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)PhysioIO_0.2.0.zip(r-4.6)PhysioIO_0.2.0.zip(r-4.5)
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✨
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:73c35a084e. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR266
source / vignettesOK266
linux-release-x86_64ERROR255
macos-release-arm64ERROR186
macos-oldrel-arm64ERROR159
windows-develERROR225
windows-releaseERROR206
windows-oldrelERROR240
wasm-releaseOK133

Exports:connectDatabasedbStatsdeleteExperimentdisconnectDatabaseinitPhysioSchemaisHDF5BackedlistBIDSSessionslistBIDSSubjectsloadExperimentmapClinicalCodesqueryExperimentsreadBIDSreadClinicalMetadataCSVreadCSVreadEDFreadElectrodePositionsCSVreadEventsCSVreadMATreadPhysioreadPhysioHDF5realizeHDF5registerExperimentvalidateBIDSvalidateClinicalMetadatawriteAssayHDF5writeBIDSwriteCSVwriteEDFwriteElectrodePositionsCSVwriteEventsCSVwriteMATwritePhysiowritePhysioHDF5

Dependencies:abindBiobaseBiocGenericsbiocmakeDBIDelayedArraydir.expiryfilelockgenericsGenomicRangesh5mreadHDF5ArrayIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsPhysioCorerhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

BIDS Format Support and DuckDB Backend

Rendered frombids-database.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-03-16
Started: 2026-03-16

Guide to Supported File Formats

Rendered fromfile-formats.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-03-16
Started: 2026-03-16

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