r-workflow-plugins

r-workflow-plugins is a monorepo of portable plugins for AI agents working on R-centered analytical and research workflows. Its broader scope covers programming, applied analysis, psychometrics, simulation, package development, and reproducible publishing.

The repository is plugin-oriented, not a package of R functions or an agent framework. A plugin is the independently distributed and versioned unit; a skill is a focused, reusable unit of agent instruction. Shared skills and references should stay portable across agent runtimes where practical, with thin runtime-specific distribution metadata.

Plugin Map

The public marketplaces distribute quarto-publishing v0.2.3, r-analytic-core v0.1.1 and quarto-bento v0.2.0, each pinned to its own plugin release tag. Four research-methods plugins now have independent v0.1.0 releases and tag-pinned catalog entries, with Codex, Claude Code and Antigravity CLI adapters. Other names remain proposals, not promised releases.

Plugin	Responsibility	Status
quarto-publishing	Quarto documents, reports, presentations, configuration, computation strategy, and render verification. Engine-aware across R/knitr, Python/Jupyter, Julia, and prose-only documents.	Published: v0.2.3
r-analytic-core	Research-first R coding: model-by-model editability, intentional repetition, proportional live verification.	Published: v0.1.1
quarto-bento	Quarto-Bento CLI/Studio, retained design, reviewed source synchronization and recovery; optional Quarto/R companions.	Published: v0.2.0
r-data-wrangling	Research data import, identifiers, labels and missing values; transformations, joins and longitudinal reshaping.	Published: v0.1.0 (2 skills)
r-applied-analysis	Descriptive/comparative analysis, ordinary regression and complex-survey inference; missing-data and mixed-model skills deferred.	Published: v0.1.0 (3 skills)
r-psychometrics	Item/reliability analysis, EFA including ordinal WLSMV, and conventional CFA/basic SEM; invariance/IRT deferred.	Published: v0.1.0 (3 skills)
r-simulation-methods	ADEMP design and failure-aware SimDesign execution and Monte Carlo evaluation.	Published: v0.1.0 (2 skills)
r-package-development	R package architecture, APIs, documentation, testing, and release-related practices.	Planned
rmarkdown-workflows	Classic R Markdown maintenance and workflows; full migration into Quarto belongs primarily to the Quarto plugin.	Planned

See the global roadmap for staged scopes, the architecture for boundaries, and the Research Methods EPIC integration evidence for the historical candidate review. The release evidence records native-host findings, corrections and the bounded support of the first releases.

Installation

Codex

Register the public marketplace:

codex plugin marketplace add brianmsm/r-workflow-plugins

The seven tagged plugins in the map are available from the catalog. Install the R coding plugin with codex plugin add r-analytic-core@r-workflow-plugins (after registering the marketplace), or use the plugin directory. Its skill can be invoked as $r-analytic-coding-principles; a natural-language alternative is “Use the research-first R coding style” followed by the task. Natural-language activation is not guaranteed.

Claude Code

claude plugin marketplace add brianmsm/r-workflow-plugins
claude plugin install quarto-publishing@r-workflow-plugins
claude plugin install r-analytic-core@r-workflow-plugins

Plugin skills are namespaced, e.g. /quarto-publishing:quarto-render-troubleshooting or /r-analytic-core:r-analytic-coding-principles.

Antigravity CLI

The four research-methods plugins include native Antigravity manifests. Install a local plugin directory extracted from its release tag with agy plugin install <directory>; see the agent setup guide. Shared skill instructions are not duplicated per host.

Gemini CLI

The plugin is not yet packaged as a native Gemini extension. Gemini CLI can use individual skills through its skill installation or linking workflow; see the agent setup guide for the distinction and example commands.

Repository Layout

• plugins/<plugin-name>/: self-contained, independently versioned plugins.
• plugins/<plugin-name>/skills/<skill-name>/SKILL.md: focused agent instructions, with optional references/, scripts/, assets/, and agent metadata.
• .agents/plugins/marketplace.json: Codex public catalog.
• .claude-plugin/marketplace.json: Claude Code public catalog.
• docs/: repository-wide architecture, roadmap, naming conventions, release policy, and agent setup.
• AGENTS.md: instructions for agents contributing to this repository.

The published marketplace entries point to plugin-specific Git release tags, not to in-progress changes on main. Work-in-progress changes belong in the relevant plugin's CHANGELOG.md under Unreleased until a new release is ready. See release process.

For quarto-publishing specifically, its own architecture describes the mature target and its roadmap describes incremental delivery. The global roadmap is not a substitute for either.