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Introduction to metalite.ae

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

Overview

metalite.ae is an R package to analyze adverse events (AE) in clinical trials, including:

AE summary.
Specific AE analysis.
AE listing.

The R package simplifies the workflow to create production-ready tables, listings, and figures discussed in the AE summary chapter and the specific AE chapter of the R for Clinical Study Reports and Submission book with full traceability.

The R package is created using the metalite data structure that provides an end-to-end software development lifecycle (SDLC) solution including defining, developing, validating, and finalizing the analysis.

Workflow

The general workflow covers:

  1. Define metadata information using metalite.
  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 example, we can create a simple AE summary table as 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
  )

Tutorials with additional examples are listed on the package website.

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.