Adverse events by System Organ Class and Preferred Term

Pre-summarised AE-by-SOC/PT table. Interleaved row order: overall "any TEAE" row first, then per-SOC blocks where each SOC row is followed by its preferred-term detail rows. Top 10 SOCs and top 5 PTs per SOC are kept; row_type marks the role of each row and indent_level carries the canonical depth (0 for overall and SOC, 1 for PT) so the downstream pipeline drives the SOC -> PT indent via col_spec(indent = "indent_level") without reconstructing it in every script. The richer SOC × PT slice exercises paginate() and the engine's horizontal-panel splitter end-to-end on a realistic submission shell.

Usage

cdisc_saf_aesocpt

Format

A data frame with 61 rows and 10 columns:

soc

System Organ Class label. Repeats across the SOC's PT rows; hide via col_spec(visible = FALSE) once label carries the same SOC text on SOC rows.

label

The row's display label. Equal to soc on the overall and SOC-summary rows; equal to the preferred-term name on PT detail rows. Promoted to the primary display column — pair with indent = "indent_level" to drive the SOC -> PT indent.

row_type

One of "overall", "soc", "pt". Partition marker; hide via col_spec(visible = FALSE).

indent_level

Integer depth (0 on overall and SOC rows, 1 on PT rows). Consumed by col_spec(indent = "indent_level") on the label column; the engine auto-hides this column at resolve time.

n_total

Integer. The row's own subject count — overall TEAE count on the overall row, the SOC's count on each SOC row, the PT's count on each PT row. Inner sort key.

soc_n

Integer. The parent SOC's count, broadcast to every row in that SOC's cluster (SOC row + its PT children) so a descending sort on soc_n keeps PTs grouped under their parent. On the overall row, equal to the overall TEAE count. Outer sort key.

placebo

Placebo arm cell text ("n (pct)").

drug_50, drug_100

Drug arms cell text.

Total

Pooled-across-arms cell text.

Source

Derived in data-raw/bundle-demo.R from pharmaverseadam::adae. Filtered to the top 10 SOCs by total incidence and the top 5 PTs per SOC. Body rows are pre-sorted with the cards-style two-level rule (arrange(desc(soc_n), soc, desc(n_total))) so the canonical render order is already baked in; the render-time sort_rows(by = c("soc_n", "n_total"), descending = c(TRUE, TRUE)) reproduces it via stable sort.

See also

cdisc_saf_aesocpt_ard for the hierarchical long ARD; cdisc_saf_n for BigN denominators.

Examples

# 95% safety pattern: SOC/PT table where `label` carries SOC text
# on SOC rows and PT text on PT rows, indented by `indent_level`.
# `soc` / `row_type` / `n_total` / `soc_n` ride along as hidden
# partition + sort keys. `sort_rows(soc_n, n_total)` clusters PTs
# under their parent SOC and orders both levels by descending count.
n <- stats::setNames(cdisc_saf_n$n, cdisc_saf_n$arm_short)

tabular(
  cdisc_saf_aesocpt,
  titles = c(
    "Table 14.3.1",
    "Adverse Events by SOC and Preferred Term",
    "Safety Population"
  )
) |>
  cols(
    label    = col_spec(
      label = "SOC / PT",
      indent = "indent_level",
      align = "left"
    ),
    soc      = col_spec(visible = FALSE),
    row_type = col_spec(visible = FALSE),
    n_total  = col_spec(visible = FALSE),
    soc_n    = col_spec(visible = FALSE),
    placebo  = col_spec(
      label = "Placebo\nN={n['placebo']}",
      align = "decimal"
    ),
    drug_50  = col_spec(
      label = "Drug 50\nN={n['drug_50']}",
      align = "decimal"
    ),
    drug_100 = col_spec(
      label = "Drug 100\nN={n['drug_100']}",
      align = "decimal"
    ),
    Total    = col_spec(
      label = "Total\nN={n['Total']}",
      align = "decimal"
    )
  ) |>
  sort_rows(
    by = c("soc_n", "n_total"),
    descending = c(TRUE, TRUE)
  )
 
