# Generate a Static AE Summary Table in GT format

    library(metalite.ae)

## Overview

This vignette demonstrates how to generate a static AE summary table in gt format reporting - The number and percentage of participants with any AEs by treatment group; - The number and percentage of participants with drug-related AEs by treatment group; - The number and percentage of participants with serious AEs by treatment group.

The workflow uses three functions from metalite.ae:

- `prepare_ae_summary()` prepares the analysis datasets.
- `format_ae_summary()` formats the results or creates mock output.
- `gt_ae_summary()` creates the GT table.

An optional extension adds risk-difference inference:

- `extend_ae_specific_inference()` adds confidence intervals and p-values based on the Miettinen and Nurminen method.

## Generate an AE summary 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_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()

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 'any'          'All AEs'
    #> 2 'rel' 'Drug-related AEs' AEREL %in% c('POSSIBLE', 'PROBABLE')
    #> 3 'ser'      'Serious AEs'                         AESER == 'Y'
    #>
    #>
    #>   Analysis function:
    #>           name                          label
    #> 1 'ae_summary' 'Table: adverse event summary'

### Step 2: Generate the GT table

`prepare_ae_summary()` uses the definitions in `meta` to calculate the summary results. `format_ae_summary()` formats those results, and `gt_ae_summary()` creates the GT table.

    prepare_ae_summary(
      meta,
      population = "apat",
      observation = "wk12",
      parameter = "any;rel;ser"
    ) |>
      format_ae_summary() |>
      gt_ae_summary(
        source = "Source:  [CDISCpilot: adam-adsl; adae]",
        analysis = "ae_summary"
      )
    #> [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-relateda 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]