Package index • PhysioCore

All functions

resultType() resultValue() biomarkerValue(): Accessors for analysis results
estimateOf() uncertaintyOf() provenanceOf() estimandOf(): Estimand / uncertainty carrier accessors
show(<AnalysisResult>): AnalysisResult: a uniform container for ecosystem analysis outputs
AnalysisResult(): Construct an AnalysisResult
EventQuery-class: EventQuery class for composable event filtering
MultiRatePhysioExperiment-class: Multi-rate multimodal container for PhysioExperiment streams
length(<MultiRatePhysioExperiment>) `[[`(<MultiRatePhysioExperiment>,<ANY>,<ANY>) dim(<MultiRatePhysioExperiment>) show(<MultiRatePhysioExperiment>): Display, size and stream-extraction methods for MultiRatePhysioExperiment
MultiRatePhysioExperiment(): Construct a MultiRatePhysioExperiment
show(<NormativeReference>): NormativeReference: stratified normative values for a metric
zScore() percentPredicted(): Normative comparisons for an observed value
NormativeReference(): Construct a NormativeReference
show(<PhysioBiomarker>): PhysioBiomarker: a single computed biomarker with metadata
PhysioBiomarker(): Construct a PhysioBiomarker
PhysioCohort-class: Multi-subject cohort / study container
length(<PhysioCohort>) `[`(<PhysioCohort>,<ANY>,<ANY>,<ANY>) show(<PhysioCohort>): Size, subsetting and display for PhysioCohort
PhysioCohort(): Construct a PhysioCohort
PhysioEvents-class: Event management for PhysioExperiment
PhysioEvents(): Create a PhysioEvents object
PhysioExperiment-class: PhysioExperiment class definition
PhysioExperiment(): Construct a PhysioExperiment object
PhysioLongitudinal-class: Longitudinal subject/session container
length(<PhysioLongitudinal>) `[`(<PhysioLongitudinal>,<ANY>,<ANY>,<ANY>) show(<PhysioLongitudinal>): Display, size and subsetting for PhysioLongitudinal
PhysioLongitudinal(): Construct a PhysioLongitudinal container
addEvents(): Add events to a PhysioExperiment object
addProvenance(): Append a provenance step, capturing an optional seed
addSession(): Add a session to a PhysioLongitudinal
addSubject(): Add a subject to a PhysioCohort
alignStreams(): Align all streams to the reference rate
appendProvenance(): Append a provenance activity
applyMontage(): Apply standard montage
as.data.frame(<PhysioExperiment>): Coerce to data.frame
as.data.frame(<PhysioBiomarker>): Coerce a PhysioBiomarker to a one-row data.frame
asMSKTracker(): Bridge a longitudinal container to a PhysioMSKNet tracker
asMultiAssayExperiment(): Coerce a PhysioLongitudinal to a MultiAssayExperiment
assaySamplingRates(): Per-assay sampling rates
blandAltman(): Bland-Altman Analysis for Method Agreement
cbindPhysio(): Combine PhysioExperiment objects by channels
changeScores(): Per-visit change scores across a longitudinal container
`channelInfo<-`(): Set channel information
channelInfo(): Channel information management for PhysioExperiment
`channelNames<-`(): Set channel names/labels
channelNames(): Get channel names/labels
checkNA(): Check for NA values in assay data
circularLinearCorrelation(): Mardia's circular-linear correlation
circularSummary(): Circular mean direction and spread
cohensD(): Cohen's d Effect Size
cohortData() `cohortData<-`(): Subject-level metadata table of a PhysioCohort
cohortDesign(): Long design table of a cohort (subjects x sessions)
commonClock(): The master clock
defaultAssay(): Retrieve the default assay name
deprecate_physio() stable: Emit a Physio-ecosystem deprecation warning or error
design(<PhysioLongitudinal>) `design<-`(<PhysioLongitudinal>): The design schema of a PhysioLongitudinal
dim(<PhysioExperiment>): Dim method for PhysioExperiment
dropChannels(): Drop channels
duration(): Get signal duration
etaSquared(): Eta-Squared Effect Size
eventQuery(): Create an EventQuery from a PhysioExperiment
extractWindow(): Extract time window
fPCA(): Functional Data Analysis (FDA) for Biomechanics
fillEdgeNA(): Fill NA values at edges
filterType(): Filter events by type
filterValue(): Filter events by value
format(<PhysioBiomarker>): Format a PhysioBiomarker as a compact string
getChannelsByType(): Get channels by type
getElectrodePositions(): Get electrode positions
getEvents(): Get events from a PhysioExperiment object
getReference(): Get reference electrode
handleNA(): Handle NA values in signal data
harmonize(): Harmonize channels, reference and montage across sessions
