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Update EG templates (#169)
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Closes #167

---------

Signed-off-by: Joe Zhu <[email protected]>
Co-authored-by: Joe Zhu <[email protected]>
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@edelarua @shajoezhu
edelarua and shajoezhu authored Nov 27, 2024
1 parent 301421d commit 3d3b610
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Showing 10 changed files with 355 additions and 336 deletions.
3 changes: 2 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ Depends:
tern (>= 0.9.6.9015)
Imports:
pharmaverseadam (>= 1.1.0),
random.cdisc.data (>= 0.3.15.9001)
random.cdisc.data (>= 0.3.16)
Suggests:
broom,
checkmate,
Expand All @@ -45,6 +45,7 @@ Suggests:
VignetteBuilder:
knitr
Remotes:
pharmaverse/pharmaverseadam@main,
insightsengineering/tern@main
biocViews:
Config/Needs/website: insightsengineering/nesttemplate
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112 changes: 56 additions & 56 deletions tests/testthat/_snaps/listing_egl01.md
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235 changes: 125 additions & 110 deletions tests/testthat/_snaps/table_egt01.md
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14 changes: 7 additions & 7 deletions tests/testthat/_snaps/table_egt02.md
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Expand Up @@ -9,10 +9,10 @@
Heart Rate (beats/min)
Low 0/84 0/72 0/94
High 4/84 (4.8%) 0/72 0/94
QT Duration (msec)
QT Duration (ms)
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)
RR Duration (ms)
Low 84/84 (100%) 72/72 (100%) 94/94 (100%)
High 0/84 0/72 0/94

Expand All @@ -27,10 +27,10 @@
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%)
QT Duration (ms)
Low 55/84 (65.5%) 44/72 (61.1%) 52/94 (55.3%)
High 37/37 (100%) 35/35 (100%) 44/44 (100%)
RR Duration (ms)
Low 12/12 (100%) 6/6 (100%) 10/10 (100%)
High 0/84 0/72 0/94

160 changes: 80 additions & 80 deletions tests/testthat/_snaps/table_egt03.md
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Expand Up @@ -3,102 +3,102 @@
Code
res
Output
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%)
LOW NORMAL HIGH Missing
———————————————————————————————————————————————————————————————————————
Placebo (N=84)
n 37 45 0 2
LOW 15 (17.9%) 14 (16.7%) 0 2 (2.4%)
NORMAL 20 (23.8%) 31 (36.9%) 0 0
HIGH 0 0 0 0
Missing 2 (2.4%) 0 0 0
Xanomeline High Dose (N=82)
n 30 50 0 2
LOW 13 (15.9%) 20 (24.4%) 0 2 (2.4%)
NORMAL 17 (20.7%) 29 (35.4%) 0 0
HIGH 0 0 0 0
Missing 0 1 (1.2%) 0 0
Xanomeline Low Dose (N=84)
n 32 51 0 1
LOW 10 (11.9%) 21 (25%) 0 1 (1.2%)
NORMAL 22 (26.2%) 28 (33.3%) 0 0
HIGH 0 0 0 0
Missing 0 2 (2.4%) 0 0

# EGT03 variant 2 is produced correctly

Code
res
Output
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%)
LOW NORMAL
—————————————————————————————————————————————————————
Placebo (N=84)
n 38 46
LOW 16 (19%) 15 (17.9%)
NORMAL 20 (23.8%) 31 (36.9%)
HIGH 0 0
Missing 2 (2.4%) 0
Xanomeline High Dose (N=82)
n 30 52
LOW 13 (15.9%) 22 (26.8%)
NORMAL 17 (20.7%) 29 (35.4%)
HIGH 0 0
Missing 0 1 (1.2%)
Xanomeline Low Dose (N=84)
n 32 52
LOW 10 (11.9%) 22 (26.2%)
NORMAL 22 (26.2%) 28 (33.3%)
HIGH 0 0
Missing 0 2 (2.4%)

# EGT03 variant 3 is produced correctly

Code
res
Output
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%)
LOW NORMAL HIGH Missing
———————————————————————————————————————————————————————————————————————
Placebo (N=84)
n 37 45 0 2
LOW 15 (17.9%) 14 (16.7%) 0 2 (2.4%)
NORMAL 20 (23.8%) 31 (36.9%) 0 0
HIGH 0 0 0 0
Missing 2 (2.4%) 0 0 0
Xanomeline High Dose (N=82)
n 30 50 0 2
LOW 13 (15.9%) 20 (24.4%) 0 2 (2.4%)
NORMAL 17 (20.7%) 29 (35.4%) 0 0
HIGH 0 0 0 0
Missing 0 1 (1.2%) 0 0
Xanomeline Low Dose (N=84)
n 32 51 0 1
LOW 10 (11.9%) 21 (25%) 0 1 (1.2%)
NORMAL 22 (26.2%) 28 (33.3%) 0 0
HIGH 0 0 0 0
Missing 0 2 (2.4%) 0 0

# EGT03 variant 4 is produced correctly

Code
res
Output
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%)
LOW NORMAL HIGH Missing
———————————————————————————————————————————————————————————————————————
Placebo (N=84)
n 37 45 0 2
LOW 15 (17.9%) 14 (16.7%) 0 2 (2.4%)
NORMAL 20 (23.8%) 31 (36.9%) 0 0
HIGH 0 0 0 0
Missing 2 (2.4%) 0 0 0
Xanomeline High Dose (N=82)
n 30 50 0 2
LOW 13 (15.9%) 20 (24.4%) 0 2 (2.4%)
NORMAL 17 (20.7%) 29 (35.4%) 0 0
HIGH 0 0 0 0
Missing 0 1 (1.2%) 0 0
Xanomeline Low Dose (N=84)
n 32 51 0 1
LOW 10 (11.9%) 21 (25%) 0 1 (1.2%)
NORMAL 22 (26.2%) 28 (33.3%) 0 0
HIGH 0 0 0 0
Missing 0 2 (2.4%) 0 0

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