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implement for lbt15
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@zdz2101
zdz2101 committed Jan 11, 2024
1 parent 5a5fefa commit 507ee8b
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144 changes: 114 additions & 30 deletions tests/testthat/_snaps/table_lbt15.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,40 +3,124 @@
Code
res
Output
Category for Lab Test
Parameter A: Drug X B: Placebo C: Combination All Patients
Direction of Abnormality (N=134) (N=134) (N=132) (N=400)
———————————————————————————————————————————————————————————————————————————————————————————————————————————
CHEMISTRY
Alanine Aminotransferase Measurement
low 32/127 (25.2%) 32/128 (25%) 32/128 (25%) 96/383 (25.1%)
high 0/134 0/134 0/132 0/400
C-Reactive Protein Measurement
low 36/127 (28.3%) 36/127 (28.3%) 42/123 (34.1%) 114/377 (30.2%)
high 34/124 (27.4%) 33/128 (25.8%) 31/129 (24%) 98/381 (25.7%)
IMMUNOLOGY
Immunoglobulin A Measurement
low 0/134 0/134 0/132 0/400
high 33/128 (25.8%) 32/124 (25.8%) 28/120 (23.3%) 93/372 (25%)
Category for Lab Test
Parameter Placebo Xanomeline High Dose Xanomeline Low Dose All Patients
Direction of Abnormality (N=86) (N=84) (N=84) (N=306)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————
CHEMISTRY
Albumin (g/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Alkaline Phosphatase (U/L)
low 0/83 0/73 0/73 0/229
high 2/83 (2.4%) 0/73 0/73 2/229 (0.9%)
Alanine Aminotransferase (U/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Aspartate Aminotransferase (U/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Bilirubin (umol/L)
low 0/83 0/73 0/73 0/229
high 1/83 (1.2%) 0/73 0/73 1/229 (0.4%)
Calcium (mmol/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Cholesterol (mmol/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Creatinine Kinase (U/L)
low 0/83 0/73 0/74 0/230
high 2/83 (2.4%) 1/73 (1.4%) 0/74 3/230 (1.3%)
Creatinine (umol/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Gamma Glutamyl Transferase (U/L)
low 0/83 0/73 0/74 0/230
high 0/82 0/73 0/74 0/229
Glucose (mmol/L)
low 0/83 0/73 0/74 0/230
high 1/82 (1.2%) 6/73 (8.2%) 1/74 (1.4%) 8/229 (3.5%)
Phosphate (mmol/L)
low 1/83 (1.2%) 0/73 0/73 1/229 (0.4%)
high 0/83 0/73 0/73 0/229
Potassium (mmol/L)
low 0/83 0/73 0/73 0/229
high 0/83 0/73 0/73 0/229
Sodium (mmol/L)
low 1/83 (1.2%) 0/73 0/74 1/230 (0.4%)
high 0/83 0/73 0/74 0/230
HEMATOLOGY
Lymphocytes (10^9/L)
low 0/81 0/71 0/74 0/226
high 0/81 0/71 0/74 0/226
Platelet (10^9/L)
low 0/83 0/73 0/72 0/228
high 0/83 0/73 0/72 0/228
Leukocytes (10^9/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230

