R/meta_example.R

In metalite: ADaM Metadata Structure

# Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
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#
# This file is part of the metalite program.
#
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#' Create an example `meta_adam` object
#'
#' This function is only for illustration purposes.
#' The r2rtf package is required.
#'
#' @return A metadata object.
#'
#' @export
#'
#' @examples
#' meta_example()
meta_example <- function() {
  adsl <- r2rtf::r2rtf_adsl
  adsl$TRTA <- adsl$TRT01A
  adsl$TRTA <- factor(adsl$TRTA,
    levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")
  )

  adae <- r2rtf::r2rtf_adae
  adae$TRTA <- factor(adae$TRTA,
    levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")
  )

  plan <- plan(
    analysis = "ae_summary", population = "apat",
    observation = c("wk12", "wk24"), parameter = "any;rel;ser"
  ) |>
    add_plan(
      analysis = "ae_specific", population = "apat",
      observation = c("wk12", "wk24"),
      parameter = c("any", "aeosi", "rel", "ser")
    )

  meta_adam(
    population = adsl,
    observation = adae
  ) |>
    define_plan(plan = plan) |>
    define_population(
      name = "apat",
      group = "TRTA",
      subset = quote(SAFFL == "Y")
    ) |>
    define_observation(
      name = "wk12",
      group = "TRTA",
      subset = quote(SAFFL == "Y"),
      label = "Weeks 0 to 12"
    ) |>
    define_observation(
      name = "wk24",
      group = "TRTA",
      subset = quote(AOCC01FL == "Y"), # just for demo, another flag shall be used.
      label = "Weeks 0 to 24"
    ) |>
    define_parameter(
      name = "rel",
      subset = quote(AEREL %in% c("POSSIBLE", "PROBABLE"))
    ) |>
    define_parameter(
      name = "aeosi",
      subset = quote(AEOSI == "Y"),
      var = "AEDECOD",
      soc = "AEBODSYS",
      term1 = "",
      term2 = "of special interest",
      label = "adverse events of special interest"
    ) |>
    define_analysis(
      name = "ae_summary",
      title = "Summary of Adverse Events"
    ) |>
    meta_build()
}