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Update snapshots, minor fixes (#145)
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Closes #144
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@edelarua
edelarua authored Nov 7, 2023
1 parent af743b9 commit 35f5440
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Showing 86 changed files with 11,611 additions and 11,723 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -18,3 +18,4 @@ _freeze
_site
.DS_Store
*.lock
*.html
3 changes: 0 additions & 3 deletions book/tables/disposition/dst01.qmd
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Expand Up @@ -51,7 +51,6 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
) %>%
count_occurrences(
"EOSSTT",
.stats = "count_fraction",
show_labels = "hidden"
) %>%
analyze_vars(
Expand All @@ -76,7 +75,6 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
) %>%
count_occurrences(
"EOSSTT",
.stats = "count_fraction",
show_labels = "hidden"
) %>%
split_rows_by("DCSREASGP", indent_mod = 1L) %>%
Expand All @@ -103,7 +101,6 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
) %>%
count_occurrences(
"EOTSTT",
.stats = "count_fraction",
show_labels = "hidden"
)
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3 changes: 1 addition & 2 deletions book/tables/efficacy/ratet01.qmd
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Expand Up @@ -32,7 +32,7 @@ anl <- df_explicit_na(anl)

```{r variant1, test = list(result_v1 = "result")}
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM", ref_group = "B: Placebo") %>%
split_cols_by("ARM", ref_group = "B: Placebo", split_fun = ref_group_position("first")) %>%
analyze_vars(
"AVAL_f",
var_labels = "Number of exacerbations per patient",
Expand Down Expand Up @@ -85,5 +85,4 @@ result
```

{{< include ../../repro.qmd >}}

:::
8 changes: 4 additions & 4 deletions book/tables/safety/enrollment01.qmd
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Expand Up @@ -57,7 +57,7 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
summarize_row_groups() %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze("INVID") %>%
analyze_vars("INVID", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID", 2L)
result <- build_table(lyt, adsl) %>%
Expand All @@ -74,7 +74,7 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze("INVID") %>%
analyze_vars("INVID", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID", 1L)
result <- build_table(lyt, adsl) %>%
Expand All @@ -93,7 +93,7 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
summarize_row_groups() %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze("INVID_INVNAM") %>%
analyze_vars("INVID_INVNAM", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID_INVNAM", 2L)
result <- build_table(lyt, adsl) %>%
Expand All @@ -110,7 +110,7 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze("INVID_INVNAM") %>%
analyze_vars("INVID_INVNAM", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID_INVNAM", 1L)
result <- build_table(lyt, adsl) %>%
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6 changes: 3 additions & 3 deletions package/tests/testthat/_snaps/adat01/markdown-snaps.md
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Expand Up @@ -11,14 +11,14 @@
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Baseline Prevalence of ADAs
Baseline evaluable patients 134 132 0 0 266
Patient with a positive sample at baseline 63 (47.0%) 64 (48.5%) NA NA 127 (47.7%)
Patient with a positive sample at baseline 63 (47.0%) 64 (48.5%) 0 0 127 (47.7%)
Patient with no positive samples at baseline 71 68 0 0 139
Incidence of Treatment Emergent ADAs
Post-baseline evaluable patients 134 132 0 0 266
Patient positive for Treatment Emergent ADA 0 0 NA NA 0
Patient positive for Treatment Emergent ADA 0 0 0 0 0
Treatment-induced ADA 0 0 0 0 0
Treatment-enhanced ADA 0 0 0 0 0
Patient negative for Treatment Emergent ADA 0 0 NA NA 0
Patient negative for Treatment Emergent ADA 0 0 0 0 0
Treatment unaffected 0 0 0 0 0
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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4 changes: 2 additions & 2 deletions package/tests/testthat/_snaps/adat02/markdown-snaps.md
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Expand Up @@ -13,8 +13,8 @@
Post-baseline evaluable patients 134 132 266
