# Subgroup Analysis for Specific AE

    library(metalite.ae)

## Overview

This vignette demonstrates how to summarize patients with drug-related AEs by subgroup. The workflow uses three functions:

- `prepare_ae_specific_subgroup()` prepares the subgroup analysis datasets.
- `format_ae_specific_subgroup()` formats the results or creates mock output.
- `tlf_ae_specific_subgroup()` creates the RTF table.

## Build metadata

    # Define metadata
    adsl <- forestly::forestly_adsl
    adae <- forestly::forestly_adae

    adsl$TRTA <- factor(
      adsl$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_specific",
      population = "apat",
      observation = "wk12",
      parameter = "rel"
    )

    meta <- metalite::meta_adam(observation = adae, population = adsl) |>
      metalite::define_plan(analysis_plan) |>
      metalite::define_population(
        name = "apat",
        var = c(
          "USUBJID", "SAFFL", "TRTA", "TRTDUR",
          "SITEID", "SEX", "RACE", "AGE"
        ),
        group = "TRTA",
        subset = SAFFL == "Y",
        label = "All Participants as Treated"
      ) |>
      metalite::define_observation(
        name = "wk12",
        var = c(
          "USUBJID", "SAFFL", "TRTA", "SEX", "AEDECOD", "AEBODSYS", "AEREL",
          "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT"
        ),
        group = "TRTA",
        subset = SAFFL == "Y",
        label = "Weeks 0 to 12"
      ) |>
      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_analysis(
        name = "ae_specific",
        title = "Participants with Drug-Related Adverse Events"
      ) |>
      metalite::meta_build()

## Generate an AE specific subgroup table

`prepare_ae_specific_subgroup()` uses the definitions in `meta` to calculate results for each subgroup. `format_ae_specific_subgroup()` formats those results, and `tlf_ae_specific_subgroup()` creates the RTF table.

    rtf_dir <- if (dir.exists("vignettes/rtf")) "vignettes/rtf" else "rtf"
    rtf_file <- file.path(rtf_dir, "ae0specific0sub0gender1.rtf")

    prepare_ae_specific_subgroup(
      meta,
      population = "apat",
      observation = "wk12",
      parameter = "rel",
      subgroup_var = "SEX",
      subgroup_header = c("TRTA", "SEX"),
      display_subgroup_total = TRUE
    ) |>
      format_ae_specific_subgroup(display = c("n", "prop")) |>
      tlf_ae_specific_subgroup(
        meddra_version = "24.0",
        source = "Source:  [CDISCpilot: adam-adsl; adae]",
        analysis = "ae_specific",
        path_outtable = rtf_file
      )
    #> The output is saved in/private/var/folders/yy/6bb11gtn52z0qwdg1_6kdbg00000gn/T/RtmpBCvLa1/Rbuild12c86435ade20/metalite.ae/vignettes/rtf/ae0specific0sub0gender1.rtf

Generated RTF file: ae0specific0sub0gender1.rtf