vagishhemmige/r-analysis-workflow
Set up, document, report and review R biomedical analysis projects: analysis plans, AGENTS.md, Quarto explainer sites, GitHub workflow, and blind clinical, statistical, coding and librarian reviews.
Write or update the explanatory Quarto website and ARCHITECTURE.md for an R analysis project. Use when a script joins the definitive workflow and needs its page, when code changes and its page or architecture must follow, when pasted code on a page should become imports from the actual script, or when the site, README or architecture needs repair, or when the analysis plan needs updating after a decision, locking, or a new data source.
Initialize or organize a new or existing R statistical or epidemiologic analysis project, including a latest RMD, partial scripts, project instructions, AGENTS.md, Quarto setup, references and gitignore. Use for resuming unfinished initialization too.
Help someone join an R analysis project, or leave one, at the level of help they choose. Use for anyone joining (including people new to R, Quarto or GitHub) and for anyone leaving or handing over work.
Build and check the reporting of an R biomedical analysis with flowchart, gtsummary, ggplot2 and ggsurvfit - the participant flow diagram, figures and survival curves with risk tables, descriptions and missingness, Table 1, two-variable, longitudinal and time-to-event summaries, fitted-model tables, and numbers quoted in prose. Does not choose models, covariates or estimands. For an independent check, use the Reporting review in the review skill.
Review an R analysis project, or a change to one, against its analysis plan, website, architecture and repository rules, using blind clinical, statistical, coding and librarian reviewers and the relevant Posit review skills. Use for code or pull-request review, plan review, citation and literature checks, site and code sync, architecture currency, repository conformance, reporting review and pre-release checks.