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