# LBT15 variant 2 works as expected

Code
res
Output
Category for Lab Test
Parameter A: Drug X B: Placebo C: Combination All Patients
Direction of Abnormality (N=134) (N=134) (N=132) (N=400)
———————————————————————————————————————————————————————————————————————————————————————————————————————————
CHEMISTRY
Alanine Aminotransferase Measurement
low 46/119 (38.7%) 54/123 (43.9%) 47/127 (37%) 147/369 (39.8%)
high 0/134 0/134 0/132 0/400
C-Reactive Protein Measurement
low 59/122 (48.4%) 56/118 (47.5%) 58/121 (47.9%) 173/361 (47.9%)
high 54/122 (44.3%) 46/122 (37.7%) 44/122 (36.1%) 144/366 (39.3%)
IMMUNOLOGY
Immunoglobulin A Measurement
low 0/134 0/134 0/132 0/400
high 47/124 (37.9%) 54/120 (45%) 47/115 (40.9%) 148/359 (41.2%)
Category for Lab Test
Parameter Placebo Xanomeline High Dose Xanomeline Low Dose All Patients
Direction of Abnormality (N=86) (N=84) (N=84) (N=306)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————
CHEMISTRY
Albumin (g/L)
low 2/83 (2.4%) 0/73 0/74 2/230 (0.9%)
high 0/83 0/73 0/74 0/230
Alkaline Phosphatase (U/L)
low 0/83 0/73 0/73 0/229
high 1/82 (1.2%) 0/72 0/73 1/227 (0.4%)
Alanine Aminotransferase (U/L)
low 0/83 0/73 0/74 0/230
high 2/83 (2.4%) 1/73 (1.4%) 0/74 3/230 (1.3%)
Aspartate Aminotransferase (U/L)
low 0/83 0/73 0/74 0/230
high 2/83 (2.4%) 1/73 (1.4%) 1/74 (1.4%) 4/230 (1.7%)
Bilirubin (umol/L)
low 0/83 0/73 0/73 0/229
high 1/83 (1.2%) 2/72 (2.8%) 1/73 (1.4%) 4/228 (1.8%)
Calcium (mmol/L)
low 0/83 2/73 (2.7%) 1/74 (1.4%) 3/230 (1.3%)
high 0/83 0/73 0/74 0/230
Cholesterol (mmol/L)
low 0/83 0/73 0/74 0/230
high 2/79 (2.5%) 0/71 2/73 (2.7%) 4/223 (1.8%)
Creatinine Kinase (U/L)
low 0/83 0/73 0/74 0/230
high 5/83 (6%) 1/73 (1.4%) 1/73 (1.4%) 7/229 (3.1%)
Creatinine (umol/L)
low 0/83 0/73 0/74 0/230
high 0/83 0/73 0/74 0/230
Gamma Glutamyl Transferase (U/L)
low 0/83 0/73 0/74 0/230
high 0/82 2/73 (2.7%) 0/74 2/229 (0.9%)
Glucose (mmol/L)
low 1/83 (1.2%) 0/73 2/74 (2.7%) 3/230 (1.3%)
high 1/82 (1.2%) 6/73 (8.2%) 1/74 (1.4%) 8/229 (3.5%)
Phosphate (mmol/L)
low 5/83 (6%) 4/73 (5.5%) 2/73 (2.7%) 11/229 (4.8%)
high 0/83 0/73 0/73 0/229
Potassium (mmol/L)
low 3/83 (3.6%) 2/73 (2.7%) 2/73 (2.7%) 7/229 (3.1%)
high 0/82 1/73 (1.4%) 0/73 1/228 (0.4%)
Sodium (mmol/L)
low 1/83 (1.2%) 0/73 0/74 1/230 (0.4%)
high 0/83 2/73 (2.7%) 0/74 2/230 (0.9%)
HEMATOLOGY
Lymphocytes (10^9/L)
low 1/80 (1.2%) 0/71 1/74 (1.4%) 2/225 (0.9%)
high 0/81 0/71 0/74 0/226
Platelet (10^9/L)
low 0/83 0/73 0/72 0/228
high 0/83 0/73 0/72 0/228
Leukocytes (10^9/L)
low 0/83 1/73 (1.4%) 1/74 (1.4%) 2/230 (0.9%)
high 0/83 0/73 0/74 0/230

4 changes: 2 additions & 2 deletions tests/testthat/test-table_lbt15.R
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@@ -1,5 +1,5 @@
adsl <- adsl_raw
adlb <- adlb_raw
adsl <- adsl_pharmaverse
adlb <- adlb_pharmaverse

adlb <- adlb %>%
mutate(
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