Summarise adverse events by arm and other grouping variables
event_count_by.Rdevent_count_by() creates a tabular summary of adverse events grouped by a
higher-level classification variable (e.g., system organ class), and counts
both the number of events and the number of unique patients per treatment arm.
Usage
event_count_by(
dt,
patient,
treat,
rows_by,
target,
.total_dt = dt,
indent = nbsp(n = 4L),
pct_dec = 1
)Arguments
- dt
A
data.frameordata.tablecontaining the adverse event data and patient-level identifiers.- patient
A string giving the name of the patient identifier variable (e.g.,
"USUBJID").- treat
A string giving the name of the treatment arm variable (e.g.,
"ARM").- rows_by
A string giving the name of the grouping variable (e.g.,
"AEBODSYS"for body system).- target
A string giving the name of the variable to report within each group (e.g.,
"AEDECOD"for preferred term).- .total_dt
A
data.frameordata.tablecontaining the denominator population. Defaults todt.- indent
A string used to indent row labels (e.g.,
" "ornbsp(n = 4L)).- pct_dec
Integer. Number of decimal places to show in percentages. Defaults to
1.
Value
A data.table with the following structure:
One row per combination of
rows_byandtargetOne row per group total (
Total number of events)One row per patient-level total (
Total number of patients with at least one event)
Columns include:
stats: character column with labelsone column per level of the
treatvariable, formatted as"n (x%)"
Examples
event_count_by(
dt = adae[adae$ANL01FL == "Y"],
patient = 'USUBJID',
treat = 'ARM',
rows_by = 'AEBODSYS',
target = 'AEDECOD',
.total_dt = adsl,
indent = ' '
)
#> stats A: Drug X B: Placebo
#> <char> <char> <char>
#> 1: cl B.2
#> 2: dcd A.1.1.1.1 0 0
#> 3: dcd A.1.1.1.2 0 0
#> 4: dcd B.1.1.1.1 0 0
#> 5: dcd B.2.1.2.1 52 (38.8%) 51 (38.1%)
#> 6: dcd B.2.2.3.1 50 (37.3%) 55 (41.0%)
#> 7: dcd C.1.1.1.3 0 0
#> 8: dcd C.2.1.2.1 0 0
#> 9: dcd D.1.1.1.1 0 0
#> 10: dcd D.1.1.4.2 0 0
#> 11: dcd D.2.1.5.3 0 0
#> 12: Total number of events 102 106
#> 13: Total number of patients with at least one event 62 (46.3%) 56 (41.8%)
#> 14: cl D.1
#> 15: dcd A.1.1.1.1 0 0
#> 16: dcd A.1.1.1.2 0 0
#> 17: dcd B.1.1.1.1 0 0
#> 18: dcd B.2.1.2.1 0 0
#> 19: dcd B.2.2.3.1 0 0
#> 20: dcd C.1.1.1.3 0 0
#> 21: dcd C.2.1.2.1 0 0
#> 22: dcd D.1.1.1.1 52 (38.8%) 40 (29.9%)
#> 23: dcd D.1.1.4.2 54 (40.3%) 44 (32.8%)
#> 24: dcd D.2.1.5.3 0 0
#> 25: Total number of events 106 84
#> 26: Total number of patients with at least one event 64 (47.8%) 54 (40.3%)
#> 27: cl A.1
#> 28: dcd A.1.1.1.1 57 (42.5%) 43 (32.1%)
#> 29: dcd A.1.1.1.2 58 (43.3%) 56 (41.8%)
#> 30: dcd B.1.1.1.1 0 0
#> 31: dcd B.2.1.2.1 0 0
#> 32: dcd B.2.2.3.1 0 0
#> 33: dcd C.1.1.1.3 0 0
#> 34: dcd C.2.1.2.1 0 0
#> 35: dcd D.1.1.1.1 0 0
