Package: PhysioIO 0.2.10

Yusuke Matsui

PhysioIO: Input and Output Functions for 'PhysioExperiment' Objects

Provides input and output capabilities for 'SummarizedExperiment'-derived physiological signal containers. Supported formats include 'EDF' and 'EDF+', 'BDF', 'GDF', 'BrainVision', 'HDF5', 'BIDS', comma-separated values, and 'MATLAB' files, together with 'DuckDB' database integration. Out-of-memory processing of large datasets is available through delayed 'HDF5' arrays.

Authors:Yusuke Matsui [aut, cre]

PhysioIO_0.2.10.tar.gz
PhysioIO_0.2.10.zip(r-4.7-any)PhysioIO_0.2.10.zip(r-4.6-any)PhysioIO_0.2.10.zip(r-4.5-any)
PhysioIO_0.2.10.tgz(r-4.6-any)PhysioIO_0.2.10.tgz(r-4.5-any)
PhysioIO_0.2.10.tar.gz(r-4.7-any)PhysioIO_0.2.10.tar.gz(r-4.6-any)
PhysioIO_0.2.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
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

Pkgdown/docs site:https://x-biosignal.github.io

On CRAN:

Conda:

softwareinfrastructuredataimportdatarepresentation

3.65 score 1 packages 70 exports 32 dependencies

Last updated from:b7e0e5b390. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK285
source / vignettesOK241
linux-releaseOK286
macos-releaseOK230
macos-oldrelOK317
windows-develOK281
windows-releaseOK278
windows-oldrelOK271
wasm-releaseOK111

Exports:attachBIDSPhysiobdfTriggerEventsconnectDatabasedbStatsdeleteExperimentdisconnectDatabasedownloadFigsharedownloadFromDOIdownloadMendeleydownloadPhysioNetdownloadZenodofigshareCollectionArticlesfromMNEhasMNEinitPhysioSchemaisHDF5BackedlistBIDSSessionslistBIDSSubjectslistWFDBRecordsloadExperimentmapClinicalCodesmendeleyDatasetFilespyMNEVersionqueryExperimentsreadBDFreadBDFStatusreadBIDSreadBIDSDerivativesreadBIDSMotionreadBIDSPhysioreadBrainVisionreadClinicalMetadataCSVreadCSVreadEDFreadElectrodePositionsCSVreadEventsCSVreadFIFreadGDFreadMATreadParquetreadPhysioreadPhysioHDF5readProvreadWFDBreadWFDBAnnotationrealizeHDF5registerExperimentregisterParquetAssaytoMNEvalidateBIDSvalidateClinicalMetadatawriteAssayHDF5writeBDFwriteBIDSwriteBIDSDerivativewriteBIDSMotionwriteBIDSPhysiowriteBrainVisionwriteCSVwriteEDFwriteElectrodePositionsCSVwriteEventsCSVwriteGDFwriteMATwriteParquetwritePhysiowritePhysioHDF5writeProvwriteWFDBwriteWFDBAnnotation

Dependencies:abindBiobaseBiocGenericsbiocmakecliDBIDelayedArraydigestdir.expiryfilelockgenericsGenomicRangesh5mreadHDF5ArrayIRangesjsonlitelatticelifecycleMatrixMatrixGenericsmatrixStatsPhysioExperimentrhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

BIDS Format Support and DuckDB Backend
Introduction | BIDS format support | What is BIDS? | Writing to and reading from a BIDS dataset | Exploring and validating a BIDS dataset | DuckDB database backend | Why use a database? | Connecting, initializing, registering, and querying | Session info
Rendered frombids-database.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Guide to Supported File Formats
Overview | A small example object | RDS (native R serialization) | CSV / TSV | EDF / EDF+ | HDF5 | MATLAB .mat files | Choosing a format | Session info
Rendered fromfile-formats.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Interoperating with MNE-Python
Why a bridge, not a rewrite | A lossless data bridge | Let MNE do the analysis, keep the result in R | MNE as a validation oracle for native ops | Toward native brain-imaging integration | Example: template (fsaverage) source localization via MNE
Rendered frommne-interop.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Readme and manuals

