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Introduction to metalite.ae

Source: vignettes/metalite-ae.Rmd
metalite-ae.Rmd

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
    analysis = "ae_specific", # Provide analysis type defined in meta$analysis
    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().