Table 14.3.1
Adverse Events by SOC and Preferred Term
Safety Population
 

SOC / PT
Placebo
N=86
Drug 50
N=96
Drug 100
N=72
Total
N=254
TOTAL SUBJECTS WITH AN EVENT
52 (60.5)
81 (84.4)
66 (91.7)
199 (78.3)
SKIN AND SUBCUTANEOUS TISSUE DISORDERS
19 (22.1)
36 (37.5)
35 (48.6)
 90 (35.4)
PRURITUS
 8 ( 9.3)
21 (21.9)
25 (34.7)
 54 (21.3)
ERYTHEMA
 8 ( 9.3)
14 (14.6)
14 (19.4)
 36 (14.2)
RASH
 5 ( 5.8)
13 (13.5)
 8 (11.1)
 26 (10.2)
HYPERHIDROSIS
 2 ( 2.3)
 4 ( 4.2)
 8 (11.1)
 14 ( 5.5)
SKIN IRRITATION
 3 ( 3.5)
 6 ( 6.2)
 5 ( 6.9)
 14 ( 5.5)
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS
15 (17.4)
36 (37.5)
30 (41.7)
 81 (31.9)
APPLICATION SITE PRURITUS
 6 ( 7.0)
23 (24.0)
21 (29.2)
 50 (19.7)
APPLICATION SITE ERYTHEMA
 3 ( 3.5)
13 (13.5)
14 (19.4)
 30 (11.8)
APPLICATION SITE DERMATITIS
 5 ( 5.8)
 9 ( 9.4)
 7 ( 9.7)
 21 ( 8.3)
APPLICATION SITE IRRITATION
 3 ( 3.5)
 9 ( 9.4)
 9 (12.5)
 21 ( 8.3)
APPLICATION SITE VESICLES
 1 ( 1.2)
 5 ( 5.2)
 5 ( 6.9)
 11 ( 4.3)
GASTROINTESTINAL DISORDERS
13 (15.1)
12 (12.5)
17 (23.6)
 42 (16.5)
DIARRHOEA
 9 (10.5)
 5 ( 5.2)
 3 ( 4.2)
 17 ( 6.7)
VOMITING
 3 ( 3.5)
 4 ( 4.2)
 6 ( 8.3)
 13 ( 5.1)
NAUSEA
 3 ( 3.5)
 3 ( 3.1)
 6 ( 8.3)
 12 ( 4.7)
ABDOMINAL PAIN
 1 ( 1.2)
 3 ( 3.1)
 1 ( 1.4)
  5 ( 2.0)
SALIVARY HYPERSECRETION
 0       
 0       
 4 ( 5.6)
  4 ( 1.6)
NERVOUS SYSTEM DISORDERS
 6 ( 7.0)
18 (18.8)
17 (23.6)
 41 (16.1)
DIZZINESS
 2 ( 2.3)
 9 ( 9.4)
10 (13.9)
 21 ( 8.3)
HEADACHE
 3 ( 3.5)
 3 ( 3.1)
 5 ( 6.9)
 11 ( 4.3)
SYNCOPE
 0       
 5 ( 5.2)
 2 ( 2.8)
  7 ( 2.8)
SOMNOLENCE
 2 ( 2.3)
 3 ( 3.1)
 1 ( 1.4)
  6 ( 2.4)
TRANSIENT ISCHAEMIC ATTACK
 0       
 2 ( 2.1)
 1 ( 1.4)
  3 ( 1.2)
CARDIAC DISORDERS
 7 ( 8.1)
12 (12.5)
14 (19.4)
 33 (13.0)
SINUS BRADYCARDIA
 2 ( 2.3)
 7 ( 7.3)
 8 (11.1)
 17 ( 6.7)
MYOCARDIAL INFARCTION
 4 ( 4.7)
 2 ( 2.1)
 4 ( 5.6)
 10 ( 3.9)
ATRIAL FIBRILLATION
 1 ( 1.2)
 2 ( 2.1)
 2 ( 2.8)
  5 ( 2.0)
SUPRAVENTRICULAR EXTRASYSTOLES
