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Create test snapshots & upgrade to testthat 3rd edition (#801)
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Closes #784 and #656
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@edelarua
edelarua authored Jan 19, 2023
1 parent 70d00c6 commit 872f99e
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -55,7 +55,7 @@ Suggests:
scda (>= 0.1.5),
scda.2022 (>= 0.1.3),
stringr,
testthat (>= 2.0)
testthat (>= 3.0)
VignetteBuilder:
knitr
RdMacros:
Expand All @@ -65,6 +65,7 @@ Remotes:
insightsengineering/scda.2022@*release,
insightsengineering/scda@*release
Config/Needs/website: insightsengineering/nesttemplate
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -17,6 +17,7 @@
repeat when paginating.
* Added `h_row_first_values` function as a more general helper function to retrieve
first values from specific rows.
* Replaced table template tests with snapshot testing.

### Bug Fixes
* Fixed bug causing incorrect ordering of numeric grade levels when missing
Expand All @@ -38,6 +39,7 @@
* Renamed `summarize_vars_in_cols` into `analyze_vars_in_cols` to reflect the
appropriate `analyze` logic.
* Exported function `format_xx`.
* Updated tests to use `testthat` 3rd edition.

# tern 0.7.10

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4 changes: 2 additions & 2 deletions R/g_step.R
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Expand Up @@ -116,14 +116,14 @@ g_step <- function(df,
name = "", values = c("CI 95%" = ci_ribbon$fill)
)
}
p <- p +
suppressMessages(p <- p +
ggplot2::geom_line(
ggplot2::aes(y = .data[["y"]], color = legend_names[1]),
linetype = est$lty
) +
scale_colour_manual(
name = "", values = c("Estimate" = "blue")
)
))

p <- p + ggplot2::labs(x = attrs$biomarker, y = attrs$estimate)
if (use_percentile) {
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1 change: 0 additions & 1 deletion tests/testthat/.gitignore
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30 changes: 30 additions & 0 deletions tests/testthat/_snaps/table_adat03.md
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# ADAT03 is produced correctly

Code
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Output
Treatment Group
Visit Total Number Samples with
of Measurable Concentration
Samples {1} Mean SD Median Minimum Maximum CV (%) Geometric Mean ≤ 15μg/mL {2}
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X (N=1206)
Day 1
938 8.227e+00 7.351e+00 1.131e+01 0.000e+00 1.986e+01 89.4 NA 738 (78.7%)
Day 2
268 1.344e+01 1.351e+00 1.330e+01 1.075e+01 1.646e+01 10.0 1.338e+01 228 (85.1%)
C: Combination (N=2112)
Day 1
1584 1.469e+01 1.237e+01 1.451e+01 0.000e+00 3.947e+01 84.3 NA 836 (52.8%)
Day 2
528 2.018e+01 7.129e+00 1.888e+01 1.073e+01 3.259e+01 35.3 1.891e+01 210 (39.8%)
Overall 3318 1.363e+01 1.059e+01 1.377e+01 0.000e+00 3.947e+01 77.7 NA 2012 (60.6%)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
{1} - footnote1
{2} - footnote2
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

107 changes: 107 additions & 0 deletions tests/testthat/_snaps/table_aet01.md
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# Safety Summary Variant 1 works as expected

Code
res
Output
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 122 (91.0%) 123 (91.8%) 120 (90.9%)
Total AEs 609 622 703
Total number of deaths 25 (18.66%) 23 (17.16%) 22 (16.67%)
Total number of patients withdrawn from study due to an AE 3 (2.24%) 6 (4.48%) 5 (3.79%)
Total number of patients with at least one
AE with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%)
Serious AE 104 (77.6%) 101 (75.4%) 99 (75.0%)
Serious AE leading to withdrawal from treatment 9 (6.7%) 6 (4.5%) 11 (8.3%)
Serious AE leading to dose modification/interruption 22 (16.4%) 26 (19.4%) 29 (22.0%)
Related Serious AE 76 (56.7%) 70 (52.2%) 75 (56.8%)
AE leading to withdrawal from treatment 27 (20.1%) 26 (19.4%) 30 (22.7%)
AE leading to dose modification/interruption 66 (49.3%) 76 (56.7%) 74 (56.1%)
Related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
Related AE leading to withdrawal from treatment 6 (4.5%) 12 (9.0%) 8 (6.1%)
Related AE leading to dose modification/interruption 29 (21.6%) 38 (28.4%) 38 (28.8%)
Grade 3-5 AE 109 (81.3%) 104 (77.6%) 109 (82.6%)

