# Generate a Static AE-Specific Table in RTF format

    library(metalite.ae)

## Overview

This vignette demonstrates how to generate a static AE-specific table reporting patients with drug-related adverse events by treatment group.

The workflow uses three functions from metalite.ae:

- `prepare_ae_specific()` prepares the analysis datasets.
- `format_ae_specific()` formats the results for reporting.
- `tlf_ae_specific()` creates the RTF table.

Related vignettes explain how to customize displayed columns and filter or sort rows. This guide also covers basic RTF customization and mock output.

## Generate an AE-specific table

The example uses ADSL and ADAE data from the forestly package.

### Step 1: Define metadata

    # 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_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", "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 = "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()

Click to show the output

    meta
    #> ADaM metadata:
    #>    .$data_population     Population data with 170 subjects
    #>    .$data_observation    Observation data with 736 records
    #>    .$plan    Analysis plan with 1 plans
    #>
    #>
    #>   Analysis population type:
    #>     name        id    group
    #> 1 'apat' 'USUBJID' 'TRT01A'
    #>                                                      var       subset
    #> 1 USUBJID, SAFFL, TRT01A, TRTDUR, SITEID, SEX, RACE, AGE SAFFL == 'Y'
    #>                           label
    #> 1 'All Participants as Treated'
    #>
    #>
    #>   Analysis observation type:
    #>     name        id  group
    #> 1 'wk12' 'USUBJID' 'TRTA'
    #>                                                                                         var
    #> 1 USUBJID, SAFFL, TRTA, AEDECOD, AEBODSYS, AEREL, AESER, AEOUT, AEACN, AESDTH, ASTDT, AENDT
    #>         subset           label
    #> 1 SAFFL == 'Y' 'Weeks 0 to 12'
    #>
    #>
    #>   Analysis parameter type:
    #>    name              label                               subset
    #> 1 'rel' 'Drug-related AEs' AEREL %in% c('POSSIBLE', 'PROBABLE')
    #>
    #>
    #>   Analysis function:
    #>            name                           label
    #> 1 'ae_specific' 'Table: specific adverse event'

### Step 2: Generate the static AE specific table

`prepare_ae_specific()` uses the population, observation, and parameter definitions in `meta` to calculate the AE-specific analysis results. It returns an `outdata` object for formatting and reporting.

`format_ae_specific()` converts the analysis results into a production-ready table dataset.

Pass the formatted output to `tlf_ae_specific()` to create the RTF table.

    rtf_dir <- if (dir.exists("vignettes/rtf")) "vignettes/rtf" else "rtf"
    rtf_file <- file.path(rtf_dir, "ae0specific1.rtf")

    outdata <- prepare_ae_specific(
      meta,
      population = "apat",
      observation = "wk12",
      parameter = "rel"
    ) |>
      format_ae_specific() |>
      tlf_ae_specific(
        meddra_version = "24.0",
        source = "Source:  [CDISCpilot: adam-adsl; adae]",
        analysis = "ae_specific", # Provide analysis type defined in meta$analysis
        path_outtable = rtf_file
      )

Generated RTF file: ae0specific1.rtf