The Metacheck Manual

Automated Checks of Research Outputs for Best Practices

A guide to Metacheck, a module based tool written in R for checking scientific manuscripts and data repositories for best practices using text search, R code, and optional LLM queries.

Welcome

This is the online book for metacheck, an R based tool that offers automated checks of best practices for research outputs such as scientific manuscripts and data repositories.

Metacheck screens scientific manuscripts or data repositories and flags potential issues for improvement. It is intended to assist researchers in in adopting best practices. It is an open source module based tool, which allows anyone to create automated checks. These checks are meant to assist, not replace, human expertise. Metacheck can currently check reporting guidelines (such as statements about COI’s, funding, and ethics approval), statistical reporting (such as p values, power analyses, or effect sizes following t-tests and F-tests), information related to references (such as PubPeer comments, or replications in the FLORA database), but it also examines the structure of repositories, data, code, and codebooks for adherence to FAIR principles. It can even perform computational reproducibility checks.

How this book is organised

• Getting Started — a simple overview of the different ways to get started with Metacheck.
• Modules — a chapter for each built-in module, with worked examples on real papers.
• Using Metacheck Locally — running everything on your own machine without sending data anywhere: checking local files, and running AI models (and RegCheck) locally with Ollama.
• Appendices — reference material: the OSF registration schemas and a function reference for new users.

As developers, we adhere to a set of values that guide the development of Metacheck, as described in the Introduction.

You can contact the Metacheck team at D.Lakens@tue.nl.