Package: PhysioIO 0.2.0

Yusuke Matsui

PhysioIO: I/O Functions for PhysioExperiment Objects

Provides comprehensive I/O capabilities for PhysioExperiment objects. Supports EDF/EDF+, HDF5, BIDS, CSV, MATLAB formats, and DuckDB database integration. Includes out-of-memory processing for large datasets via HDF5Array.

Authors:Yusuke Matsui

PhysioIO_0.2.0.tar.gz
PhysioIO_0.2.0.zip(r-4.7-any)PhysioIO_0.2.0.zip(r-4.6-any)PhysioIO_0.2.0.zip(r-4.5-any)
PhysioIO_0.2.0.tgz(r-4.6-any)PhysioIO_0.2.0.tgz(r-4.5-any)
PhysioIO_0.2.0.tar.gz(r-4.7-any)PhysioIO_0.2.0.tar.gz(r-4.6-any)
PhysioIO_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PhysioIO/json (API)

# Install 'PhysioIO' in R:
install.packages('PhysioIO', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/x-biosignal/physioio/issues

On CRAN:

Conda:

3.00 score 33 exports 28 dependencies

Last updated from:65efe48176. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR257
source / vignettesOK205
linux-release-x86_64ERROR259
macos-release-arm64ERROR216
macos-oldrel-arm64ERROR156
windows-develERROR212
windows-releaseERROR201
windows-oldrelERROR192
wasm-releaseOK128

Exports:connectDatabasedbStatsdeleteExperimentdisconnectDatabaseinitPhysioSchemaisHDF5BackedlistBIDSSessionslistBIDSSubjectsloadExperimentmapClinicalCodesqueryExperimentsreadBIDSreadClinicalMetadataCSVreadCSVreadEDFreadElectrodePositionsCSVreadEventsCSVreadMATreadPhysioreadPhysioHDF5realizeHDF5registerExperimentvalidateBIDSvalidateClinicalMetadatawriteAssayHDF5writeBIDSwriteCSVwriteEDFwriteElectrodePositionsCSVwriteEventsCSVwriteMATwritePhysiowritePhysioHDF5

Dependencies:abindBiobaseBiocGenericsbiocmakeDBIDelayedArraydir.expiryfilelockgenericsGenomicRangesh5mreadHDF5ArrayIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsPhysioCorerhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

BIDS Format Support and DuckDB Backend
Introduction | BIDS format support | What is BIDS? | Reading from a BIDS dataset | Writing to BIDS format | Exploring a BIDS dataset | Validating BIDS compliance | DuckDB database backend | Why use a database? | Connecting and initializing | Database schema | Registering experiments | Querying experiments | Loading experiments from the database | Managing experiments | Disconnecting | Combining BIDS and DuckDB | Session info
Rendered frombids-database.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Guide to Supported File Formats
Overview | EDF / EDF+ | Reading EDF files | Writing EDF files | HDF5 | Writing to HDF5 | Reading from HDF5 | Selective assay I/O | CSV / TSV | Reading CSV | Writing CSV | Events and electrode positions | MATLAB .mat files | Reading .mat files | Writing .mat files | Clinical metadata CSV | Reading and validating clinical metadata | Harmonizing clinical codes across sites | RDS (native R serialization) | Choosing a format | Session info
Rendered fromfile-formats.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Readme and manuals

Help Manual

Help pageTopics
Package on-load hook.onLoad
Lightweight database interfaceconnectDatabase disconnectDatabase
Get database statisticsdbStats
Delete experiment from databasedeleteExperiment
DuckDB Schema Management for PhysioExperimentinitPhysioSchema
Check if assays are HDF5-backedisHDF5Backed
List sessions for a subject in BIDS datasetlistBIDSSessions
List subjects in a BIDS datasetlistBIDSSubjects
Load experiment from databaseloadExperiment
Harmonize clinical codes across sitesmapClinicalCodes
Query experiments from databasequeryExperiments
BIDS Format Support for PhysioExperimentreadBIDS
Clinical metadata CSV I/O and validationreadClinicalMetadataCSV
CSV/TSV I/O for PhysioExperimentreadCSV
EDF/EDF+ file I/OreadEDF
Read electrode positions from CSVreadElectrodePositionsCSV
Read events from CSV/TSV filereadEventsCSV
Read PhysioExperiment from MATLAB .mat filereadMAT
Read PhysioExperiment from HDF5readPhysioHDF5
Realize HDF5-backed data to memoryrealizeHDF5
Register a PhysioExperiment in the databaseregisterExperiment
Validate BIDS dataset structurevalidateBIDS
Validate clinical metadatavalidateClinicalMetadata
Write assay to HDF5 filewriteAssayHDF5
Write PhysioExperiment to BIDS formatwriteBIDS
Write PhysioExperiment to CSV filewriteCSV
Write EDF filewriteEDF
Write electrode positions to CSVwriteElectrodePositionsCSV
Write events to CSV filewriteEventsCSV
Write PhysioExperiment to MATLAB .mat filewriteMAT
Basic read/write helpersreadPhysio writePhysio
HDF5 Backend for PhysioExperimentwritePhysioHDF5