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Fix failing adat02 template #270

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merged 7 commits into from
Oct 10, 2024
Merged

Fix failing adat02 template #270

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084b946
Fix failing adat02 template
edelarua Oct 9, 2024
02f2fc3
Works for stable and development
edelarua Oct 9, 2024
17c46b6
Update development snapshot
edelarua Oct 9, 2024
37c3c06
Update outdated snapshots
edelarua Oct 9, 2024
a4a3946
Fix rbmit01 for development
edelarua Oct 9, 2024
97e0039
Update snapshots
edelarua Oct 10, 2024
611856e
Stable ADA snapshots changed after rcd release
edelarua Oct 10, 2024
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2 changes: 1 addition & 1 deletion book/tables/ADA/adat02.qmd
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Expand Up @@ -84,7 +84,7 @@ lyt_adab <- basic_table(show_colcounts = TRUE) %>%
lyt_adab_ti <- basic_table(show_colcounts = TRUE) %>%
split_cols_by(
"ACTARM",
split_fun = keep_split_levels(c("A: Drug X", "C: Combination", "<Missing>")) # temp fix
split_fun = keep_split_levels(levels(adab_ti$ACTARM)[-2]) # temp fix
) %>%
count_patients_with_flags(
"USUBJID",
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4 changes: 2 additions & 2 deletions book/tables/efficacy/rbmit01.qmd
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Expand Up @@ -112,8 +112,8 @@ Define which imputation method to use, then create samples for the imputation pa

```{r, warning = FALSE, opts.label = "skip_test_strict"}
#| code-fold: show

draws_method <- method_bayes(seed = 123)
set.seed(123)
draws_method <- method_bayes()

draws_obj <- rbmi::draws(
data = data_full,
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32 changes: 16 additions & 16 deletions package/tests/testthat/_snaps/development/tables-ADA-adat01.md
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Expand Up @@ -5,22 +5,22 @@
Output
Baseline Prevalence and Incidence of Treatment Emergent ADA

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X C: Combination <Missing> B: Placebo All Drug X
(N=134) (N=132) (N=0) (N=134) (N=266)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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%) 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 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 0 0 0
Treatment unaffected 0 0 0 0 0
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X C: Combination All Drug X B: Placebo All Patients
(N=134) (N=132) (N=266) (N=134) (N=400)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Baseline Prevalence of ADAs
Baseline evaluable patients 134 132 266 0 266
Patient with a positive sample at baseline 63 (47.0%) 64 (48.5%) 127 (47.7%) 0 127 (47.7%)
Patient with no positive samples at baseline 71 68 139 0 139
Incidence of Treatment Emergent ADAs
Post-baseline evaluable patients 134 132 266 0 266
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 0 0 0
Treatment unaffected 0 0 0 0 0
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies) Baseline evaluable patient = a patient with an ADA assay result from a baseline sample(s)
Post-baseline evaluable patient = a patient with an ADA assay result from at least one post-baseline sample Number of patients positive for Treatment Emergent
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24 changes: 12 additions & 12 deletions package/tests/testthat/_snaps/development/tables-ADA-adat02.md
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Expand Up @@ -6,18 +6,18 @@
Summary of Patients with Treatment-Induced ADA, PK Population
Protocol: A: Drug X Antibody

—————————————————————————————————————————————————————————————————————————————
A: Drug X C: Combination <Missing>
(N=134) (N=132) (N=0)
—————————————————————————————————————————————————————————————————————————————
Post-baseline evaluable patients 134 132 266
Treatment-induced ADA patients 0 0 64 (24.1%)
Treatment-induced ADA patients with
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
—————————————————————————————————————————————————————————————————————————————
—————————————————————————————————————————————————————————————————
A: Drug X C: Combination
(N=134) (N=132)
—————————————————————————————————————————————————————————————————
Post-baseline evaluable patients 134 132
Treatment-induced ADA patients 38 (28.4%) 26 (19.7%)
Treatment-induced ADA patients with
Transient ADA 0 0
Persistent ADA 0 0
Median time to onset of ADA (weeks) 0.1 0.1
ADA titer range (min - max) NA NA
—————————————————————————————————————————————————————————————————

ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic
Antibodies)
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36 changes: 18 additions & 18 deletions package/tests/testthat/_snaps/development/tables-ADA-adat04a.md
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Expand Up @@ -6,24 +6,24 @@
Baseline Prevalence and Incidence of Treatment Emergent NAbs
Protocol: A: Drug X Antibody

—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X C: Combination <Missing> B: Placebo All Drug X
(N=134) (N=132) (N=0) (N=134) (N=266)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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 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 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 0 0 0
Treatment unaffected 0 0 0 0 0
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X C: Combination All Drug X B: Placebo All Patients
(N=134) (N=132) (N=266) (N=134) (N=400)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Baseline Prevalence of NAbs
Baseline evaluable patients for ADA 134 132 266 0 266
Patients with a positive ADA sample at baseline 63 64 127 0 127
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 134 132 266 0 266
Patients positive for ADA 66 59 125 0 125
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 0 0 0
Treatment unaffected 0 0 0 0 0
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

NAb = Neutralizing Antibodies ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies) Baseline evaluable patient for ADA = a patient with an ADA assay result from a baseline sample(s)
Baseline evaluable patient for NAb = a patient with a NAb assay result from a baseline sample(s)
Expand Down
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