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Merged
edelarua merged 26 commits into from
Nov 14, 2024
Merged

Use pharmaverseadam data in safety templates - part 2 #154

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97c72cb
Update EGT* templates - EGT04 to be updated after refactor
edelarua Jul 26, 2024
8c4b617
Update VST* templates
edelarua Jul 26, 2024
15250ad
Update EXT01 - to be updated after refactor
edelarua Jul 26, 2024
e509eab
Merge branch 'main' into 147_pv_safety_pt_2@main
edelarua Oct 15, 2024
9d7e349
Update tests
edelarua Oct 16, 2024
a277ed5
Fix egt03/04
edelarua Oct 16, 2024
efe0dca
[skip style] [skip vbump] Restyle files
github-actions[bot] Oct 16, 2024
f631eb8
Empty commit
edelarua Oct 16, 2024
1fe9629
Merge branch 'main' into 147_pv_safety_pt_2@main
shajoezhu Oct 29, 2024
759b3cf
Update DESCRIPTION
shajoezhu Oct 29, 2024
c7771bd
Update snapshots
edelarua Nov 6, 2024
f5d89d5
egt03 N counts
edelarua Nov 6, 2024
9a68e6d
Update snaps
edelarua Nov 6, 2024
44f9e9e
Update tern version
edelarua Nov 6, 2024
d66b7bd
Update vst01 snapshot
edelarua Nov 6, 2024
6821fac
Merge branch 'main' into 147_pv_safety_pt_2@main
shajoezhu Nov 7, 2024
7440f8f
Merge branch 'main' into 147_pv_safety_pt_2@main
shajoezhu Nov 7, 2024
a0263d4
egt05_qtcat filter by timepoint
edelarua Nov 7, 2024
4f6a558
Merge branch 'main' into 147_pv_safety_pt_2@main
edelarua Nov 7, 2024
be0d4dc
Fix snaps
edelarua Nov 7, 2024
2379180
Merge branch 'main' into 147_pv_safety_pt_2@main
shajoezhu Nov 8, 2024
a88766f
Merge branch 'main' into 147_pv_safety_pt_2@main
edelarua Nov 8, 2024
dcb018e
Empty commit
edelarua Nov 11, 2024
0a75273
Merge remote-tracking branch 'origin/147_pv_safety_pt_2@main' into 14…
edelarua Nov 11, 2024
968a147
Empty commit
edelarua Nov 14, 2024
1c9fce1
use r-deps
shajoezhu Nov 14, 2024
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8 changes: 8 additions & 0 deletions .github/workflows/docs.yaml
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Expand Up @@ -41,3 +41,11 @@ jobs:
REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
with:
additional-unit-test-report-directories: unit-test-report-non-cran
deps-installation-method: setup-r-dependencies
lookup-refs: |
insightsengineering/random.cdisc.data
insightsengineering/rtables
insightsengineering/formatters
insightsengineering/tern
insightsengineering/rlistings
pharmaverse/pharmaverseadam
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -24,7 +24,7 @@ Depends:
formatters (>= 0.5.9),
R (>= 4.2),
rlistings (>= 0.2.9),
rtables (>= 0.6.8),
rtables (>= 0.6.10),
tern (>= 0.9.6.9015)
Imports:
pharmaverseadam (>= 1.1.0),
Expand Down
241 changes: 143 additions & 98 deletions tests/testthat/_snaps/table_egt01.md
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48 changes: 24 additions & 24 deletions tests/testthat/_snaps/table_egt02.md
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Expand Up @@ -3,34 +3,34 @@
Code
res
Output
Assessment A: Drug X B: Placebo C: Combination
Abnormality (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————
Heart Rate
Low 40/134 (29.9%) 43/134 (32.1%) 37/132 (28%)
High 39/134 (29.1%) 45/134 (33.6%) 36/132 (27.3%)
QT Duration
Low 33/134 (24.6%) 44/134 (32.8%) 47/132 (35.6%)
High 30/134 (22.4%) 42/134 (31.3%) 34/132 (25.8%)
RR Duration
Low 45/134 (33.6%) 26/134 (19.4%) 38/132 (28.8%)
High 29/134 (21.6%) 49/134 (36.6%) 27/132 (20.5%)
Assessment Placebo Xanomeline High Dose Xanomeline Low Dose
Abnormality (N=86) (N=72) (N=96)
———————————————————————————————————————————————————————————————————————————————————
Heart Rate (beats/min)
Low 0/84 0/72 0/94
High 4/84 (4.8%) 0/72 0/94
QT Duration (msec)
Low 55/84 (65.5%) 44/72 (61.1%) 52/94 (55.3%)
High 84/84 (100%) 72/72 (100%) 93/94 (98.9%)
RR Duration (msec)
Low 84/84 (100%) 72/72 (100%) 94/94 (100%)
High 0/84 0/72 0/94

