AET04 Table 1 (Default) Adverse Events by Highest NCI CTACAE AE Grade Table 1aet04_1.RdThe AET04 table provides an overview of adverse event with the highest NCI CTCAE grade per individual.
aet04_1(
adam_db,
armvar = .study$actualarm,
group_grades = .study$group_grades,
lbl_overall = .study$lbl_overall,
prune_0 = TRUE,
deco = std_deco("AET04"),
.study = list(actualarm = "ACTARM", lbl_overall = NULL, group_grades = NULL)
)
aet04_1_lyt(
armvar = .study$actualarm,
lbl_aebodsys = "AEBODSYS",
lbl_aedecod = "AEDECOD",
group_grades = .study$group_grades,
lbl_overall = .study$lbl_overall,
deco = std_deco("AET04"),
.study = list(actualarm = "ACTARM", lbl_overall = NULL, group_grades = NULL)
)
aet04_1_pre(adam_db)(dm) object containing the ADaM datasets
(character) variable used for column splitting
(list) putting in correspondence severity levels and labels.
(character) label used for overall column, if set to NULL the overall column is omitted
(logical) remove 0 count rows
(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.
Numbers represent absolute numbers of patients and fraction of N, or absolute number of event when specified.
Remove zero-count rows unless overridden with prune_0 = FALSE.
Split columns by arm, typically ACTARM.
Does not include a total column by default.
Sort Body System or Organ Class and Dictionary-Derived Term by highest overall frequencies. Analysis Toxicity Grade is sorted by severity.
aet04_1_lyt: aet04_1 Layout
aet04_1_pre: aet04_1 Preprocessing
library(dm)
db <- syn_test_data() %>%
aet04_1_pre()
aet04_1(db)
#> Adverse Events by Highest NCI CTCAE Grade: {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 Grade 122 (91%) 123 (91.8%) 120 (90.9%)
#> Grade 1-2 13 (9.7%) 19 (14.2%) 11 (8.3%)
#> 1 7 (5.2%) 9 (6.7%) 4 (3%)
#> 2 6 (4.5%) 10 (7.5%) 7 (5.3%)
#> Grade 3-4 33 (24.6%) 34 (25.4%) 34 (25.8%)
#> 3 18 (13.4%) 14 (10.4%) 16 (12.1%)
#> 4 15 (11.2%) 20 (14.9%) 18 (13.6%)
#> Grade 5 76 (56.7%) 70 (52.2%) 75 (56.8%)
#> cl A.1
#> Any Grade 78 (58.2%) 75 (56%) 89 (67.4%)
#> Grade 1-2 78 (58.2%) 75 (56%) 89 (67.4%)
#> 1 30 (22.4%) 27 (20.1%) 39 (29.5%)
#> 2 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> dcd A.1.1.1.1
#> Any Grade 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> Grade 1-2 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> 1 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> dcd A.1.1.1.2
#> Any Grade 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> Grade 1-2 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> 2 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> cl B.2
#> Any Grade 79 (59%) 74 (55.2%) 85 (64.4%)
#> Grade 1-2 30 (22.4%) 30 (22.4%) 33 (25%)
#> 1 30 (22.4%) 30 (22.4%) 33 (25%)
#> Grade 3-4 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> 3 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> dcd B.2.2.3.1
#> Any Grade 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> Grade 1-2 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> 1 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> dcd B.2.1.2.1
#> Any Grade 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> Grade 3-4 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> 3 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> cl D.1
#> Any Grade 79 (59%) 67 (50%) 80 (60.6%)
#> Grade 3-4 29 (21.6%) 25 (18.7%) 29 (22%)
#> 3 29 (21.6%) 25 (18.7%) 29 (22%)
#> Grade 5 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> dcd D.1.1.1.1
#> Any Grade 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> Grade 5 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> dcd D.1.1.4.2
#> Any Grade 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> Grade 3-4 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> 3 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> cl D.2
#> Any Grade 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> Grade 1-2 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> 1 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> dcd D.2.1.5.3
#> Any Grade 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> Grade 1-2 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> 1 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> cl B.1
#> Any Grade 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> Grade 5 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> dcd B.1.1.1.1
#> Any Grade 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> Grade 5 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> cl C.2
#> Any Grade 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> Grade 1-2 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> 2 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> dcd C.2.1.2.1
#> Any Grade 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> Grade 1-2 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> 2 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> cl C.1
#> Any Grade 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> Grade 3-4 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> 4 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> dcd C.1.1.1.3
#> Any Grade 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> Grade 3-4 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> 4 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 highest grade for this patient. To the SOC Overall row counts, a patient contributes only with the AE occuring with the highest grade within the SOC. Percentages are based on N in the column headings. 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).
