PhysioRecipes

A growing, version-controlled database of reproducible analysis case studies built on the PhysioExperiment ecosystem and public data. Each entry is a self-contained scientific unit — a proposition, the question and goal it answers, the challenge and the ecosystem approach that solves it, and the conclusion, figures and tables — backed end-to-end by the reproducibility substrate so that every reported number traces to an artifact and the whole pipeline replays byte-identically.

The collection is published as an x-biosignal resource: a Quarto gallery (one page per case) plus a companion R data package that ships the verified run bundles (so a reader can re-run or audit any case).

Installation

The ecosystem builds on Bioconductor, so its repositories have to be on the list as well -- without them the install stops at SummarizedExperiment.

install.packages("BiocManager", repos = "https://cloud.r-project.org")
install.packages(
  "PhysioRecipes",
  repos = c("https://x-biosignal.r-universe.dev", BiocManager::repositories())
)

From GitHub instead:

install.packages("remotes", repos = "https://cloud.r-project.org")
remotes::install_github("x-biosignal/PhysioRecipes")

Why

1. Track record. Demonstrate, on public gold-standard datasets, that the ecosystem reproduces established analyses — and does so reproducibly.
2. A reusable corpus. Each case is a recipe others can lift and adapt.
3. A research pipeline. Reproduction routinely surfaces important open questions (e.g. metric definitions on which tools legitimately disagree). Cases that raise a significant unresolved question are escalated to a paper, carrying the same substrate-grade rigor (see SCHEMA.md → Escalation).

The unit

Every case follows the same structure — defined in SCHEMA.md and scaffolded by TEMPLATE.qmd:

Section	What it holds
Proposition	the central claim the case establishes
Question & goal	what is asked and why it matters
Challenge & approach	the difficulty, and the ecosystem op-DAG that resolves it
Data	the public dataset + citation
Results	figures/tables, every number traced to an artifact
Conclusion	the verified claims (GROUNDED / not)
Open questions	unresolved questions — the escalation queue to papers
Reproduce	the frozen op-DAG + byte-identical replay + verification badge

Layout

PhysioRecipes/
├── README.md            # this file
├── SCHEMA.md            # the case-unit contract (metadata + narrative sections)
├── TEMPLATE.qmd         # copy this to start a new case
├── _quarto.yml          # gallery site config
└── cases/
    └── <id>/
        ├── index.qmd    # the narrative unit (renders to one gallery page)
        ├── case.json    # structured DB record (validates against SCHEMA.md)
        └── bundle/      # the substrate run bundle (prereg/manifest/opdag/claims/verification)

Status

Bootstrapping. First worked case: cases/ecg-hrv-mitbih (ECG/HRV on the MIT-BIH Arrhythmia Database). Gallery rendering and the companion data package run in CI once a handful of cases exist; public release to x-biosignal follows the ecosystem's develop→verify→publish flow.