diff --git a/README.Rmd b/README.Rmd index cb77f76..74dfbc3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,19 +16,15 @@ knitr::opts_chunk$set( ) ``` -# appendMCP +# appendMCP - [![R-CMD-check](https://github.com/johnsonandjohnson/appendMCP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/johnsonandjohnson/appendMCP/actions/workflows/R-CMD-check.yaml) [![License: GPL (≥ 3)](https://img.shields.io/badge/License-GPL%20(%3E%3D%203)-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) -**appendMCP** generates analysis documentation for graphical multiple -comparison procedures (MCPs) in clinical -trials with group sequential designs (GSDs). 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). +**appendMCP** generates analysis documentation for clinical trials conducted using graphical multiple comparison procedures (MCPs) within a group sequential design (GSD) setting. +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). ## Installation @@ -39,8 +35,7 @@ remotes::install_github("johnsonandjohnson/appendMCP") ## Quick Start -The core workflow is three steps: load a configuration, process it, and -generate a report. +The core workflow is three steps: load a configuration, process it, and generate a report. ```{r eval=FALSE} library(appendMCP) @@ -50,21 +45,17 @@ results <- process_config(config) generate_report(results) ``` -This produces an HTML report in your working directory containing -summary tables, the graphical testing procedure diagram, information -fraction plots, alpha spending visualizations, and operating -characteristics. +This produces an HTML report in your working directory containing summary tables, the graphical testing procedure diagram, information fraction plots, alpha spending visualizations, and operating characteristics. ## 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 +- **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. @@ -86,8 +77,7 @@ results$er_figure # Enrollment rate ## Scaffolding a New Study -`create_study()` copies a configuration and report template into a -project folder and generates a ready-to-run analysis script: +`create_study()` copies a configuration and report template into a project folder and generates a ready-to-run analysis script: ```{r eval=FALSE} create_study( @@ -110,8 +100,7 @@ list_rmd_template_repository() # built-in report templates ## Using a Custom Configuration -A configuration is an R list assigned to a single variable in a `.R` -file. The required fields are: +A configuration is an R list assigned to a single variable in a `.R` file. The required fields are: | Field | Description | |---|---| diff --git a/README.md b/README.md index f9dd265..58317b9 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,21 @@ -# appendMCP +# appendMCP - [![R-CMD-check](https://github.com/johnsonandjohnson/appendMCP/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/johnsonandjohnson/appendMCP/actions/workflows/R-CMD-check.yaml) [![License: GPL (≥ 3)](https://img.shields.io/badge/License-GPL%20(%3E%3D%203)-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) -**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). +**appendMCP** generates analysis documentation for clinical trials +conducted using graphical multiple comparison procedures (MCPs) within a +group sequential design (GSD) setting. 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). ## Installation @@ -44,17 +44,17 @@ characteristics. ## What the Package Produces -- **Table 1** — Hypothesis summary (endpoint, type, spending function) -- **Table 2** — Analysis schedule by hypothesis (timing, information +- **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 +- **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 +- **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 +- **Table 6a / 6b:** Simulation-based operating characteristics by analysis and overall -- **Plots** — Graph diagram, information fractions, alpha spending, +- **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. @@ -136,4 +136,3 @@ vignette("configuration-guide", package = "appendMCP") - Full documentation site: - Report a bug: -