Help Manual

Help pageTopics
Attach a physio recording to a main recording as an aligned streamattachBIDSPhysio
Extract trigger events from a BioSemi Status channelbdfTriggerEvents
Lightweight database interfaceconnectDatabase disconnectDatabase
Get database statisticsdbStats
Delete experiment from databasedeleteExperiment
Download files from a public figshare articledownloadFigshare
Download a dataset from its DOI (figshare, Zenodo or Mendeley Data)downloadFromDOI
Download files from a Mendeley Data datasetdownloadMendeley
Download a WFDB record from PhysioNetdownloadPhysioNet
Download files from a public Zenodo recorddownloadZenodo
List the articles in a public figshare collectionfigshareCollectionArticles
Convert an MNE-Python Raw object to a PhysioExperimentfromMNE
Is the Python 'mne' module available?hasMNE
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
List the records in a WFDB RECORDS filelistWFDBRecords
Load experiment from databaseloadExperiment
Harmonize clinical codes across sitesmapClinicalCodes
List the files of a public Mendeley Data datasetmendeleyDatasetFiles
Version of the available Python 'mne' modulepyMNEVersion
Query experiments from databasequeryExperiments
Read BDF (BioSemi Data Format) filereadBDF
Read the BioSemi Status channel of a BDF filereadBDFStatus
BIDS Format Support for PhysioExperimentreadBIDS
Read the derivative recordings of a subjectreadBIDSDerivatives
Read a Motion-BIDS recordingreadBIDSMotion
Read a BIDS continuous physiological recordingreadBIDSPhysio
BrainVision File Format I/O for PhysioExperimentreadBrainVision
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 an Elekta/Neuromag/MNE FIF (FIFF) filereadFIF
GDF (General Data Format) File I/O for PhysioExperimentreadGDF
Read PhysioExperiment from MATLAB .mat filereadMAT
Read a PhysioExperiment from a Parquet dataset directoryreadParquet
Read PhysioExperiment from HDF5readPhysioHDF5
Read a W3C PROV interchange file back into a provenance tablereadProv
Read a WFDB recordreadWFDB
Read a WFDB annotation filereadWFDBAnnotation
Realize HDF5-backed data to memoryrealizeHDF5
Register a PhysioExperiment in the databaseregisterExperiment
Register a Parquet-backed assay as a DuckDB view for out-of-core queriesregisterParquetAssay
Convert a PhysioExperiment to an MNE-Python RawArraytoMNE
Validate BIDS dataset structurevalidateBIDS
Validate clinical metadatavalidateClinicalMetadata
Write assay to HDF5 filewriteAssayHDF5
Write BDF (BioSemi Data Format) filewriteBDF
Write PhysioExperiment to BIDS formatwriteBIDS
Write a BIDS derivative recordingwriteBIDSDerivative
Write a Motion-BIDS recordingwriteBIDSMotion
Write a BIDS continuous physiological recordingwriteBIDSPhysio
Write PhysioExperiment to BrainVision formatwriteBrainVision
Write PhysioExperiment to CSV filewriteCSV
Write EDF filewriteEDF
Write electrode positions to CSVwriteElectrodePositionsCSV
Write events to CSV filewriteEventsCSV
Write PhysioExperiment to GDF formatwriteGDF
Write PhysioExperiment to MATLAB .mat filewriteMAT
Write a PhysioExperiment to a Parquet dataset directorywriteParquet
Basic read/write helpersreadPhysio writePhysio
HDF5 Backend for PhysioExperimentwritePhysioHDF5
Serialize a provenance trail to a W3C PROV interchange filewriteProv
Write a WFDB recordwriteWFDB
Write a WFDB annotation filewriteWFDBAnnotation