AE summary table — gt_ae_summary • metalite.ae

AE summary table

Usage

gt_ae_summary(
  outdata,
  source,
  analysis,
  title = c("analysis", "observation", "population"),
  footnotes = NULL
)

Arguments

outdata: An outdata object created by prepare_ae_specific().
source: A character value of the data source.
analysis: One of analysis name existing at outdata$meta$analysis
title: Term "analysis", "observation"and "population") for collecting title from metadata or a character vector of table titles.
footnotes: A character vector of table footnotes.

Value

RTF file and the source dataset for AE summary table.

Examples

library(gt)
#' # Define metadata
adsl <- forestly::forestly_adsl
adae <- forestly::forestly_adae

adsl$TRT01A <- factor(
  adsl$TRT01A,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)
adae$TRTA <- factor(
  adae$TRTA,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)

analysis_plan <- metalite::plan(
  analysis = "ae_summary",
  population = "apat",
  observation = "wk12",
  parameter = "any;rel;ser"
)

meta <- metalite::meta_adam(observation = adae, population = adsl) |>
  metalite::define_plan(analysis_plan) |>
  metalite::define_population(
    name = "apat",
    var = c(
      "USUBJID", "SAFFL", "TRT01A", "TRTDUR",
      "SITEID", "SEX", "RACE", "AGE"
    ),
    group = "TRT01A",
    subset = SAFFL == "Y",
    label = "All Participants as Treated"
  ) |>
  metalite::define_observation(
    name = "wk12",
    var = c(
      "USUBJID", "SAFFL", "TRTA", "AEDECOD", "AEBODSYS", "AEREL",
      "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT"
    ),
    group = "TRTA",
    subset = SAFFL == "Y",
    label = "Weeks 0 to 12"
  ) |>
  metalite::define_parameter(
    name = "any",
    term1 = "",
    term2 = "",
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "All AEs"
  ) |>
  metalite::define_parameter(
    name = "rel",
    term1 = "Drug-Related",
    term2 = "",
    subset = AEREL %in% c("POSSIBLE", "PROBABLE"),
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "Drug-related AEs"
  ) |>
  metalite::define_parameter(
    name = "ser",
    term1 = "Serious",
    term2 = "",
    subset = AESER == "Y",
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "Serious AEs"
  ) |>
  metalite::define_analysis(
    name = "ae_summary",
    title = "Adverse Event Summary"
  ) |>
  metalite::meta_build()

outdata <- prepare_ae_summary(meta,
  population = "apat",
  observation = "wk12",
  parameter = "any;rel;ser"
)
#> any
#> rel
#> ser
outdata |>
  format_ae_summary() |>
  gt_ae_summary(
    analysis = "ae_summary",
    source = "Source:  [CDISCpilot: adam-adsl; adae]"
  )
#> [1] "Adverse Event Summary"       "Weeks 0 to 12"              
#> [3] "All Participants as Treated"


  Adverse Event Summary

Weeks 0 to 12

All Participants as Treated
    

      
        Low Dose
      
      
        Placebo
      
      
        Total
      
    
n
      (%)
      n
      (%)
      n
      (%)
    
Participants in population
84


86


170

with one or more adverse events
77
(91.7)
69
(80.2)
146
(85.9)
with no adverse events
7
 (8.3)
17
(19.8)
24
(14.1)
with drug-related^a adverse events
73
(86.9)
44
(51.2)
117
(68.8)
with serious adverse events
1
 (1.2)
0
 (0.0)
1
 (0.6)
^aDetermined by the investigator to be related to the drug.
    
Source:  [CDISCpilot: adam-adsl; adae]

	Low Dose		Placebo		Total
Adverse Event Summary Weeks 0 to 12 All Participants as Treated
	n	(%)	n	(%)	n	(%)
Participants in population	84		86		170
with one or more adverse events	77	(91.7)	69	(80.2)	146	(85.9)
with no adverse events	7	(8.3)	17	(19.8)	24	(14.1)
with drug-related^a adverse events	73	(86.9)	44	(51.2)	117	(68.8)
with serious adverse events	1	(1.2)	0	(0.0)	1	(0.6)
^aDetermined by the investigator to be related to the drug.
Source: [CDISCpilot: adam-adsl; adae]