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Introduction to metalite.sl

metalite.sl.Rmd
library(metalite)
library(metalite.sl)
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
#>   object 'type_sum.accel' not found

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")
  )

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().