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Use pharmaverseadam data in safety templates - part 2 (#154)
Closes #147
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‎.github/workflows/docs.yaml‎

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REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
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with:
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additional-unit-test-report-directories: unit-test-report-non-cran
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deps-installation-method: setup-r-dependencies
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lookup-refs: |
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insightsengineering/random.cdisc.data
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insightsengineering/rtables
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insightsengineering/formatters
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insightsengineering/tern
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insightsengineering/rlistings
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pharmaverse/pharmaverseadam

‎DESCRIPTION‎

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formatters (>= 0.5.9),
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R (>= 4.2),
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rlistings (>= 0.2.9),
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rtables (>= 0.6.8),
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rtables (>= 0.6.10),
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tern (>= 0.9.6.9015)
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Imports:
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pharmaverseadam (>= 1.1.0),

‎tests/testthat/_snaps/table_egt01.md‎

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‎tests/testthat/_snaps/table_egt02.md‎

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Assessment A: Drug X B: Placebo C: Combination
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Abnormality (N=134) (N=134) (N=132)
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————————————————————————————————————————————————————————————————
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Heart Rate
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Low 40/134 (29.9%) 43/134 (32.1%) 37/132 (28%)
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High 39/134 (29.1%) 45/134 (33.6%) 36/132 (27.3%)
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QT Duration
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Low 33/134 (24.6%) 44/134 (32.8%) 47/132 (35.6%)
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High 30/134 (22.4%) 42/134 (31.3%) 34/132 (25.8%)
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RR Duration
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Low 45/134 (33.6%) 26/134 (19.4%) 38/132 (28.8%)
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High 29/134 (21.6%) 49/134 (36.6%) 27/132 (20.5%)
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Assessment Placebo Xanomeline High Dose Xanomeline Low Dose
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Abnormality (N=86) (N=72) (N=96)
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———————————————————————————————————————————————————————————————————————————————————
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Heart Rate (beats/min)
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Low 0/84 0/72 0/94
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High 4/84 (4.8%) 0/72 0/94
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QT Duration (msec)
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Low 55/84 (65.5%) 44/72 (61.1%) 52/94 (55.3%)
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High 84/84 (100%) 72/72 (100%) 93/94 (98.9%)
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RR Duration (msec)
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Low 84/84 (100%) 72/72 (100%) 94/94 (100%)
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High 0/84 0/72 0/94
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# (EGT02) 2. Among Subjects Without Abnormality at Baseline
2020

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Code
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Output
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Assessment A: Drug X B: Placebo C: Combination
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Abnormality (N=134) (N=134) (N=132)
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————————————————————————————————————————————————————————————————
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Heart Rate
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Low 39/128 (30.5%) 42/124 (33.9%) 33/117 (28.2%)
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High 37/127 (29.1%) 43/129 (33.3%) 31/122 (25.4%)
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QT Duration
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Low 29/113 (25.7%) 42/126 (33.3%) 43/124 (34.7%)
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High 30/125 (24%) 40/130 (30.8%) 30/119 (25.2%)
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RR Duration
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Low 45/129 (34.9%) 26/123 (21.1%) 37/126 (29.4%)
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High 27/127 (21.3%) 43/122 (35.2%) 25/125 (20%)
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Assessment Placebo Xanomeline High Dose Xanomeline Low Dose
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Abnormality (N=86) (N=72) (N=96)
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———————————————————————————————————————————————————————————————————————————————————
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Heart Rate (beats/min)
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Low 0/84 0/72 0/94
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High 4/84 (4.8%) 0/72 0/94
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QT Duration (msec)
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Low 52/84 (61.9%) 44/72 (61.1%) 51/94 (54.3%)
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High 83/84 (98.8%) 72/72 (100%) 90/94 (95.7%)
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RR Duration (msec)
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Low 84/84 (100%) 72/72 (100%) 94/94 (100%)
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High 0/84 0/72 0/94
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‎tests/testthat/_snaps/table_egt03.md‎

