AET03 Table 1 (Default) Advert Events by Greatest Intensity Table 1aet03_1.RdAn adverse events table categorized by System Organ Class, Dictionary-Derived Term and Greatest intensity.
aet03_1(
adam_db,
armvar = .study$actualarm,
prune_0 = TRUE,
lbl_overall = .study$lbl_overall,
deco = std_deco("AET03"),
.study = list(actualarm = "ACTARM", lbl_overall = NULL)
)
aet03_1_lyt(
armvar = .study$actualarm,
lbl_aebodsys = "",
lbl_aedecod = "",
severity_grade = .study$severity_grade,
lbl_overall = .study$lbl_overall,
deco = std_deco("AET03"),
.study = list(actualarm = "ACTARM", lbl_overall = NULL, severity_grade = c("MILD",
"MODERATE", "SEVERE", "LIFE THREATENING"))
)
aet03_1_pre(adam_db)(dm) object containing the ADaM datasets
(character) variable used for column splitting
(logical) remove 0 count rows
(character) label used for overall column, if set to NULL the overall column is omitted
(character) decoration with title, subtitles and main_footer content
(list) with default values for the arguments of the function
(character) text label for AEBODSYS.
(character) text label for AEDECOD.
(vector of character) describing the severity levels present in the data set.
Default Adverse Events by Greatest Intensity table.
Numbers represent absolute numbers of patients and fraction of N.
Remove zero-count rows unless overridden with prune_0 = FALSE.
Split columns by arm.
Does not include a total column by default.
Sort by Body System or Organ Class (SOC) and Dictionary-Derived Term (PT).
aet03_1_lyt: aet03_1 Layout
aet03_1_pre: aet03_1 Preprocessing
library(dm)
db <- syn_test_data() %>%
aet03_1_pre()
aet03_1(db)
#> Adverse Events by Greatest Intensity: {Specify Population}
#> Protocol: {{protocol}}
#>
#> —————————————————————————————————————————————————————————————————————
#> MedDRA System Organ Class A: Drug X B: Placebo C: Combination
#> MedDRA Preferred Term (N=134) (N=134) (N=132)
#> —————————————————————————————————————————————————————————————————————
#> - Any Intensity - 122 (91%) 123 (91.8%) 120 (90.9%)
#> MILD 7 (5.2%) 9 (6.7%) 4 (3%)
#> MODERATE 24 (17.9%) 24 (17.9%) 23 (17.4%)
#> SEVERE 91 (67.9%) 90 (67.2%) 93 (70.5%)
#> cl A.1
#> - Any Intensity - 78 (58.2%) 75 (56%) 89 (67.4%)
#> MILD 30 (22.4%) 27 (20.1%) 39 (29.5%)
#> MODERATE 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> dcd A.1.1.1.1
#> - Any Intensity - 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> MILD 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> dcd A.1.1.1.2
#> - Any Intensity - 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> MODERATE 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> cl B.2
#> - Any Intensity - 79 (59%) 74 (55.2%) 85 (64.4%)
#> MILD 30 (22.4%) 30 (22.4%) 33 (25%)
#> MODERATE 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> dcd B.2.2.3.1
#> - Any Intensity - 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> MILD 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> dcd B.2.1.2.1
#> - Any Intensity - 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> MODERATE 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> cl D.1
#> - Any Intensity - 79 (59%) 67 (50%) 80 (60.6%)
#> MODERATE 29 (21.6%) 25 (18.7%) 29 (22%)
#> SEVERE 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> dcd D.1.1.1.1
#> - Any Intensity - 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> SEVERE 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> dcd D.1.1.4.2
#> - Any Intensity - 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> MODERATE 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> cl D.2
#> - Any Intensity - 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> MILD 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> dcd D.2.1.5.3
#> - Any Intensity - 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> MILD 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> cl B.1
#> - Any Intensity - 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> SEVERE 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> dcd B.1.1.1.1
#> - Any Intensity - 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> SEVERE 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> cl C.2
#> - Any Intensity - 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> MODERATE 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> dcd C.2.1.2.1
#> - Any Intensity - 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> MODERATE 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> cl C.1
#> - Any Intensity - 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> SEVERE 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> dcd C.1.1.1.3
#> - Any Intensity - 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> SEVERE 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> —————————————————————————————————————————————————————————————————————
#>
#> Investigator text for AEs encoded using MedDRA version xx.x. All counts represent patients. Multiple occurrences of the same AE in one individual are counted once at the greatest intensity for this preferred term. To the SOC Overall row counts, a patient contributes only with the AE occuring with the greatest intensity within the SOC. Standard footnote defining AEs included in table (e.g., includes AEs with onset from first dose of study drug through 7 days after last dose of study drug).
