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Use pharmaverseadam data in safety templates - part 2 #154

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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
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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 @@
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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 6/84 (7.1%) 4/72 (5.6%) 6/94 (6.4%)
QT Duration (msec)
Low 23/84 (27.4%) 15/72 (20.8%) 21/94 (22.3%)
High 70/84 (83.3%) 66/72 (91.7%) 85/94 (90.4%)
RR Duration (msec)
Low 84/84 (100%) 71/72 (98.6%) 90/94 (95.7%)
High 0/84 0/72 0/94

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

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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 5/84 (6%) 4/72 (5.6%) 6/94 (6.4%)
QT Duration (msec)
Low 23/84 (27.4%) 15/72 (20.8%) 20/94 (21.3%)
High 69/84 (82.1%) 65/72 (90.3%) 81/94 (86.2%)
RR Duration (msec)
Low 83/84 (98.8%) 71/72 (98.6%) 90/94 (95.7%)
High 0/84 0/72 0/94

157 changes: 80 additions & 77 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=336)
n 0 331 3 2
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 0 243 (72.3%) 2 (0.6%) 0
HIGH 0 5 (1.5%) 0 0
Missing 0 0 0 2 (0.6%)
Xanomeline High Dose (N=324)
n 0 321 3 0
LOW 0 80 (24.7%) 1 (0.3%) 0
NORMAL 0 241 (74.4%) 2 (0.6%) 0
HIGH 0 0 0 0
Missing 0 0 0 0
Xanomeline Low Dose (N=336)
n 1 326 6 3
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 1 (0.3%) 242 (72%) 5 (1.5%) 0
HIGH 0 1 (0.3%) 0 0
Missing 0 0 0 3 (0.9%)

# EGT03 variant 2 is produced correctly

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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 LOW HIGH
————————————————————————————————————————————————————————————————
Placebo (N=336)
n 333 0 3
LOW 83 (24.7%) 0 1 (0.3%)
NORMAL 243 (72.3%) 0 2 (0.6%)
HIGH 5 (1.5%) 0 0
Missing 2 (0.6%) 0 0
Xanomeline High Dose (N=324)
n 321 0 3
LOW 80 (24.7%) 0 1 (0.3%)
NORMAL 241 (74.4%) 0 2 (0.6%)
HIGH 0 0 0
Missing 0 0 0
Xanomeline Low Dose (N=336)
n 329 1 6
LOW 83 (24.7%) 0 1 (0.3%)
NORMAL 242 (72%) 1 (0.3%) 5 (1.5%)
HIGH 1 (0.3%) 0 0
Missing 3 (0.9%) 0 0

# EGT03 variant 3 is produced correctly

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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=336)
n 0 331 3 2
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 0 243 (72.3%) 2 (0.6%) 0
HIGH 0 5 (1.5%) 0 0
Missing 0 0 0 2 (0.6%)
Xanomeline High Dose (N=324)
n 0 321 3 0
LOW 0 80 (24.7%) 1 (0.3%) 0
NORMAL 0 241 (74.4%) 2 (0.6%) 0
HIGH 0 0 0 0
Missing 0 0 0 0
Comment on lines +60 to +71
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let's check if this is expected, and if it makes sense

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zero counts for low

Xanomeline Low Dose (N=336)
n 1 326 6 3
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 1 (0.3%) 242 (72%) 5 (1.5%) 0
HIGH 0 1 (0.3%) 0 0
Missing 0 0 0 3 (0.9%)

# EGT03 variant 4 is produced correctly

Code
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Output
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
LOW NORMAL HIGH Missing
———————————————————————————————————————————————————————————————————————————
Placebo (N=336)
n 0 331 3 2
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 0 243 (72.3%) 2 (0.6%) 0
HIGH 0 5 (1.5%) 0 0
Missing 0 0 0 2 (0.6%)
Xanomeline High Dose (N=324)
n 0 321 3 0
LOW 0 80 (24.7%) 1 (0.3%) 0
NORMAL 0 241 (74.4%) 2 (0.6%) 0
HIGH 0 0 0 0
Comment on lines +87 to +96
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zero counts for low , lets check

Missing 0 0 0 0
Xanomeline Low Dose (N=336)
n 1 326 6 3
LOW 0 83 (24.7%) 1 (0.3%) 0
NORMAL 1 (0.3%) 242 (72%) 5 (1.5%) 0
HIGH 0 1 (0.3%) 0 0
Missing 0 0 0 3 (0.9%)

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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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=145)
Normal 73 (50.3%) 0 1 (0.7%)
Abnormal 38 (26.2%) 1 (0.7%) 2 (1.4%)
Missing 30 (20.7%) 0 0
Xanomeline High Dose (N=113)
Normal 45 (39.8%) 9 (8%) 1 (0.9%)
Abnormal 27 (23.9%) 7 (6.2%) 0
Missing 23 (20.4%) 1 (0.9%) 0
Xanomeline Low Dose (N=119)
Normal 52 (43.7%) 8 (6.7%) 0
Abnormal 30 (25.2%) 3 (2.5%) 0
Missing 25 (21%) 0 1 (0.8%)

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