aet04_1(
db,
prune_0 = FALSE,
lbl_overall = "All Patients",
group_grades = list(
"Any Grade" = c("1", "2", "3", "4", "5"),
"Grade 1-2" = c("1", "2"),
"Grade 3-5" = c("3", "4", "5")
)
)
#> Adverse Events by Highest NCI CTCAE Grade: {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 Grade 122 (91%) 123 (91.8%) 120 (90.9%) 365 (91.2%)
#> Grade 1-2 13 (9.7%) 19 (14.2%) 11 (8.3%) 43 (10.8%)
#> 1 7 (5.2%) 9 (6.7%) 4 (3%) 20 (5%)
#> 2 6 (4.5%) 10 (7.5%) 7 (5.3%) 23 (5.8%)
#> Grade 3-5 109 (81.3%) 104 (77.6%) 109 (82.6%) 322 (80.5%)
#> 3 18 (13.4%) 14 (10.4%) 16 (12.1%) 48 (12%)
#> 4 15 (11.2%) 20 (14.9%) 18 (13.6%) 53 (13.2%)
#> 5 76 (56.7%) 70 (52.2%) 75 (56.8%) 221 (55.2%)
#> cl A.1
#> Any Grade 78 (58.2%) 75 (56%) 89 (67.4%) 242 (60.5%)
#> Grade 1-2 78 (58.2%) 75 (56%) 89 (67.4%) 242 (60.5%)
#> 1 30 (22.4%) 27 (20.1%) 39 (29.5%) 96 (24%)
#> 2 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd A.1.1.1.1
#> Any Grade 50 (37.3%) 45 (33.6%) 63 (47.7%) 158 (39.5%)
#> Grade 1-2 50 (37.3%) 45 (33.6%) 63 (47.7%) 158 (39.5%)
#> 1 50 (37.3%) 45 (33.6%) 63 (47.7%) 158 (39.5%)
#> 2 0 0 0 0
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd A.1.1.1.2
#> Any Grade 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> Grade 1-2 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> 1 0 0 0 0
#> 2 48 (35.8%) 48 (35.8%) 50 (37.9%) 146 (36.5%)
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> cl B.2
#> Any Grade 79 (59%) 74 (55.2%) 85 (64.4%) 238 (59.5%)
#> Grade 1-2 30 (22.4%) 30 (22.4%) 33 (25%) 93 (23.2%)
#> 1 30 (22.4%) 30 (22.4%) 33 (25%) 93 (23.2%)
#> 2 0 0 0 0
#> Grade 3-5 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> 3 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd B.2.2.3.1
#> Any Grade 48 (35.8%) 54 (40.3%) 51 (38.6%) 153 (38.2%)
#> Grade 1-2 48 (35.8%) 54 (40.3%) 51 (38.6%) 153 (38.2%)
#> 1 48 (35.8%) 54 (40.3%) 51 (38.6%) 153 (38.2%)
#> 2 0 0 0 0
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd B.2.1.2.1
#> Any Grade 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> 3 49 (36.6%) 44 (32.8%) 52 (39.4%) 145 (36.2%)
#> 4 0 0 0 0
#> 5 0 0 0 0
#> cl D.1
#> Any Grade 79 (59%) 67 (50%) 80 (60.6%) 226 (56.5%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 79 (59%) 67 (50%) 80 (60.6%) 226 (56.5%)
#> 3 29 (21.6%) 25 (18.7%) 29 (22%) 83 (20.8%)
#> 4 0 0 0 0
#> 5 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> dcd D.1.1.1.1
#> Any Grade 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 50 (37.3%) 42 (31.3%) 51 (38.6%) 143 (35.8%)
#> dcd D.1.1.4.2
#> Any Grade 48 (35.8%) 42 (31.3%) 50 (37.9%) 140 (35%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 48 (35.8%) 42 (31.3%) 50 (37.9%) 140 (35%)
#> 3 48 (35.8%) 42 (31.3%) 50 (37.9%) 140 (35%)
#> 4 0 0 0 0
#> 5 0 0 0 0
#> cl D.2
#> Any Grade 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> Grade 1-2 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> 1 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> 2 0 0 0 0
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd D.2.1.5.3
#> Any Grade 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> Grade 1-2 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> 1 47 (35.1%) 58 (43.3%) 57 (43.2%) 162 (40.5%)
#> 2 0 0 0 0
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> cl B.1
#> Any Grade 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> dcd B.1.1.1.1
#> Any Grade 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 47 (35.1%) 49 (36.6%) 43 (32.6%) 139 (34.8%)
#> cl C.2
#> Any Grade 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> Grade 1-2 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> 1 0 0 0 0
#> 2 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> dcd C.2.1.2.1
#> Any Grade 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> Grade 1-2 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> 1 0 0 0 0
#> 2 35 (26.1%) 48 (35.8%) 55 (41.7%) 138 (34.5%)
#> Grade 3-5 0 0 0 0
#> 3 0 0 0 0
#> 4 0 0 0 0
#> 5 0 0 0 0
#> cl C.1
#> Any Grade 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> 3 0 0 0 0
#> 4 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> 5 0 0 0 0
#> dcd C.1.1.1.3
#> Any Grade 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> Grade 1-2 0 0 0 0
#> 1 0 0 0 0
#> 2 0 0 0 0
#> Grade 3-5 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> 3 0 0 0 0
#> 4 43 (32.1%) 46 (34.3%) 43 (32.6%) 132 (33%)
#> 5 0 0 0 0
#> —————————————————————————————————————————————————————————————————————————————————————
#>
#> 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 highest grade for this patient. To the SOC Overall row counts, a patient contributes only with the AE occuring with the highest grade within the SOC. Percentages are based on N in the column headings. 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).
aet04_1_lyt(armvar = "ACTARM")
#> A Pre-data Table Layout
#>
#> Column-Split Structure:
#> ACTARM (lvls)
#>
#> Row-Split Structure:
#> AEBODSYS (lvls) -> AEDECOD (lvls) -> AETOXGR (** analysis **)
#>
syn_test_data() %>%
aet04_1_pre()
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adae`, `adaette`, `adcm`, `addv`, … (15 total)
#> Columns: 846
#> Primary keys: 2
#> Foreign keys: 1