#> 36: dcd D.1.1.4.2 0 0
#> 37: dcd D.2.1.5.3 0 0
#> 38: Total number of events 115 99
#> 39: Total number of patients with at least one event 68 (50.7%) 58 (43.3%)
#> 40: cl D.2
#> 41: dcd A.1.1.1.1 0 0
#> 42: dcd A.1.1.1.2 0 0
#> 43: dcd B.1.1.1.1 0 0
#> 44: dcd B.2.1.2.1 0 0
#> 45: dcd B.2.2.3.1 0 0
#> 46: dcd C.1.1.1.3 0 0
#> 47: dcd C.2.1.2.1 0 0
#> 48: dcd D.1.1.1.1 0 0
#> 49: dcd D.1.1.4.2 0 0
#> 50: dcd D.2.1.5.3 49 (36.6%) 57 (42.5%)
#> 51: Total number of events 49 57
#> 52: Total number of patients with at least one event 37 (27.6%) 46 (34.3%)
#> 53: cl B.1
#> 54: dcd A.1.1.1.1 0 0
#> 55: dcd A.1.1.1.2 0 0
#> 56: dcd B.1.1.1.1 44 (32.8%) 43 (32.1%)
#> 57: dcd B.2.1.2.1 0 0
#> 58: dcd B.2.2.3.1 0 0
#> 59: dcd C.1.1.1.3 0 0
#> 60: dcd C.2.1.2.1 0 0
#> 61: dcd D.1.1.1.1 0 0
#> 62: dcd D.1.1.4.2 0 0
#> 63: dcd D.2.1.5.3 0 0
#> 64: Total number of events 44 43
#> 65: Total number of patients with at least one event 38 (28.4%) 37 (27.6%)
#> 66: cl C.2
#> 67: dcd A.1.1.1.1 0 0
#> 68: dcd A.1.1.1.2 0 0
#> 69: dcd B.1.1.1.1 0 0
#> 70: dcd B.2.1.2.1 0 0
#> 71: dcd B.2.2.3.1 0 0
#> 72: dcd C.1.1.1.3 0 0
#> 73: dcd C.2.1.2.1 39 (29.1%) 40 (29.9%)
#> 74: dcd D.1.1.1.1 0 0
#> 75: dcd D.1.1.4.2 0 0
#> 76: dcd D.2.1.5.3 0 0
#> 77: Total number of events 39 40
#> 78: Total number of patients with at least one event 28 (20.9%) 36 (26.9%)
#> 79: cl C.1
#> 80: dcd A.1.1.1.1 0 0
#> 81: dcd A.1.1.1.2 0 0
#> 82: dcd B.1.1.1.1 0 0
#> 83: dcd B.2.1.2.1 0 0
#> 84: dcd B.2.2.3.1 0 0
#> 85: dcd C.1.1.1.3 47 (35.1%) 51 (38.1%)
#> 86: dcd C.2.1.2.1 0 0
#> 87: dcd D.1.1.1.1 0 0
#> 88: dcd D.1.1.4.2 0 0
#> 89: dcd D.2.1.5.3 0 0
#> 90: Total number of events 47 51
#> 91: Total number of patients with at least one event 36 (26.9%) 34 (25.4%)
#> stats A: Drug X B: Placebo
#> C: Combination
#> <char>
#> 1:
#> 2: 0
#> 3: 0
#> 4: 0
#> 5: 59 (44.7%)
#> 6: 68 (51.5%)
#> 7: 0
#> 8: 0
#> 9: 0
#> 10: 0
#> 11: 0
#> 12: 127
#> 13: 74 (56.1%)
#> 14:
#> 15: 0
#> 16: 0
#> 17: 0
#> 18: 0
#> 19: 0
#> 20: 0
#> 21: 0
#> 22: 64 (48.5%)
#> 23: 50 (37.9%)
#> 24: 0
#> 25: 114
#> 26: 68 (51.5%)
#> 27:
#> 28: 74 (56.1%)
#> 29: 63 (47.7%)
#> 30: 0
#> 31: 0
#> 32: 0
#> 33: 0
#> 34: 0
#> 35: 0
#> 36: 0
#> 37: 0
#> 38: 137
#> 39: 76 (57.6%)
#> 40:
#> 41: 0
#> 42: 0
#> 43: 0
#> 44: 0
#> 45: 0
#> 46: 0
#> 47: 0
#> 48: 0
#> 49: 0
#> 50: 65 (49.2%)
#> 51: 65
#> 52: 50 (37.9%)
#> 53:
#> 54: 0
#> 55: 0
#> 56: 50 (37.9%)
#> 57: 0
#> 58: 0
#> 59: 0
#> 60: 0
#> 61: 0
#> 62: 0
#> 63: 0
#> 64: 50
#> 65: 36 (27.3%)
#> 66:
#> 67: 0
#> 68: 0
#> 69: 0
#> 70: 0
#> 71: 0
#> 72: 0
#> 73: 57 (43.2%)
#> 74: 0
#> 75: 0
#> 76: 0
#> 77: 57
#> 78: 48 (36.4%)
#> 79:
#> 80: 0
#> 81: 0
#> 82: 0
#> 83: 0
#> 84: 0
#> 85: 54 (40.9%)
#> 86: 0
#> 87: 0
#> 88: 0
#> 89: 0
#> 90: 54
#> 91: 36 (27.3%)
#> C: Combination