# Introduction to metalite.ae

## Overview

metalite.ae is an R package designed for the analysis of adverse events (AE) in clinical trials. It operates on ADaM datasets and adheres to the metalite structure. The package encompasses the following components:

AE summary.
Specific AE analysis.
AE listing.

The R package streamlines the process of generating production-ready tables, listings, and figures as outlined in the AE summary chapter and the specific AE chapter of the R for Clinical Study Reports and Submission book. It ensures complete traceability throughout the development lifecycle, leveraging the metalite data structure.

This R package offers a comprehensive software development lifecycle (SDLC) solution, encompassing activities such as definition, development, validation, and finalization of the analysis.

## Highlighted features

- Avoid duplicated input by using metadata structure.
  - For example, define analysis population once to use in all adverse events analysis.
- Consistent input and output in standard functions.
- Streamlines mock table generation.

## Workflow

The overall workflow includes the following steps:

1. Define metadata information using metalite R package.
2. Prepare outdata using `prepare_*()` functions.
3. Extend outdata using `extend_*()` functions (optional).
4. Format outdata using `format_*()` functions.
5. Create TLFs using `tlf_*()` functions.

For instance, we can illustrate the creation of a straightforward AE summary table as shown below.

    meta_ae_example() |> # Example AE data created using metalite
      prepare_ae_summary(
        population = "apat", # Select population by keywords
        observation = "wk12", # Select observation by keywords
        parameter = "any;rel;ser" # Select AE terms by keywords
      ) |>
      format_ae_summary() |>
      tlf_ae_summary(
        source = "Source:  [CDISCpilot: adam-adsl; adae]", # Define data source
        path_outtable = "ae0summary.rtf" # Define output
      )

Additional examples and tutorials can be found on the package website, offering further guidance and illustrations.

## Input

To implement the workflow in metalite.ae, it is necessary to establish a metadata structure using the metalite R package. For detailed instructions, please consult the metalite tutorial and refer to the source code of the function `meta_ae_example()`.