{"id":51169243,"url":"https://github.com/johnsonandjohnson/appendmcp","last_synced_at":"2026-06-26T23:01:45.718Z","repository":{"id":361220007,"uuid":"1243626935","full_name":"johnsonandjohnson/appendMCP","owner":"johnsonandjohnson","description":"Graphical multiple comparison procedures for group sequential design clinical trials","archived":false,"fork":false,"pushed_at":"2026-05-29T17:44:39.000Z","size":1967,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-29T18:12:54.195Z","etag":null,"topics":["group-sequential-designs","multiple-testing","report-generation-by-template"],"latest_commit_sha":null,"homepage":"https://johnsonandjohnson.github.io/appendMCP/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/johnsonandjohnson.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-05-19T14:10:32.000Z","updated_at":"2026-05-29T17:40:33.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/johnsonandjohnson/appendMCP","commit_stats":null,"previous_names":["johnsonandjohnson/appendmcp"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/johnsonandjohnson/appendMCP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnsonandjohnson%2FappendMCP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnsonandjohnson%2FappendMCP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnsonandjohnson%2FappendMCP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnsonandjohnson%2FappendMCP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/johnsonandjohnson","download_url":"https://codeload.github.com/johnsonandjohnson/appendMCP/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnsonandjohnson%2FappendMCP/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34835779,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-26T02:00:06.560Z","response_time":106,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["group-sequential-designs","multiple-testing","report-generation-by-template"],"created_at":"2026-06-26T23:01:43.968Z","updated_at":"2026-06-26T23:01:45.712Z","avatar_url":"https://github.com/johnsonandjohnson.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\neditor_options: \n  markdown: \n    wrap: 72\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# appendMCP\n\n\u003c!-- badges: start --\u003e\n\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"150\" /\u003e\n[![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)\n[![License: GPL (\u0026ge; 3)](https://img.shields.io/badge/License-GPL%20(%3E%3D%203)-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\u003c!-- badges: end --\u003e\n\n**appendMCP** generates analysis documentation for graphical multiple\ncomparison procedures (MCPs) in group sequential design (GSD) clinical\ntrials. Given a study configuration, it produces summary tables,\ndiagnostic plots, and a fully formatted R Markdown report suitable for\nappending to a statistical analysis plan (SAP).\n\n## Installation\n\n```{r eval=FALSE}\n# install.packages(\"remotes\")\nremotes::install_github(\"johnsonandjohnson/appendMCP\")\n```\n\n## Quick Start\n\nThe core workflow is three steps: load a configuration, process it, and\ngenerate a report.\n\n```{r eval=FALSE}\nlibrary(appendMCP)\n\nconfig  \u003c- load_config_from_repository(\"example_study\")\nresults \u003c- process_config(config)\ngenerate_report(results)\n```\n\nThis produces an HTML report in your working directory containing\nsummary tables, the graphical testing procedure diagram, information\nfraction plots, alpha spending visualizations, and operating\ncharacteristics.\n\n## What the Package Produces\n\n- **Table 1** — Hypothesis summary (endpoint, type, spending function)\n- **Table 2** — Analysis schedule by hypothesis (timing, information fractions)\n- **Table 3** — Analysis schedule by analysis (all hypotheses at each look)\n- **Table 4** — Weight scenarios under the graphical MCP\n- **Table 5** — Boundary specifications (nominal p-values, information fractions, local power)\n- **Table 6a / 6b** — Simulation-based operating characteristics by analysis and overall\n- **Plots** — Graph diagram, information fractions, alpha spending, enrollment,\n  time-to-event and binary endpoint distributions\n\nTables are returned as `huxtable` objects ready for Word or HTML output.\n\n## Exploring Results\n\n```{r eval=FALSE}\n# Individual tables\nresults$tables$table1   # Hypothesis summary\nresults$tables$table2   # Schedule by hypothesis\nresults$tables$table5   # Boundary specifications (nominal p-values, local power)\n\n# Plots (top-level fields on the results object)\nresults$graph_figure          # Graphical MCP diagram\nresults$information_figure    # Information fraction over time\nresults$alpha_spend_figure    # Alpha spending functions\nresults$tte_figure            # Time-to-event distributions\nresults$er_figure             # Enrollment rate\n```\n\n## Scaffolding a New Study\n\n`create_study()` copies a configuration and report template into a\nproject folder and generates a ready-to-run analysis script:\n\n```{r eval=FALSE}\ncreate_study(\n  config       = \"example_study\",   # built-in config, or path to your own .R file\n  rmd_template = \"gsd_default\",     # built-in template, or path to your own .Rmd\n  output_dir   = \"my_study\"\n)\n# Creates:\n#   my_study/study_config.R    — edit this to define your study\n#   my_study/render_config.R   — run this to execute the analysis\n#   my_study/report.Rmd        — the report template\n```\n\n## Available Built-in Configurations and Templates\n\n```{r eval=FALSE}\nlist_config_repository()        # built-in study configurations\nlist_rmd_template_repository()  # built-in report templates\n```\n\n## Using a Custom Configuration\n\nA configuration is an R list assigned to a single variable in a `.R`\nfile. The required fields are:\n\n| Field | Description |\n|---|---|\n| `study_name` | Study identifier string |\n| `alpha` | One-sided significance level (e.g. `0.025`) |\n| `analyses` | Data frame of analysis specifications |\n| `hypotheses` | Data frame of hypothesis definitions |\n| `enroll_rate` | Data frame of enrollment rates by stratum |\n| `graph` | List with `g` (transition matrix) and `w` (initial weights) |\n| `distribution_tte` | Time-to-event distributions (required if any TTE endpoint) |\n| `distribution_bin` | Binary endpoint distributions (required if any binary endpoint) |\n\nSee the built-in example for a complete, annotated configuration:\n\n```{r eval=FALSE}\nconfig \u003c- load_config_from_repository(\"example_study\")\nstr(config, max.level = 1)\n```\n\nOr read the configuration guide vignette:\n\n```{r eval=FALSE}\nvignette(\"configuration-guide\", package = \"appendMCP\")\n```\n\n## Getting Help\n\n- Function reference: `?process_config`, `?create_study`, `?generate_report`\n- Vignettes: `browseVignettes(\"appendMCP\")`\n- Full documentation site: \u003chttps://johnsonandjohnson.github.io/appendMCP\u003e\n- Report a bug: \u003chttps://github.com/johnsonandjohnson/appendMCP/issues\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjohnsonandjohnson%2Fappendmcp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjohnsonandjohnson%2Fappendmcp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjohnsonandjohnson%2Fappendmcp/lists"}