 (2.2%) 6 (4.5%) 5 (3.8%) 14 (3.5%)
Death 25 (18.7%) 23 (17.2%) 22 (16.7%) 70 (17.5%)
Lack Of Efficacy 2 (1.5%) 2 (1.5%) 3 (2.3%) 7 (1.8%)
Physician Decision 2 (1.5%) 3 (2.2%) 2 (1.5%) 7 (1.8%)
Protocol Violation 5 (3.7%) 3 (2.2%) 4 (3%) 12 (3%)
Withdrawal By Parent/Guardian 4 (3%) 2 (1.5%) 1 (0.8%) 7 (1.8%)
Withdrawal By Subject 1 (0.7%) 1 (0.7%) 1 (0.8%) 3 (0.8%)

---

Code
t_ds_slide(adsl = testdata$adsl, split_by_study = TRUE)
Output
Discontinue table
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
AB12345-1 AB12345-2
A: Drug X B: Placebo C: Combination A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Received Treatment 62 (100.00%) 74 (100.00%) 64 (100.00%) 72 (100.00%) 60 (100.00%) 68 (100.00%)
On-study Status 2 (3.2%) 0 (0.0%) 1 (1.6%) 1 (1.4%) 2 (3.3%) 3 (4.4%)
On Treatment 0 0 0 0 0 0
In Follow-up 2 (3.2%) 0 1 (1.6%) 1 (1.4%) 2 (3.3%) 3 (4.4%)
Discontinued the study 19 (30.6%) 24 (32.4%) 15 (23.4%) 23 (31.9%) 16 (26.7%) 23 (33.8%)
Adverse Event 2 (3.2%) 4 (5.4%) 4 (6.2%) 1 (1.4%) 2 (3.3%) 1 (1.5%)
Death 12 (19.4%) 13 (17.6%) 7 (10.9%) 13 (18.1%) 10 (16.7%) 15 (22.1%)
Lack Of Efficacy 1 (1.6%) 2 (2.7%) 0 1 (1.4%) 0 3 (4.4%)
Physician Decision 2 (3.2%) 2 (2.7%) 0 0 1 (1.7%) 2 (2.9%)
Protocol Violation 1 (1.6%) 2 (2.7%) 2 (3.1%) 4 (5.6%) 1 (1.7%) 2 (2.9%)
Withdrawal By Parent/Guardian 1 (1.6%) 1 (1.4%) 1 (1.6%) 3 (4.2%) 1 (1.7%) 0
Withdrawal By Subject 0 0 1 (1.6%) 1 (1.4%) 1 (1.7%) 0

---

Code
t_ds_slide(adsl = testdata$adsl, split_by_study = TRUE, side_by_side = TRUE)
Condition
Warning in `build_table_header()`:
split_by_study argument will be ignored
Output
Discontinue table
————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X B: Placebo C: Combination All Patients
————————————————————————————————————————————————————————————————————————————————————————————————
Received Treatment 134 (100.00%) 134 (100.00%) 132 (100.00%) 400 (100.00%)
On-study Status 3 (2.2%) 2 (1.5%) 4 (3.0%) 9 (2.2%)
On Treatment 0 0 0 0
In Follow-up 3 (2.2%) 2 (1.5%) 4 (3%) 9 (2.2%)
Discontinued the study 42 (31.3%) 40 (29.9%) 38 (28.8%) 120 (30.0%)
Adverse Event 3 (2.2%) 6 (4.5%) 5 (3.8%) 14 (3.5%)
Death 25 (18.7%) 23 (17.2%) 22 (16.7%) 70 (17.5%)
Lack Of Efficacy 2 (1.5%) 2 (1.5%) 3 (2.3%) 7 (1.8%)
Physician Decision 2 (1.5%) 3 (2.2%) 2 (1.5%) 7 (1.8%)
Protocol Violation 5 (3.7%) 3 (2.2%) 4 (3%) 12 (3%)
Withdrawal By Parent/Guardian 4 (3%) 2 (1.5%) 1 (0.8%) 7 (1.8%)
Withdrawal By Subject 1 (0.7%) 1 (0.7%) 1 (0.8%) 3 (0.8%)

2 changes: 1 addition & 1 deletion tests/testthat/setup.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ adsl <- eg_adsl %>%
mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo", "C: Combination"))) %>%
preprocess_t_dd() %>%
mutate(DISTRTFL = sample(c("Y", "N"), size = length(TRT01A), replace = TRUE, prob = c(.1, .9))) %>%
# preprocess_t_ds() %>%
preprocess_t_ds() %>%
mutate(
DTRFL = if_else(EOTSTT == "DISCONTINUED", "Y", "N"),
TRTSDT = as.Date(TRTSDTM)
Expand Down
5 changes: 3 additions & 2 deletions tests/testthat/test-filter_spec-verbose.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,10 @@ test_that("Listing print correctly", {
full_spec <- spec_file %>%
read_spec()

expect_snapshot(full_spec %>%
testthat::expect_snapshot(full_spec %>%
filter_spec(., program %in% c(
"t_ds_slide",
"t_ds_trt_slide"
"t_ds_trt_slide",
"i_am_wrong"
), verbose = TRUE))
})
115 changes: 115 additions & 0 deletions tests/testthat/test-g_mean_slides.R
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,115 @@
# data setup
library(dplyr)
library(ggplot2)
library(svglite)

adeg <- testdata$adeg %>% filter(PARAMCD == "QT")
advs <- testdata$advs %>% filter(PARAMCD == "WEIGHT")
adlb <- testdata$adlb %>% filter(PARAMCD == "IGA")