# (EGT02) 2. Among Subjects Without Abnormality at Baseline

Code
res
Output
Assessment A: Drug X B: Placebo C: Combination
Abnormality (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————
Heart Rate
Low 39/128 (30.5%) 42/124 (33.9%) 33/117 (28.2%)
High 37/127 (29.1%) 43/129 (33.3%) 31/122 (25.4%)
QT Duration
Low 29/113 (25.7%) 42/126 (33.3%) 43/124 (34.7%)
High 30/125 (24%) 40/130 (30.8%) 30/119 (25.2%)
RR Duration
Low 45/129 (34.9%) 26/123 (21.1%) 37/126 (29.4%)
High 27/127 (21.3%) 43/122 (35.2%) 25/125 (20%)
Assessment Placebo Xanomeline High Dose Xanomeline Low Dose
Abnormality (N=86) (N=72) (N=96)
———————————————————————————————————————————————————————————————————————————————————
Heart Rate (beats/min)
Low 0/84 0/72 0/94
High 4/84 (4.8%) 0/72 0/94
QT Duration (msec)
Low 52/84 (61.9%) 44/72 (61.1%) 51/94 (54.3%)
High 83/84 (98.8%) 72/72 (100%) 90/94 (95.7%)
RR Duration (msec)
Low 84/84 (100%) 72/72 (100%) 94/94 (100%)
High 0/84 0/72 0/94

155 changes: 79 additions & 76 deletions tests/testthat/_snaps/table_egt03.md
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Expand Up @@ -3,99 +3,102 @@
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Output
LOW NORMAL HIGH Missing
——————————————————————————————————————————————————————————————————
A: Drug X (N=134)
n 40 92 0 2
LOW 1 (0.7%) 5 (3.7%) 0 0
NORMAL 36 (26.9%) 83 (61.9%) 0 1 (0.7%)
HIGH 2 (1.5%) 4 (3%) 0 0
Missing 1 (0.7%) 0 0 1 (0.7%)
B: Placebo (N=134)
n 43 89 0 2
LOW 1 (0.7%) 9 (6.7%) 0 0
NORMAL 40 (29.9%) 75 (56%) 0 2 (1.5%)
HIGH 1 (0.7%) 4 (3%) 0 0
Missing 1 (0.7%) 1 (0.7%) 0 0
C: Combination (N=132)
n 37 94 0 1
LOW 4 (3%) 11 (8.3%) 0 0
NORMAL 31 (23.5%) 75 (56.8%) 0 0
HIGH 1 (0.8%) 8 (6.1%) 0 1 (0.8%)
Missing 1 (0.8%) 0 0 0
LOW NORMAL HIGH Missing
—————————————————————————————————————————————————————————————————
Placebo (N=86)
n 0 333 0 3
LOW 0 84 (25%) 0 0
NORMAL 0 249 (74.1%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 3 (0.9%)
Xanomeline High Dose (N=84)
n 0 327 0 1
LOW 0 82 (25%) 0 0
NORMAL 0 245 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)
Xanomeline Low Dose (N=84)
n 0 335 0 1
LOW 0 84 (25%) 0 0
NORMAL 0 251 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)

# EGT03 variant 2 is produced correctly

Code
res
Output
LOW NORMAL HIGH
———————————————————————————————————————————————————————
A: Drug X (N=134)
n 40 94 0
LOW 1 (0.7%) 5 (3.7%) 0
NORMAL 36 (26.9%) 84 (62.7%) 0
HIGH 2 (1.5%) 4 (3%) 0
Missing 1 (0.7%) 1 (0.7%) 0
B: Placebo (N=134)
n 43 91 0
LOW 1 (0.7%) 9 (6.7%) 0
NORMAL 40 (29.9%) 77 (57.5%) 0
HIGH 1 (0.7%) 4 (3%) 0
Missing 1 (0.7%) 1 (0.7%) 0
C: Combination (N=132)
n 37 95 0
LOW 4 (3%) 11 (8.3%) 0
NORMAL 31 (23.5%) 75 (56.8%) 0
HIGH 1 (0.8%) 9 (6.8%) 0
Missing 1 (0.8%) 0 0
NORMAL
—————————————————————————————————————————
Placebo (N=86)
n 336
LOW 84 (25%)
NORMAL 249 (74.1%)
HIGH 0
Missing 3 (0.9%)
Xanomeline High Dose (N=84)
n 328
LOW 82 (25%)
NORMAL 245 (74.7%)
HIGH 0
Missing 1 (0.3%)
Xanomeline Low Dose (N=84)
n 336
LOW 84 (25%)
NORMAL 251 (74.7%)
HIGH 0
Missing 1 (0.3%)