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LOW NORMAL HIGH Missing
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——————————————————————————————————————————————————————————————————
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A: Drug X (N=134)
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n 40 92 0 2
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LOW 1 (0.7%) 5 (3.7%) 0 0
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NORMAL 36 (26.9%) 83 (61.9%) 0 1 (0.7%)
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HIGH 2 (1.5%) 4 (3%) 0 0
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Missing 1 (0.7%) 0 0 1 (0.7%)
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B: Placebo (N=134)
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n 43 89 0 2
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LOW 1 (0.7%) 9 (6.7%) 0 0
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NORMAL 40 (29.9%) 75 (56%) 0 2 (1.5%)
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HIGH 1 (0.7%) 4 (3%) 0 0
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Missing 1 (0.7%) 1 (0.7%) 0 0
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C: Combination (N=132)
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n 37 94 0 1
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LOW 4 (3%) 11 (8.3%) 0 0
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NORMAL 31 (23.5%) 75 (56.8%) 0 0
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HIGH 1 (0.8%) 8 (6.1%) 0 1 (0.8%)
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Missing 1 (0.8%) 0 0 0
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LOW NORMAL HIGH Missing
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—————————————————————————————————————————————————————————————————
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Placebo (N=86)
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n 0 333 0 3
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LOW 0 84 (25%) 0 0
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NORMAL 0 249 (74.1%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 3 (0.9%)
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Xanomeline High Dose (N=84)
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n 0 327 0 1
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LOW 0 82 (25%) 0 0
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NORMAL 0 245 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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Xanomeline Low Dose (N=84)
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n 0 335 0 1
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LOW 0 84 (25%) 0 0
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NORMAL 0 251 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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# EGT03 variant 2 is produced correctly
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Output
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LOW NORMAL HIGH
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A: Drug X (N=134)
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n 40 94 0
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LOW 1 (0.7%) 5 (3.7%) 0
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NORMAL 36 (26.9%) 84 (62.7%) 0
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HIGH 2 (1.5%) 4 (3%) 0
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Missing 1 (0.7%) 1 (0.7%) 0
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B: Placebo (N=134)
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n 43 91 0
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LOW 1 (0.7%) 9 (6.7%) 0
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NORMAL 40 (29.9%) 77 (57.5%) 0
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HIGH 1 (0.7%) 4 (3%) 0
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Missing 1 (0.7%) 1 (0.7%) 0
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C: Combination (N=132)
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n 37 95 0
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LOW 4 (3%) 11 (8.3%) 0
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NORMAL 31 (23.5%) 75 (56.8%) 0
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HIGH 1 (0.8%) 9 (6.8%) 0
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Missing 1 (0.8%) 0 0
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NORMAL
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—————————————————————————————————————————
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Placebo (N=86)
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n 336
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LOW 84 (25%)
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NORMAL 249 (74.1%)
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HIGH 0
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Missing 3 (0.9%)
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Xanomeline High Dose (N=84)
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n 328
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LOW 82 (25%)
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NORMAL 245 (74.7%)
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HIGH 0
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Missing 1 (0.3%)
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Xanomeline Low Dose (N=84)
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n 336
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LOW 84 (25%)
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NORMAL 251 (74.7%)
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HIGH 0
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Missing 1 (0.3%)
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# EGT03 variant 3 is produced correctly
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LOW NORMAL HIGH Missing
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A: Drug X (N=134)
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n 39 93 0 2
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LOW 1 (0.7%) 5 (3.7%) 0 0
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NORMAL 36 (26.9%) 84 (62.7%) 0 1 (0.7%)
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HIGH 2 (1.5%) 4 (3%) 0 1 (0.7%)
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B: Placebo (N=134)
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n 42 90 0 2
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LOW 1 (0.7%) 9 (6.7%) 0 0
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NORMAL 40 (29.9%) 77 (57.5%) 0 2 (1.5%)
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HIGH 1 (0.7%) 4 (3%) 0 0
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C: Combination (N=132)
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n 36 95 0 1
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LOW 4 (3%) 11 (8.3%) 0 0
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NORMAL 31 (23.5%) 75 (56.8%) 0 1 (0.8%)
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HIGH 1 (0.8%) 9 (6.8%) 0 0
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LOW NORMAL HIGH Missing
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—————————————————————————————————————————————————————————————————
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Placebo (N=86)
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n 0 333 0 3
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LOW 0 84 (25%) 0 0
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NORMAL 0 249 (74.1%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 3 (0.9%)
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Xanomeline High Dose (N=84)
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n 0 327 0 1
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LOW 0 82 (25%) 0 0
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NORMAL 0 245 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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Xanomeline Low Dose (N=84)
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n 0 335 0 1
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LOW 0 84 (25%) 0 0
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NORMAL 0 251 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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# EGT03 variant 4 is produced correctly
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LOW NORMAL HIGH Missing
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LOW NORMAL HIGH Missing
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—————————————————————————————————————————————————————————————————
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A: Drug X (N=134)
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n 0 95 37 2
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LOW 0 2 (1.5%) 4 (3%) 0
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NORMAL 0 88 (65.7%) 31 (23.1%) 1 (0.7%)
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HIGH 0 5 (3.7%) 1 (0.7%) 0
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Missing 0 0 1 (0.7%) 1 (0.7%)
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B: Placebo (N=134)
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n 0 88 44 2
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LOW 0 8 (6%) 2 (1.5%) 0
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NORMAL 0 76 (56.7%) 39 (29.1%) 2 (1.5%)
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HIGH 0 3 (2.2%) 2 (1.5%) 0
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Missing 0 1 (0.7%) 1 (0.7%) 0
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C: Combination (N=132)
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n 0 96 35 1
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LOW 0 12 (9.1%) 3 (2.3%) 0
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NORMAL 0 79 (59.8%) 27 (20.5%) 0
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HIGH 0 5 (3.8%) 4 (3%) 1 (0.8%)
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Missing 0 0 1 (0.8%) 0
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Placebo (N=86)
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n 0 333 0 3
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LOW 0 84 (25%) 0 0
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NORMAL 0 249 (74.1%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 3 (0.9%)
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Xanomeline High Dose (N=84)
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n 0 327 0 1
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LOW 0 82 (25%) 0 0
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NORMAL 0 245 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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Xanomeline Low Dose (N=84)
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n 0 335 0 1
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LOW 0 84 (25%) 0 0
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NORMAL 0 251 (74.7%) 0 0
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HIGH 0 0 0 0
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Missing 0 0 0 1 (0.3%)
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‎tests/testthat/_snaps/table_egt04.md‎