aet03_1(db, lbl_overall = "All Patients")
#> Adverse Events by Greatest Intensity: {Specify Population}
#> Protocol: {{protocol}}
#>
#> ————————————————————————————————————————————————————————————————————————————————————
#> MedDRA System Organ Class A: Drug X B: Placebo C: Combination All Patients
#> MedDRA Preferred Term (N=134) (N=134) (N=132) (N=400)
#> ————————————————————————————————————————————————————————————————————————————————————
#> - Any Intensity - 122 (91%) 123 (91.8%) 120 (90.9%) 365 (91.2%)
#> MILD 7 (5.2%) 9 (6.7%) 4 (3%) 20 (5%)
#> MODERATE 24 (17.9%) 24 (17.9%) 23 (17.4%) 71 (17.8%)
#> SEVERE 91 (67.9%) 90 (67.2%) 93 (70.5%) 274 (68.5%)
#> cl A.1
#> - Any Intensity - 78 (58.2%) 75 (56%) 89 (67.4%) 242 (60.5%)
#> MILD 30 (22.4%) 27 (20.1%) 39 (29.5%) 96 (24%)
#> MODERATE 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> dcd A.1.1.1.1
#> - Any Intensity - 50 (37.3%) 45 (33.6%) 63 (47.7%) 158 (39.5%)
#> MILD 50 (37.3%) 45 (33.6%) 63 (47.7%) 158 (39.5%)
#> dcd A.1.1.1.2
#> - Any Intensity - 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> MODERATE 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> cl B.2
#> - Any Intensity - 79 (59%) 74 (55.2%) 85 (64.4%) 238 (59.5%)
#> MILD 30 (22.4%) 30 (22.4%) 33 (25%) 93 (23.2%)
#> MODERATE 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> dcd B.2.2.3.1
#> - Any Intensity - 48 (35.8%) 54 (40.3%) 51 (38.6%) 153 (38.2%)
#> MILD 48 (35.8%) 54 (40.3%) 51 (38.6%) 153 (38.2%)
#> dcd B.2.1.2.1
#> - Any Intensity - 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> MODERATE 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> cl D.1
#> - Any Intensity - 79 (59%) 67 (50%) 80 (60.6%) 226 (56.5%)
#> MODERATE 29 (21.6%) 25 (18.7%) 29 (22%) 83 (20.8%)
#> SEVERE 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> dcd D.1.1.1.1
#> - Any Intensity - 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> SEVERE 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> dcd D.1.1.4.2
#> - Any Intensity - 48 (35.8%) 42 (31.3%) 50 (37.9%) 140 (35%)
#> MODERATE 48 (35.8%) 42 (31.3%) 50 (37.9%) 140 (35%)
#> cl D.2
#> - Any Intensity - 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> MILD 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> dcd D.2.1.5.3
#> - Any Intensity - 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> MILD 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> cl B.1
#> - Any Intensity - 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> SEVERE 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> dcd B.1.1.1.1
#> - Any Intensity - 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> SEVERE 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> cl C.2
#> - Any Intensity - 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> MODERATE 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> dcd C.2.1.2.1
#> - Any Intensity - 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> MODERATE 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> cl C.1
#> - Any Intensity - 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> SEVERE 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> dcd C.1.1.1.3
#> - Any Intensity - 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> SEVERE 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> ————————————————————————————————————————————————————————————————————————————————————
#>
#> Investigator text for AEs encoded using MedDRA version xx.x. All counts represent patients. Multiple occurrences of the same AE in one individual are counted once at the greatest intensity for this preferred term. To the SOC Overall row counts, a patient contributes only with the AE occuring with the greatest intensity within the SOC. Standard footnote defining AEs included in table (e.g., includes AEs with onset from first dose of study drug through 7 days after last dose of study drug).
aet03_1_lyt(
armvar = "ACTARM",
lbl_aebodsys = "Body System or Organ Class",
lbl_aedecod = "Dictionary-Derived Term",
lbl_overall = NULL,
deco = std_deco("AET03")
)
#> A Pre-data Table Layout
#>
#> Column-Split Structure:
#> ACTARM (lvls)
#>
#> Row-Split Structure:
#> AEBODSYS (lvls) -> AEDECOD (lvls)
#>
syn_test_data() %>%
aet03_1_pre()
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adae`, `adaette`, `adcm`, `addv`, … (15 total)
#> Columns: 846
#> Primary keys: 2
#> Foreign keys: 1