# EGT03 variant 3 is produced correctly

Code
res
Output
LOW NORMAL HIGH Missing
——————————————————————————————————————————————————————————————————
A: Drug X (N=134)
n 39 93 0 2
LOW 1 (0.7%) 5 (3.7%) 0 0
NORMAL 36 (26.9%) 84 (62.7%) 0 1 (0.7%)
HIGH 2 (1.5%) 4 (3%) 0 1 (0.7%)
B: Placebo (N=134)
n 42 90 0 2
LOW 1 (0.7%) 9 (6.7%) 0 0
NORMAL 40 (29.9%) 77 (57.5%) 0 2 (1.5%)
HIGH 1 (0.7%) 4 (3%) 0 0
C: Combination (N=132)
n 36 95 0 1
LOW 4 (3%) 11 (8.3%) 0 0
NORMAL 31 (23.5%) 75 (56.8%) 0 1 (0.8%)
HIGH 1 (0.8%) 9 (6.8%) 0 0
LOW NORMAL HIGH Missing
—————————————————————————————————————————————————————————————————
Placebo (N=86)
n 0 333 0 3
LOW 0 84 (25%) 0 0
NORMAL 0 249 (74.1%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 3 (0.9%)
Xanomeline High Dose (N=84)
n 0 327 0 1
LOW 0 82 (25%) 0 0
NORMAL 0 245 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)
Xanomeline Low Dose (N=84)
n 0 335 0 1
LOW 0 84 (25%) 0 0
NORMAL 0 251 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)

# EGT03 variant 4 is produced correctly

Code
res
Output
LOW NORMAL HIGH Missing
LOW NORMAL HIGH Missing
—————————————————————————————————————————————————————————————————
A: Drug X (N=134)
n 0 95 37 2
LOW 0 2 (1.5%) 4 (3%) 0
NORMAL 0 88 (65.7%) 31 (23.1%) 1 (0.7%)
HIGH 0 5 (3.7%) 1 (0.7%) 0
Missing 0 0 1 (0.7%) 1 (0.7%)
B: Placebo (N=134)
n 0 88 44 2
LOW 0 8 (6%) 2 (1.5%) 0
NORMAL 0 76 (56.7%) 39 (29.1%) 2 (1.5%)
HIGH 0 3 (2.2%) 2 (1.5%) 0
Missing 0 1 (0.7%) 1 (0.7%) 0
C: Combination (N=132)
n 0 96 35 1
LOW 0 12 (9.1%) 3 (2.3%) 0
NORMAL 0 79 (59.8%) 27 (20.5%) 0
HIGH 0 5 (3.8%) 4 (3%) 1 (0.8%)
Missing 0 0 1 (0.8%) 0
Placebo (N=86)
n 0 333 0 3
LOW 0 84 (25%) 0 0
NORMAL 0 249 (74.1%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 3 (0.9%)
Xanomeline High Dose (N=84)
n 0 327 0 1
LOW 0 82 (25%) 0 0
NORMAL 0 245 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)
Xanomeline Low Dose (N=84)
n 0 335 0 1
LOW 0 84 (25%) 0 0
NORMAL 0 251 (74.7%) 0 0
HIGH 0 0 0 0
Missing 0 0 0 1 (0.3%)

28 changes: 14 additions & 14 deletions tests/testthat/_snaps/table_egt04.md
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Expand Up @@ -3,18 +3,18 @@
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Output
Normal Abnormal Missing
———————————————————————————————————————————————————————————
A: Drug X (N=134)
Normal 20 (14.9%) 81 (60.4%) 1 (0.7%)
Abnormal 11 (8.2%) 19 (14.2%) 0
Missing 0 1 (0.7%) 1 (0.7%)
B: Placebo (N=134)
Normal 18 (13.4%) 81 (60.4%) 2 (1.5%)
Abnormal 3 (2.2%) 28 (20.9%) 0
Missing 0 2 (1.5%) 0
C: Combination (N=132)
Normal 26 (19.7%) 69 (52.3%) 1 (0.8%)
Abnormal 6 (4.5%) 29 (22%) 0
Missing 1 (0.8%) 0 0
Normal Abnormal Missing
—————————————————————————————————————————————————————————————
Placebo (N=147)
Normal 0 79 (53.7%) 0
Abnormal 0 46 (31.3%) 0
Missing 0 22 (15%) 0
Xanomeline High Dose (N=120)
Normal 0 62 (51.7%) 1 (0.8%)
Abnormal 0 40 (33.3%) 1 (0.8%)
Missing 0 16 (13.3%) 0
Xanomeline Low Dose (N=111)
Normal 0 58 (52.3%) 0
Abnormal 0 26 (23.4%) 2 (1.8%)
Missing 0 24 (21.6%) 1 (0.9%)

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