Treatment-induced ADA patients 0 0 64 (24.1%)
Treatment-induced ADA patients with
Transient ADA NA NA 0
Persistent ADA NA NA 0
Transient ADA 0 0 0
Persistent ADA 0 0 0
Median time to onset of ADA (weeks) NA NA 0.1
ADA titer range (min - max) NA NA NA
—————————————————————————————————————————————————————————————————————————————
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11 changes: 5 additions & 6 deletions package/tests/testthat/_snaps/adat03/markdown-snaps.md
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Expand Up @@ -9,19 +9,18 @@
Analyte: R1800000
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Treatment Group
Visit Total Number Samples with
of Measurable Concentration
Samples {1} Mean SD Median Minimum Maximum CV (%) Geometric Mean ≤ 15μg/mL {2}
Total Number Samples with
Treatment Group of Measurable Concentration
Visit Samples {1} Mean SD Median Minimum Maximum CV (%) Geometric Mean ≤ 15μg/mL {2}
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X (N=536)
Day 1 402 0 0 0 0 0 NA NA 402 (100%)
Day 2 134 16.2 1.63 16.2 12.6 19.9 10.0 16.1 39 (29.1%)
C: Combination (N=792)
Day 1 528 0 0 0 0 0 NA NA 528 (100%)
Day 2 264 24.7 8.65 22.5 12.6 39.5 35.0 23.2 28 (10.6%)
Overall 1328 6.54 11.0 0 0 39.5 167.5 NA 997 (75.1%)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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6 changes: 3 additions & 3 deletions package/tests/testthat/_snaps/adat04a/markdown-snaps.md
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Expand Up @@ -13,15 +13,15 @@
Baseline Prevalence of NAbs
Baseline evaluable patients for ADA 134 132 0 0 266
Patients with a positive ADA sample at baseline 63 64 0 0 127
Patients with a positive NAb sample at baseline 0 0 NA NA 0
Patients with a positive NAb sample at baseline 0 0 0 0 0
Patient with no positive NAb samples at baseline 0 0 0 0 0
Incidence of Treatment Emergent NAbs
Post-baseline evaluable patients for ADA 134 132 0 0 266
Patients positive for ADA 66 59 0 0 125
Patients positive for Treatment Emergent NAb 0 0 NA NA 0
Patients positive for Treatment Emergent NAb 0 0 0 0 0
Treatment-induced NAb 0 0 0 0 0
Treatment-enhanced NAb 0 0 0 0 0
Patients negative for NAb 0 0 NA NA 0
Patients negative for NAb 0 0 0 0 0
Treatment unaffected 0 0 0 0 0
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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4 changes: 2 additions & 2 deletions package/tests/testthat/_snaps/adat04b/markdown-snaps.md
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Expand Up @@ -13,12 +13,12 @@
Baseline Prevalence of NAbs
Baseline evaluable patients for ADA 134 132 0 0 266
Patients with a positive ADA sample at baseline 63 64 0 0 127
Patients with a positive NAb sample at baseline 0 0 NA NA 0
Patients with a positive NAb sample at baseline 0 0 0 0 0
Patients with no positive NAb sample at baseline 0 0 0 0 0
Incidence of NAbs
Post-baseline evaluable patients for ADA 134 132 0 0 266
Patients positive for ADA 66 59 0 0 125
Patients positive for NAb 0 0 NA NA 0
Patients positive for NAb 0 0 0 0 0
Patients negative for NAb 134 132 0 0 266
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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4 changes: 2 additions & 2 deletions package/tests/testthat/_snaps/aet01_aesi/markdown-snaps.md
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Expand Up @@ -118,8 +118,8 @@
Code
print(data_snap[[i]])
Output
Standardized MedDRA Query A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
Standardized MedDRA Query (N=134) (N=134) (N=132)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
C.1.1.1.3/B.2.2.3.1 AESI (BROAD)
Total number of patients with at least one AE 58 (43.3%) 60 (44.8%) 66 (50.0%)
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4 changes: 2 additions & 2 deletions package/tests/testthat/_snaps/aet02/markdown-snaps.md
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Expand Up @@ -199,8 +199,8 @@
Code
print(data_snap[[i]])
Output
MedDRA Preferred Term A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
MedDRA Preferred Term (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 100 (74.6%) 98 (73.1%) 103 (78.0%)
Total number of events 502 480 604
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