# tests
path_to_test <- "_snaps"

## adeg
## Test 1: Test graph creation of `g_eg_slide` (eg mean plot) ----
test_that("g_mean_slides Test 1: Test graph creation of `g_eg_slide` (eg mean plot)", {
testthat::expect_silent(geg <- withr::with_options(
opts_partial_match_old,
g_eg_slide(testdata$adsl, adeg, arm = "TRT01P", paramcd = "PARAMCD")
))

expect_snapshot_ggplot(title = "g_eg_test", geg, width = 10, height = 8)
})


## Test 2: Test error of `g_eg_slide` ----
test_that("g_mean_slides Test 2: Test error of `g_eg_slide`", {
testthat::expect_error(g_eg_slide(testdata$adsl, adeg, arm = TRT01P))
})

## adlb
## Test 3: Test graph creation of `g_lb_slide` (lab mean plot) ----
test_that("g_mean_slides Test 3: Test graph creation of `g_lb_slide` (lab mean plot)", {
testthat::expect_silent(glb <- withr::with_options(
opts_partial_match_old,
g_lb_slide(testdata$adsl, adlb, arm = "TRT01P", paramcd = "PARAMCD")
))

expect_snapshot_ggplot(title = "g_lb_test", glb, width = 10, height = 8)
})


## Test 4: Test graph creation of `g_lb_slide` (lab change from baseline plot) ----
test_that("g_mean_slides Test 4: Test graph creation of `g_lb_slide` (lab change from baseline plot)", {
testthat::expect_silent(plot_lb_chg <- withr::with_options(
opts_partial_match_old,
g_lb_slide(
testdata$adsl, adlb,
arm = "TRT01P",
paramcd = "PARAMCD",
y = "CHG",
subtitle = "Plot of change from baseline and 95% Confidence Limit by Visit."
)
))

expect_snapshot_ggplot(title = "g_lb_chg_test", plot_lb_chg, width = 10, height = 8)
})



## Test 5: Test error of `g_lb_slide` ----
test_that("g_mean_slides Test 5: Test error of `g_lb_slide`", {
expect_error(g_lb_slide(testdata$adsl, adlb, arm = TRT01P))
})

## advs
## Test 6: Test graph creation of `g_vs_slide` (vital sign mean plot) ----
test_that("g_mean_slides Test 6: Test graph creation of `g_vs_slide` (vital sign mean plot)", {
testthat::expect_silent(gvs <- withr::with_options(
opts_partial_match_old,
g_vs_slide(testdata$adsl, advs, arm = "TRT01P", paramcd = "PARAMCD")
))

expect_snapshot_ggplot(title = "g_vs_test", gvs, width = 10, height = 8)
})

## Test 7: Test error of `g_vs_slide` ----
test_that("g_mean_slides Test 7: Test error of `g_vs_slide`", {
expect_error(g_vs_slide(testdata$adsl, advs, arm = TRT01P))
})

## general
## Test 8: Test graph creation of `g_mean_slide` (vital sign mean plot) ----
test_that("g_mean_slides Test 8: Test graph creation of `g_mean_slide` (vital sign mean plot)", {
testthat::expect_silent(gm1 <- withr::with_options(
opts_partial_match_old,
g_mean_general(testdata$adsl,
adeg,
variables = tern::control_lineplot_vars(
group_var = "TRT01P",
paramcd = "PARAMCD"
)
)
))

expect_snapshot_ggplot(title = "g_mean_general_test", gm1, width = 10, height = 8)

testthat::expect_silent(gm2 <- withr::with_options(
opts_partial_match_old,
g_mean_general(testdata$adsl,
adeg,
variables = tern::control_lineplot_vars(
group_var = "TRT01P",
paramcd = "PARAMCD"
),
subtitle_add_unit = FALSE
)
))

expect_snapshot_ggplot(title = "g_mean_nounit_test", gm2, width = 10, height = 8)
})

## Test 9: Test error of general function `g_mean_slide` ----
test_that("g_mean_slides Test 9: Test error of general function `g_mean_slide`", {
expect_error(g_eg_slide(testdata$adsl, adeg, arm = TRT01P))
})
16 changes: 16 additions & 0 deletions tests/testthat/test-t_ds_slide.R
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
test_that("Test table creation of t_ds_slide", {
expect_snapshot(t_ds_slide(adsl = testdata$adsl))
})

test_that("Test table creation of t_ds_slide", {
expect_snapshot(t_ds_slide(adsl = testdata$adsl, side_by_side = TRUE))
})

test_that("Test table creation of t_ds_slide", {
expect_snapshot(t_ds_slide(adsl = testdata$adsl, split_by_study = TRUE))
})

test_that("Test table creation of t_ds_slide", {
expect_snapshot(t_ds_slide(adsl = testdata$adsl, split_by_study = TRUE, side_by_side = TRUE))
expect_warning(t_ds_slide(adsl = testdata$adsl, split_by_study = TRUE, side_by_side = TRUE))
})

0 comments on commit d21214f

Please sign in to comment.