AET01 Table 2 (Supplementary) Overview of Deaths and Adverse Events Summary Table 2.aet01_2.RdOverview of death and summary of adverse events with medical concepts.
aet01_2(
adam_db,
armvar = .study$actualarm,
lbl_overall = .study$lbl_overall,
prune_0 = FALSE,
deco = std_deco("AET01"),
safety_var = .study$safety_var,
lbl_safety_var = var_labels_for(adam_db$adae, safety_var),
medconcept_var = .study$medconcept_var,
lbl_medconcept_var = var_labels_for(adam_db$adae, medconcept_var),
.study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
"SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "SEV"),
medconcept_var = c("SMQ01", "SMQ02", "CQ01"))
)
aet01_2_lyt(
armvar = .study$actualarm,
lbl_overall = .study$lbl_overall,
deco = std_deco("AET01"),
safety_var = .study$safety_var,
lbl_safety_var = .study$lbl_safety_var,
medconcept_var = .study$medconcept_var,
lbl_medconcept_var = .study$lbl_medconcept_var,
.study = list(actualarm = "ACTARM", lbl_overall = NULL, safety_var = c("FATAL",
"SER", "SERWD", "SERDSM", "RELSER", "WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35",
"CTC45", "SEV"), lbl_safety_var = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER",
"WD", "DSM", "REL", "RELWD", "RELDSM", "CTC35", "CTC45", "SEV"), medconcept_var =
c("SMQ01", "SMQ02", "CQ01"), lbl_medconcept_var = c("SMQ01", "SMQ02", "CQ01"))
)
aet01_2_pre(adam_db)(dm) object containing the ADaM datasets
(character) variable used for column splitting
(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
(character) the safety variables to be summarized.
(character) the labels of the safety variables to be summarized.
(character) the medical concept variables to be summarized.
(character) the label of the medical concept variables to be summarized.
(list) with default values for the arguments of the function
Does not remove rows with zero counts by default.
aet01_2_lyt: aet01_2 Layout
aet01_2_pre: aet01_2 Preprocessing
library(dm)
db <- syn_test_data() %>%
aet01_2_pre()
aet01_2(db, armvar = "ARM", prune_0 = FALSE)
#> Overview of Deaths and Adverse Events: {Specify Population}
#> Protocol: {{protocol}}
#>
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X B: Placebo C: Combination
#> (N=134) (N=134) (N=132)
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> Total number of patients with at least one AE 122 (91%) 123 (91.8%) 120 (90.9%)
#> Total number of AEs 609 622 703
#> Total number of deaths 22 (16.4%) 26 (19.4%) 19 (14.4%)
#> Total number of patients withdrawn from study due to an AE 6 (4.5%) 1 (0.7%) 2 (1.5%)
#> Total number of patients with at least one
#> AE with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%)
#> Serious AE 104 (77.6%) 101 (75.4%) 99 (75%)
#> Serious AE leading to withdrawal from treatment 8 (6%) 8 (6%) 7 (5.3%)
#> Serious AE leading to dose modification/interruption 36 (26.9%) 31 (23.1%) 26 (19.7%)
#> Related Serious AE 76 (56.7%) 70 (52.2%) 75 (56.8%)
#> AE leading to withdrawal from treatment 23 (17.2%) 24 (17.9%) 27 (20.5%)
#> AE leading to dose modification/interruption 72 (53.7%) 65 (48.5%) 76 (57.6%)
#> Related AE 105 (78.4%) 108 (80.6%) 109 (82.6%)
#> Related AE leading to withdrawal from treatment 6 (4.5%) 9 (6.7%) 13 (9.8%)
#> Related AE leading to dose modification/interruption 31 (23.1%) 31 (23.1%) 32 (24.2%)
#> Severe AE (at greatest intensity) 91 (67.9%) 90 (67.2%) 93 (70.5%)
#> Total number of patients with at least one
#> C.1.1.1.3/B.2.2.3.1 AESI (BROAD) 72 (53.7%) 79 (59%) 75 (56.8%)
#> SMQ 02 Reference Name 0 0 0
#> D.2.1.5.3/A.1.1.1.1 AESI 74 (55.2%) 80 (59.7%) 87 (65.9%)
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> Investigator text for AEs encoded using MedDRA version xx.x. Percentages are based on N in the column headings.
#> Multiple occurrences of the same AE in one individual are counted only once except for "Total number of AEs" row in which multiple occurrences of the same AE are counted separately. 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).
aet01_1_lyt(
armvar = "ACTARM",
lbl_overall = NULL,
deco = std_deco("AET01")
)
#> $lyt_adae
#> A Pre-data Table Layout
#>
#> Column-Split Structure:
#> ACTARM (lvls)
#>
#> Row-Split Structure:
#> USUBJID (** analysis **)
#>
#>
#> $lyt_adsl
#> A Pre-data Table Layout
#>
#> Column-Split Structure:
#> ACTARM (lvls)
#>
#> Row-Split Structure:
#> USUBJID:USUBJID (** multivar analysis **)
#>
#>
syn_test_data() %>%
aet01_2_pre()
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adae`, `adaette`, `adcm`, `addv`, … (15 total)
#> Columns: 862
#> Primary keys: 2
#> Foreign keys: 1