harmonizeChannels(): Harmonize channels across sessions
harmonizeMontage(): Harmonize the montage across sessions
harmonizeReference(): Harmonize the reference across sessions
harmonizeReport(): Report the channels dropped / renamed per session by harmonization
hasNA(): Check if data contains any NA values
icc(): Intraclass Correlation Coefficient (ICC)
is.PhysioBiomarker(): Test whether an object is a PhysioBiomarker
length(<PhysioExperiment>): Length method for PhysioExperiment
logStep(): Record an analysis step in the provenance log
mdc(): Minimal Detectable Change (MDC)
mvarFit(): Fit an MVAR model (user-facing)
mvarOrderSelect(): MVAR model-order selection by AIC / BIC
mvarTransfer(): MVAR transfer function and spectra (user-facing)
nChannels(): Get number of channels
nEvents(): Get number of events
nStreams(): Number of streams
naSummary(): Get NA summary for all assays
normativeLookup(): Look up normative values for a biomarker
physioBiomarker(): Construct a reliability-characterised biomarker
physioPalette(): Colorblind-safe palettes (qualitative, sequential, diverging)
pickChannels(): Pick specific channels
print(<fpca_result>): Print fPCA result
provenance() `provenance<-`(): Provenance / audit trail for PhysioExperiment objects
provenanceHash(): Deterministic hash of the provenance audit trail
rayleighTest(): Rayleigh test for a preferred direction
rbindPhysio(): Combine PhysioExperiment objects by time
reconstructFPCA(): Reconstruct waveforms from fPCA
recordActivity(): Record a PROV activity around an operation
registerCurves(): Curve registration (time warping)
registerOperation() getOperation() availableOperations() unregisterOperation(): Register and dispatch named operations
registerReader() getReader() availableReaders() unregisterReader(): Register and dispatch file readers
registerWriter() getWriter() availableWriters() unregisterWriter(): Register and dispatch file writers
removeEvents(): Remove events from a PhysioExperiment object
renameChannels(): Rename channels
replaceNA(): Replace NA values in assay
resampleToCommon(): Resample all streams onto a single common-rate view
resolveQuery(): Resolve an EventQuery to get filtered events
samplesToTime(): Convert sample indices to times
samplingRate() `samplingRate<-`(): Accessors for PhysioExperiment
scale_color_physio() scale_colour_physio() scale_fill_physio(): Colorblind-safe discrete colour / fill scales for ggplot2
sem(): Standard Error of Measurement (SEM)
session(): Retrieve a single session by visit label or id
sessions() `sessions<-`(): Access the sessions of a PhysioLongitudinal
setAssaySamplingRate(): Set the sampling rate of a specific assay
setChannelTypes(): Set channel types
setChannelUnits(): Set channel units
setElectrodePositions(): Set electrode positions
setEvents(): Set events for a PhysioExperiment object
setReference(): Set reference electrode
show(<PhysioEvents>): Show method for PhysioEvents
show(<PhysioExperiment>): S4 Methods for PhysioExperiment
streamNames(): Names of the streams
streamRates(): Per-stream sampling rates
streamTimeIndex(): Sample times of a stream on the shared clock
streams() `streams<-`(): Access the streams of a MultiRatePhysioExperiment
`[`(<PhysioExperiment>,<ANY>,<ANY>,<ANY>): Subset PhysioExperiment by time indices
subject(): Retrieve a single subject's longitudinal record by id
subjectData() `subjectData<-`(): Subject-level metadata
subjectIds() nSubjects() groups(): Subject ids, subject count and group labels of a PhysioCohort
subjects() `subjects<-`(): Subjects of a PhysioCohort
subsetCohort(): Subset a PhysioCohort by group (or a predicate on colData)
summary(<PhysioExperiment>): Summary statistics for PhysioExperiment
theme_physio(): A clean, accessible ggplot2 theme for x-biosignal figures
timeIndex(): Time index helper
timeToSamples(): Convert event times to sample indices
watsonWilliamsTest(): Watson-Williams test for equal mean directions
waveformCMC(): Coefficient of multiple correlation for repeated waveforms (Kadaba CMC)
waveformICC(): Pointwise intraclass correlation across the movement cycle
waveformReliability(): Waveform reliability report: CMC, ICC / SEM / MDC curves
withProvenance(): Carry a provenance log onto a derived object and record a step
wpliEstimate(): Weighted phase-lag index estimator (raw and debiased)