# Safety Summary Variant 2 (with Medical Concepts Section) works as expected

Code
res
Output
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 122 (91.0%) 123 (91.8%) 120 (90.9%)
Total AEs 609 622 703
Total number of deaths 25 (18.66%) 23 (17.16%) 22 (16.67%)
Total number of patients withdrawn from study due to an AE 3 (2.24%) 6 (4.48%) 5 (3.79%)
Total number of patients with at least one
AE with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%)
Serious AE 104 (77.6%) 101 (75.4%) 99 (75.0%)
Serious AE leading to withdrawal from treatment 9 (6.7%) 6 (4.5%) 11 (8.3%)
Serious AE leading to dose modification/interruption 22 (16.4%) 26 (19.4%) 29 (22.0%)
Related Serious AE 76 (56.7%) 70 (52.2%) 75 (56.8%)
AE leading to withdrawal from treatment 27 (20.1%) 26 (19.4%) 30 (22.7%)
AE leading to dose modification/interruption 66 (49.3%) 76 (56.7%) 74 (56.1%)
Related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
Related AE leading to withdrawal from treatment 6 (4.5%) 12 (9.0%) 8 (6.1%)
Related AE leading to dose modification/interruption 29 (21.6%) 38 (28.4%) 38 (28.8%)
Grade 3-5 AE 109 (81.3%) 104 (77.6%) 109 (82.6%)
Total number of patients with at least one
C.1.1.1.3/B.2.2.3.1 AESI (BROAD) 72 (53.7%) 79 (59.0%) 75 (56.8%)
SMQ 02 Reference Name 0 0 0
D.2.1.5.3/A.1.1.1.1 AESI 74 (55.2%) 80 (59.7%) 87 (65.9%)

# Safety Summary Variant 3 (with Modified Rows) works as expected

Code
res
Output
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 122 (91.0%) 123 (91.8%) 120 (90.9%)
Total AEs 609 622 703
Total number of deaths 25 (18.66%) 23 (17.16%) 22 (16.67%)
Total number of patients withdrawn from study due to an AE 3 (2.24%) 6 (4.48%) 5 (3.79%)
Total number of patients withdrawn informed consent 1 (0.75%) 1 (0.75%) 1 (0.76%)
Total number of patients with at least one
AE with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%)
Serious AE 104 (77.6%) 101 (75.4%) 99 (75.0%)
AE leading to withdrawal from treatment 27 (20.1%) 26 (19.4%) 30 (22.7%)
Related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
Grade 3-5 AE 109 (81.3%) 104 (77.6%) 109 (82.6%)
Grade 4/5 AE 91 (67.9%) 90 (67.2%) 93 (70.5%)

# Safety Summary Variant 4 (with Rows Counting Events and Additional Sections) works as expected

Code
res
Output
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 122 (91.0%) 123 (91.8%) 120 (90.9%)
Total AEs 609 622 703
Total number of deaths 25 (18.66%) 23 (17.16%) 22 (16.67%)
Total number of patients withdrawn from study due to an AE 3 (2.24%) 6 (4.48%) 5 (3.79%)
Total number of patients with at least one
AE with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%)
Serious AE 104 (77.6%) 101 (75.4%) 99 (75.0%)
AE leading to withdrawal from treatment 27 (20.1%) 26 (19.4%) 30 (22.7%)
AE leading to dose modification/interruption 66 (49.3%) 76 (56.7%) 74 (56.1%)
Related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
Grade 3-5 AE 109 (81.3%) 104 (77.6%) 109 (82.6%)
Total number of unique preferred terms which are
Serious AE 4 4 4
AE leading to dose modification/interruption 8 8 8
Related AE 5 5 5
Grade 3-5 AE 5 5 5
Grade 4/5 3 3 3
Total number of adverse events which are
Serious AE 249 255 282
AE leading to dose modification/interruption 116 122 137
Related AE 282 299 336
Grade 3-5 AE 303 291 327
Grade 4/5 172 174 197

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