Sepages pipeline methodological guide

Overview

This vignette briefly introduces the preprocessing methodology developed for the SEPAGES study.

For full details, including theoretical background, code examples, and recommendations, please refer to the complete documentation available online:

👉 SEPAGES pipeline documentation (bookdown)

Structure of the book

The online documentation includes the following chapters:

• Example data structure
• Handling values below LOD
• Standardising on protocol variables
• Recommended variable names
• References

The book is updated regularly and contains reproducible code, figures, and links to relevant references.

Citation

If you wish to cite the preprocessing methodology, please cite:

Rolland M., SEPAGES preprocessing pipeline, 2025. Available at:
https://bookdown.org/mj_rolland/sepages_pipeline_doc/