Package: PhysioStream 0.9.4

Yusuke Matsui

PhysioStream: Governed Real-Time Streams for Physiological Data

Provides validated stream metadata, source and sink contracts, a bounded single-producer/single-consumer ring buffer, deterministic in-process loopback streams, capability-gated Lab Streaming Layer inlets and outlets, marker-event capture, governed Extensible Data Format read/write, and conversion of buffered physiological samples to PhysioExperiment objects, with explicit robust clock-offset, drift, jitter, multi-stream synchronization, transactional causal processing pipelines, explicit backpressure, monotonic latency measurement, and governed loopback, MQTT, and TTL stimulation-command outlets with arm, dead-man, maximum, duplicate-ID, and refractory interlocks, plus causal EMG-onset, EEG-ERD, and phase-target detectors bound to commit-before-stimulation closed-loop session control and provenance, with a bounded live biofeedback scope and marker-anchored video-time synchronization.

Authors:Yusuke Matsui [aut, cre]

# Install 'PhysioStream' in R:

install.packages('PhysioStream', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

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

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.18 score 1 packages 94 exports 28 dependencies

Last updated from:197f7b9569. Checks:13 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	202
linux-devel-x86_64	ERROR	245
source / vignettes	OK	333
linux-release-arm64	ERROR	204
linux-release-x86_64	ERROR	290
macos-release-arm64	ERROR	265
macos-release-x86_64	ERROR	411
macos-oldrel-arm64	ERROR	186
macos-oldrel-x86_64	ERROR	375
windows-devel-arm64	ERROR	383
windows-devel-x86_64	ERROR	377
windows-release-arm64	ERROR	366
windows-release-x86_64	ERROR	294
windows-oldrel-x86_64	ERROR	308
wasm-release	OK	112

Exports:armTrigger bandpassRmsOp biofeedbackFrame biofeedbackScope biofeedbackStart biofeedbackState biofeedbackStep biofeedbackStop biofeedbackUpdate clockOffset closedLoop closedLoopEmergencyStop closedLoopFlush closedLoopLog closedLoopProvenance closedLoopStart closedLoopState closedLoopStep closedLoopStop dejitter disarmTrigger driftCorrect emergencyStop emgOnsetOp erdIntentOp incrementalPCA lmsFilter loopbackFeed loopbackSource loopbackTrigger lslAvailable lslBackendInfo lslInlet lslMarkerEvents lslOutlet lslPull lslPush lslResolveStreams measureLatency mqttAvailable mqttBackendInfo mqttTrigger nlmsFilter onChunk onlineICA phaseTargetOp pipelineEnqueue pipelineReset pipelineRun pipelineState pipelineStep processorReset processorState readXDF ringBuffer ringCapacity ringFill ringPeek ringPull ringPush ringReset ringStats rlsFilter sendStim show signalSyncTime slidingSTFT streamChannels streamClose streamDtype streamInfo streamName streamOpen streamPipeline streamPull streamPush streamRate streamSnapshot streamState streamType syncDiagnostics syncStreams triggerClose triggerHeartbeat triggerOpen triggerState ttlTrigger videoSync videoSyncTime videoSyncViewer welchOnline writeXDF xdfAvailable xdfBackendInfo

Dependencies:abind Biobase BiocGenerics cli DelayedArray digest generics GenomicRanges IRanges jsonlite lattice lifecycle MASS Matrix MatrixGenerics matrixStats PhysioExperiment PhysioPreprocess Rcpp rlang S4Arrays S4Vectors Seqinfo signal SparseArray SummarizedExperiment xml2 XVector

