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Generate analysis documentation for graphical MCPs in group sequential trials

appendMCP.Rd

appendMCP generates analysis documentation for graphical multiple comparison procedures (MCPs) in group sequential design (GSD) clinical trials. Given a study configuration, it produces summary tables, diagnostic plots, and a fully formatted R Markdown report suitable for appending to a statistical analysis plan (SAP).

Main Functions

load_config_from_repository

Load built-in configurations

process_config

Process design configurations and calculate operating characteristics

generate_report

Generate comprehensive HTML or Word reports

create_study

Scaffold a new study from built-in templates

Quick Start


library(appendMCP)

config  <- load_config_from_repository("example_study")
results <- process_config(config)
generate_report(results)

What the Package Produces

Table 1

Hypothesis summary (endpoint, type, spending function)

Table 2

Analysis schedule by hypothesis (timing, information fractions)

Table 3

Analysis schedule by analysis (all hypotheses at each look)

Table 4

Weight scenarios under the graphical MCP

Table 5

Boundary specifications (nominal p-values, information fractions, local power)

Table 6a / 6b

Simulation-based operating characteristics by analysis and overall

Plots

Graph diagram, information fractions, alpha spending, enrollment, time-to-event and binary endpoint distributions

Tables are returned as huxtable objects ready for Word or HTML output.

Configuration Structure

A valid configuration must include:

  • analyses: Analysis specifications (data frame)

  • hypotheses: Hypothesis definitions (data frame)

  • enroll_rate: Enrollment rates by strata (data frame)

  • graph: Graphical testing procedure (list with g matrix and w weights)

  • distribution_tte and/or distribution_bin: Distribution parameters (data frame)

Author

Maintainer: Yevgen Tymofyeyev ytymofye@its.jnj.com

Authors:

Examples

if (FALSE) { # \dontrun{
# List available templates
list_config_repository()
list_rmd_template_repository()

# Load and process a study
config  <- load_config_from_repository("example_study")
results <- process_config(config)

# Explore results
results$tables$table1        # Hypothesis summary
results$tables$table5        # Boundary specifications
results$graph_figure         # Graphical MCP diagram
results$alpha_spend_figure   # Alpha spending functions

# Generate report
generate_report(results)

# Scaffold a new study
create_study(
  config       = "example_study",
  rmd_template = "gsd_detailed",
  output_dir   = "my_study"
)
} # }