 1 ( 1.2)
 1 ( 1.0)
 1 ( 1.4)
  3 ( 1.2)
VENTRICULAR EXTRASYSTOLES
 0       
 2 ( 2.1)
 1 ( 1.4)
  3 ( 1.2)
INFECTIONS AND INFESTATIONS
12 (14.0)
 6 ( 6.2)
11 (15.3)
 29 (11.4)
NASOPHARYNGITIS
 2 ( 2.3)
 4 ( 4.2)
 6 ( 8.3)
 12 ( 4.7)
UPPER RESPIRATORY TRACT INFECTION
 6 ( 7.0)
 1 ( 1.0)
 3 ( 4.2)
 10 ( 3.9)
INFLUENZA
 1 ( 1.2)
 1 ( 1.0)
 1 ( 1.4)
  3 ( 1.2)
URINARY TRACT INFECTION
 2 ( 2.3)
 0       
 1 ( 1.4)
  3 ( 1.2)
CYSTITIS
 1 ( 1.2)
 0       
 1 ( 1.4)
  2 ( 0.8)
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS
 5 ( 5.8)
 8 ( 8.3)
 9 (12.5)
 22 ( 8.7)
COUGH
 1 ( 1.2)
 5 ( 5.2)
 5 ( 6.9)
 11 ( 4.3)
NASAL CONGESTION
 3 ( 3.5)
 1 ( 1.0)
 3 ( 4.2)
  7 ( 2.8)
DYSPNOEA
 1 ( 1.2)
 1 ( 1.0)
 1 ( 1.4)
  3 ( 1.2)
EPISTAXIS
 0       
 1 ( 1.0)
 2 ( 2.8)
  3 ( 1.2)
PHARYNGOLARYNGEAL PAIN
 0       
 1 ( 1.0)
 1 ( 1.4)
  2 ( 0.8)
PSYCHIATRIC DISORDERS
 7 ( 8.1)
 9 ( 9.4)
 3 ( 4.2)
 19 ( 7.5)
CONFUSIONAL STATE
 2 ( 2.3)
 3 ( 3.1)
 1 ( 1.4)
  6 ( 2.4)
AGITATION
 2 ( 2.3)
 3 ( 3.1)
 0       
  5 ( 2.0)
INSOMNIA
 2 ( 2.3)
 0       
 2 ( 2.8)
  4 ( 1.6)
ANXIETY
 0       
 3 ( 3.1)
 0       
  3 ( 1.2)
DELUSION
 1 ( 1.2)
 0       
 1 ( 1.4)
  2 ( 0.8)
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS
 3 ( 3.5)
 6 ( 6.2)
 5 ( 6.9)
 14 ( 5.5)
BACK PAIN
 1 ( 1.2)
 1 ( 1.0)
 3 ( 4.2)
  5 ( 2.0)
ARTHRALGIA
 1 ( 1.2)
 2 ( 2.1)
 1 ( 1.4)
  4 ( 1.6)
SHOULDER PAIN
 1 ( 1.2)
 2 ( 2.1)
 0       
  3 ( 1.2)
MUSCLE SPASMS
 0       
 1 ( 1.0)
 1 ( 1.4)
  2 ( 0.8)
ARTHRITIS
 0       
 0       
 1 ( 1.4)
  1 ( 0.4)
INVESTIGATIONS
 5 ( 5.8)
 4 ( 4.2)
 3 ( 4.2)
 12 ( 4.7)
ELECTROCARDIOGRAM ST SEGMENT DEPRESSION
 4 ( 4.7)
 1 ( 1.0)
 0       
  5 ( 2.0)
ELECTROCARDIOGRAM T WAVE INVERSION
 2 ( 2.3)
 1 ( 1.0)
 1 ( 1.4)
  4 ( 1.6)
BLOOD GLUCOSE INCREASED
 0       
 1 ( 1.0)
 1 ( 1.4)
  2 ( 0.8)
ELECTROCARDIOGRAM T WAVE AMPLITUDE DECREASED
 1 ( 1.2)
 1 ( 1.0)
 0       
  2 ( 0.8)
BIOPSY
 0       
 0       
 1 ( 1.4)
  1 ( 0.4)