An offline streaming workflow

Rendered fromoffline-streaming.Rmdusingknitr::rmarkdown

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

Help page	Topics
Arm, heartbeat, disarm, or emergency-stop a trigger	armTrigger disarmTrigger emergencyStop triggerHeartbeat
Construct the compiled causal SOS plus rolling-RMS operation	bandpassRmsOp
Start, step, and stop a biofeedback runtime	biofeedback-lifecycle biofeedbackStart biofeedbackStep biofeedbackStop
Inspect a biofeedback frame or portable state	biofeedback-state biofeedbackFrame biofeedbackState
Construct and optionally launch a governed live biofeedback scope	biofeedbackScope
Publish a bounded external feedback update	biofeedbackUpdate
Estimate a governed stream-clock mapping	clockOffset
Run a governed closed-loop session	closed-loop-lifecycle closedLoopEmergencyStop closedLoopFlush closedLoopStart closedLoopStep closedLoopStop
Inspect governed closed-loop state and audit	closed-loop-state closedLoopLog closedLoopState
Construct a governed detector-to-stimulation controller	closedLoop
Append a stopped closed-loop session to PhysioExperiment provenance	closedLoopProvenance
Regularize stream timestamps on a nominal grid	dejitter
Apply a governed stream-clock model	driftCorrect
Construct a causal streaming EMG-onset detector	emgOnsetOp
Construct a causal streaming EEG ERD detector	erdIntentOp
Incremental principal-component analysis	incrementalPCA
Stateful least-mean-squares adaptive filter	lmsFilter
Feed a loopback source	loopbackFeed
Construct a loopback source	loopbackSource
Deterministic in-process stream source	LoopbackSource-class
Construct a deterministic governed loopback trigger	loopbackTrigger
Test Lab Streaming Layer backend availability	lslAvailable
Report the configured LSL backend	lslBackendInfo
Construct an LSL inlet	lslInlet
Lab Streaming Layer inlet	LSLInlet-class
Convert buffered LSL markers to PhysioEvents	lslMarkerEvents
Construct an LSL outlet	lslOutlet
Lab Streaming Layer outlet	LSLOutlet-class
Pull one LSL chunk into an inlet buffer	lslPull
Push samples or markers through an LSL outlet	lslPush
Resolve visible Lab Streaming Layer streams	lslResolveStreams
Measure governed ingest-to-emit pipeline latency	measureLatency
Test or describe the configured MQTT backend	mqttAvailable mqttBackendInfo
Construct a governed MQTT stimulation-command trigger	mqttTrigger
Stateful normalized LMS adaptive filter	nlmsFilter
Register a causal per-chunk operation	onChunk
Online recursive independent-component analysis	onlineICA
Construct a causal phase-target detector	phaseTargetOp
Inspect or reset governed pipeline state	pipeline-state pipelineReset pipelineState
Enqueue one bounded input chunk	pipelineEnqueue
Pull from a configured source and process synchronously	pipelineRun
Process queued chunks synchronously	pipelineStep
Inspect or reset governed streaming processor state	processorReset processorState
Read an Extensible Data Format file	readXDF
Pull or inspect buffered samples	ring-read ringPeek ringPull
Ring-buffer capacity and occupancy	ring-state ringCapacity ringFill ringStats
Construct a native ring buffer	ringBuffer
Live bounded ring buffer	RingBuffer-class
Push samples into a ring buffer	ringPush
Reset unread ring-buffer state	ringReset
Stateful recursive-least-squares adaptive filter	rlsFilter
Send a governed stimulation command	sendStim
Sliding short-time Fourier transform	slidingSTFT
Stream metadata accessors	stream-metadata streamChannels streamDtype streamName streamRate streamType
Stream endpoint lifecycle and transport operations	stream-operations streamClose streamClose,LoopbackSource-method streamClose,LSLInlet-method streamClose,LSLOutlet-method streamClose,StreamEndpoint-method streamOpen streamOpen,LoopbackSource-method streamOpen,LSLInlet-method streamOpen,LSLOutlet-method streamOpen,StreamEndpoint-method streamPull streamPull,LoopbackSource-method streamPull,LSLInlet-method streamPull,StreamEndpoint-method streamPush streamPush,LoopbackSource-method streamPush,LSLOutlet-method streamPush,StreamEndpoint-method streamState streamState,LSLInlet-method streamState,LSLOutlet-method streamState,StreamEndpoint-method
Virtual stream endpoint	StreamEndpoint-class
Construct or retrieve stream metadata	streamInfo streamInfo,character-method streamInfo,RingBuffer-method streamInfo,StreamEndpoint-method streamInfo,StreamInfo-method
Validated stream metadata	show,StreamInfo-method StreamInfo-class
Construct a governed synchronous stream-processing pipeline	streamPipeline
Virtual stream sink	StreamSink-class
Snapshot an open numeric stream	streamSnapshot
Virtual stream source	StreamSource-class
Summarize governed stream synchronization	syncDiagnostics
Synchronize a multi-rate stream container	syncStreams
Open or close a governed stimulation trigger	triggerClose triggerOpen
Inspect governed trigger state	triggerState
Construct a governed TTL stimulation-command trigger	ttlTrigger
Map between synchronized signal and video time	signalSyncTime video-sync-map videoSyncTime
Fit a governed marker-anchored video/signal time map	videoSync
Launch a synchronized video and signal viewer	videoSyncViewer
Exponentially weighted online Welch spectrum	welchOnline
Write an Extensible Data Format file	writeXDF
Test XDF backend availability	xdfAvailable
Report the configured XDF backend	xdfBackendInfo

Package: PhysioStream 0.9.4

PhysioStream: Governed Real-Time Streams for Physiological Data

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