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mjg211 merged 1 commit into from
Aug 14, 2026
Merged

Fixed badges in README and formatted other text. #7

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39 changes: 14 additions & 25 deletions README.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,19 +16,15 @@ knitr::opts_chunk$set(
)
```

# appendMCP
# appendMCP <img src="man/figures/logo.png" align="right" height="150"/>

<!-- badges: start -->
<img src="man/figures/logo.png" align="right" height="150" />
[![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 (&ge; 3)](https://img.shields.io/badge/License-GPL%20(%3E%3D%203)-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
<!-- badges: end -->

**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

Expand All @@ -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)
Expand All @@ -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.

Expand All @@ -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(
Expand All @@ -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 |
|---|---|
Expand Down
29 changes: 14 additions & 15 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@

<!-- README.md is generated from README.Rmd. Please edit that file -->

# appendMCP
# appendMCP <img src="man/figures/logo.png" align="right" height="150"/>

<!-- badges: start -->

<img src="man/figures/logo.png" align="right" height="150" />
[![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)
<!-- badges: end -->

**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

Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -136,4 +136,3 @@ vignette("configuration-guide", package = "appendMCP")
- Full documentation site:
<https://johnsonandjohnson.github.io/appendMCP>
- Report a bug: <https://github.com/johnsonandjohnson/appendMCP/issues>

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