A tiny local lake | Store and retrieve a PhysioExperiment | Store a run bundle with internal lineage | Where to go next
Package: PhysioLake 0.1.3
Yusuke Matsui
PhysioLake: Versioned, Lineage-Tracked Data Management for the Physio Ecosystem
Integrates the PhysioExperiment ecosystem with 'OmicsLake', a versioned, on-disk data-management engine built on 'DuckDB', 'Apache Arrow' and 'Parquet' with automatic dataset-level lineage tracking. Rather than reimplementing a data lake, PhysioLake inherits the domain-agnostic OmicsLake core (storage backend, snapshots and time-travel, cross-dataset lineage, query layer) and registers physiology-specific adapters and utilities: 'PhysioExperiment' objects are stored and retrieved with full fidelity, preserving the sampling-rate slot and the W3C-PROV provenance held in object metadata. This connects the ecosystem's per-object (micro) provenance with the lake's cross-dataset (macro) lineage.
Authors:
PhysioLake_0.1.3.tar.gz
PhysioLake_0.1.3.zip(r-4.7-any)PhysioLake_0.1.3.zip(r-4.6-any)PhysioLake_0.1.3.zip(r-4.5-any)
PhysioLake_0.1.3.tgz(r-4.6-any)PhysioLake_0.1.3.tgz(r-4.5-any)
PhysioLake_0.1.3.tar.gz(r-4.7-any)PhysioLake_0.1.3.tar.gz(r-4.6-any)
PhysioLake_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioLake/json (API)
| # Install 'PhysioLake' in R: |
| install.packages('PhysioLake', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/x-biosignal/physiolake/issues
Last updated from:106fdbe2ba. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 232 | ||
| source / vignettes | OK | 265 | ||
| linux-release | NOTE | 253 | ||
| macos-release | NOTE | 242 | ||
| macos-oldrel | NOTE | 190 | ||
| windows-devel | NOTE | 193 | ||
| windows-release | NOTE | 138 | ||
| windows-oldrel | NOTE | 172 | ||
| wasm-release | OK | 141 |
Exports:PhysioExperimentAdapterphysioProvenancephysioPutphysioPutBundleregisterPhysioAdapters
Dependencies:abindBiobaseBiocGenericscliDelayedArraydigestgenericsGenomicRangesIRangeslatticelifecycleMatrixMatrixGenericsmatrixStatsPhysioExperimentR6rlangS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| PhysioExperiment adapter for OmicsLake | PhysioExperimentAdapter |
| Retrieve the provenance op-DAG stored for a lake object | physioProvenance |
| Store a Physio object in a lake with its provenance linked in the lineage | physioPut |
| Store a reproducibility-substrate / PhysioAgent run bundle in a lake | physioPutBundle |
| Register the Physio adapters with OmicsLake | registerPhysioAdapters |