Introduction to metalite.sl

In metalite.sl: Subject-Level Analysis Using 'metalite'

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  out.width = "100%",
  dpi = 150,
  eval = TRUE
)

library(metalite)
library(metalite.sl)

Overview

metalite.sl R package designed for the analysis & reporting of subject-level analysis in clinical trials. It operates on ADaM datasets and adheres to the metalite structure. The package encompasses the following components:

Baseline Characteristics.

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 subject level analysis.
• Consistent input and output in standard functions.
• Provide workflow to add interactive features to subject-level analysis table.

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 Baseline characteristic table as shown below.

meta_sl_example() |>
  prepare_base_char(
    population = "apat",
    analysis = "base_char",
    parameter = "age;gender"
  ) |>
  format_base_char() |>
  rtf_base_char(
    source = "Source: [CDISCpilot: adam-adsl]",
    path_outdata = tempfile(fileext = ".Rdata"),
    path_outtable = tempfile(fileext = ".rtf")
  )

knitr::include_graphics("pdf/base0char.pdf")

An example for interactive baseline characteristic table:

react_base_char(
  metadata_sl = meta_sl_example(),
  metadata_ae = metalite.ae::meta_ae_example(),
  population = "apat",
  observation = "wk12",
  display_total = TRUE,
  sl_parameter = "age;race",
  ae_subgroup = c("age", "race"),
  ae_specific = "rel",
  width = 1200
)

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

Input

To implement the workflow in metalite.sl, 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_sl_example().

metalite.sl documentation built on April 3, 2025, 8:52 p.m.