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Normal Abnormal Missing
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A: Drug X (N=134)
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Normal 20 (14.9%) 81 (60.4%) 1 (0.7%)
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Abnormal 11 (8.2%) 19 (14.2%) 0
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Missing 0 1 (0.7%) 1 (0.7%)
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B: Placebo (N=134)
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Normal 18 (13.4%) 81 (60.4%) 2 (1.5%)
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Abnormal 3 (2.2%) 28 (20.9%) 0
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Missing 0 2 (1.5%) 0
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C: Combination (N=132)
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Normal 26 (19.7%) 69 (52.3%) 1 (0.8%)
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Abnormal 6 (4.5%) 29 (22%) 0
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Missing 1 (0.8%) 0 0
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Normal Abnormal Missing
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—————————————————————————————————————————————————————————————
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Placebo (N=147)
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Normal 0 79 (53.7%) 0
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Abnormal 0 46 (31.3%) 0
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Missing 0 22 (15%) 0
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Xanomeline High Dose (N=120)
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Normal 0 62 (51.7%) 1 (0.8%)
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Abnormal 0 40 (33.3%) 1 (0.8%)
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Missing 0 16 (13.3%) 0
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Xanomeline Low Dose (N=111)
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Normal 0 58 (52.3%) 0
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Abnormal 0 26 (23.4%) 2 (1.8%)
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Missing 0 24 (21.6%) 1 (0.9%)
2020

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