Skip to contents

Create Adverse Event Summary Table

Source: R/safety_summary.R
create_ae_summary_table.Rd

Generate AE summary tables for clinical study reports.

Usage

create_ae_summary_table(
  data,
  adsl = NULL,
  type = c("overview", "soc", "soc_pt", "pt", "common", "severity", "relationship",
    "sae", "discontinuation", "deaths", "comparison"),
  trt_var = ph_default("trt_var"),
  n_top = ph_default("n_top"),
  soc = NULL,
  title = NULL,
  footnotes = character(),
  theme = "hta",
  ref_group = NULL,
  by = "pt",
  threshold = 0,
  sort_by = "incidence",
  conf_level = ph_default("conf_level"),
  include_nnh = TRUE,
  soc_order = NULL,
  severity_levels = c("MILD", "MODERATE", "SEVERE"),
  ...
)

Arguments

data

ADAE data frame or ADaMData object containing ADaM Adverse Events dataset

adsl

ADSL data frame or ADaMData object (optional, required for some table types like "deaths", "comparison", or for denominator calculation)

type

Character string specifying table type:

  • "overview" - Summary of TEAEs, related AEs, SAEs, discontinuations

  • "soc" - AEs by System Organ Class

  • "soc_pt" - AEs by SOC and Preferred Term (hierarchical)

  • "pt" - AEs by Preferred Term only

  • "common" - Most frequently reported AEs

  • "severity" - AEs by maximum severity

  • "relationship" - AEs by relationship to study drug

  • "sae" - Serious Adverse Events

  • "discontinuation" - AEs leading to discontinuation

  • "deaths" - Deaths summary (requires adsl)

  • "comparison" - AE comparison with RD/RR (requires adsl)

trt_var

Treatment variable name (default: "TRT01P")

n_top

For type="common", number of top PTs to show (default: 15)

soc

For type="pt", filter to specific SOC (optional)

title

Table title (auto-generated if NULL)

footnotes

Character vector of footnotes (optional)

theme

Theme for table styling (default: "hta")

ref_group

For type="comparison", reference group for comparisons

by

For type="comparison", grouping level: "soc", "pt", or "overall"

threshold

For type="comparison", minimum incidence pct (default: 0)

sort_by

For type="comparison", sort by "rd", "rr", or "incidence"

conf_level

For type="comparison", confidence level (default: 0.95)

include_nnh

For type="comparison", include NNH column (default: TRUE)

soc_order

For type="soc" or type="soc_pt", custom ordering of SOCs (character vector). If NULL, SOCs are sorted alphabetically (default: NULL)

severity_levels

For type="severity", severity levels ordering (character vector). Default: c("MILD", "MODERATE", "SEVERE")

...

Additional arguments passed to create_clinical_table()

Value

A ClinicalTable object

Examples

if (FALSE) { # \dontrun{
# AE Overview
overview <- create_ae_summary_table(data, adsl, type = "overview")

# SOC table
soc_table <- create_ae_summary_table(data, adsl, type = "soc")

# SOC/PT hierarchical table
soc_pt <- create_ae_summary_table(data, adsl, type = "soc_pt")

# Most common AEs (top 20)
common <- create_ae_summary_table(data, adsl, type = "common", n_top = 20)

# SAE table
sae <- create_ae_summary_table(data, adsl, type = "sae")

# AE comparison with risk differences
comparison <- create_ae_summary_table(
  data, adsl,
  type = "comparison",
  ref_group = "Placebo",
  by = "pt",
  threshold = 5
)

# SOC table with custom ordering
soc_ordered <- create_ae_summary_table(
  data, adsl,
  type = "soc",
  soc_order = c(
    "Infections",
    "Nervous system disorders",
    "Gastrointestinal disorders"
  )
)
} # }