{ "_id": "6ac10a5d552a13804ac7ec5f", "Package": "PhysioExperiment", "Title": "Shared Data Model for Physiological Signal Analysis", "Version": "2.3.1", "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Matsui\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mail.to.matsui@gmail.com\")", "Description": "Provides the shared data model for the Physio ecosystem:\nthe PhysioExperiment class, a 'SummarizedExperiment' extension\nfor multi-modal physiological signal data (such as\nelectroencephalography, electromyography, and\nelectrocardiography), together with the containers for multiple\nsimultaneously recorded streams, repeated sessions of one\nsubject, and cohorts of subjects. Includes core accessors,\nchannel and event management, provenance, and basic 'S4'\nmethods. Domain packages apply specialized methods to these\nshared containers and are installed separately.", "biocViews": "Software, Infrastructure, DataRepresentation, TimeCourse", "VignetteBuilder": "knitr", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Collate": "'PhysioExperiment-class.R' 'PhysioExperiment-accessors.R'\n'PhysioExperiment-methods.R' 'provenance.R'\n'MultiPhysioExperiment-class.R' 'container-migration.R'\n'trials.R' 'multirate-accessors.R' 'PhysioLongitudinal-class.R'\n'PhysioCohort-class.R' 'channels.R' 'harmonize.R'\n'change-scores.R' 'events.R' 'event-query.R' 'utils-signal.R'\n'utils-mvar.R' 'utils-na.R' 'clinimetrics.R'\n'analysis-result.R' 'normative.R' 'biomarker.R' 'vis-theme.R'\n'registry.R' 'lifecycle.R' 'stats-circular.R'\n'stats-reliability.R' 'stats-fda.R' 'zzz.R'", "RoxygenNote": "7.3.3", "URL": "https://github.com/x-biosignal/PhysioExperiment,\nhttps://x-biosignal.r-universe.dev/PhysioExperiment", "BugReports": "https://github.com/x-biosignal/PhysioExperiment/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://x-biosignal.r-universe.dev", "Date/Publication": "2026-10-03 13:11:53 UTC", "RemoteUrl": "https://github.com/x-biosignal/PhysioExperiment", "RemoteRef": "HEAD", "RemoteSha": "e65059e55edbd9bf0568f094cdeb97124805084c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-03 13:42:10 UTC", "User": "root" }, "Author": "Yusuke Matsui [aut, cre]", "Maintainer": "Yusuke Matsui ", "_user": "x-biosignal", "_type": "src", "_file": "PhysioExperiment_2.3.1.tar.gz", "_fileid": "https://r2.ropensci.org/8dbb6fff7912fbc7d468370a29e19b55b165af1dc93e5357f029af24429224ab", "_filesize": 823657, "_sha256": "8dbb6fff7912fbc7d468370a29e19b55b165af1dc93e5357f029af24429224ab", "_expires": "2027-01-11T13:59:55.000Z", "_created": "2026-10-03T13:42:10.000Z", "_published": "2026-10-03T13:59:57.596Z", "_jobs": [ { "job": 111214538681, "time": 235, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11275723056" }, { "job": 111214538653, "time": 274, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11275633330" }, { "job": 111214538643, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11276050340" }, { "job": 111214538586, "time": 253, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11275815897" }, { "job": 111213846316, "time": 247, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11275388456" }, { "job": 111214538624, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11274864149" }, { "job": 111214538684, "time": 180, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11274994254" }, { "job": 111214538665, "time": 290, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11275157688" }, { "job": 111214538679, "time": 236, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11275668284" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296", "_status": "success", "_upstream": "https://github.com/x-biosignal/PhysioExperiment", "_commit": { "id": "e65059e55edbd9bf0568f094cdeb97124805084c", "author": "Yusuke Matsui ", "committer": "Yusuke Matsui ", "message": "Release snapshot\n", "time": 1791033113 }, "_maintainer": { "name": "Yusuke Matsui", "email": "mail.to.matsui@gmail.com", "login": "ymatts", "description": "Data scientist", "uuid": 5744286 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "testthat", "version": ">= 3.2.0", "role": "Suggests" }, { "package": "abind", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "farver", "role": "Suggests" }, { "package": "colorspace", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "MultiAssayExperiment", "role": "Suggests" }, { "package": "PhysioMSKNet", "role": "Suggests" } ], "_owner": "x-biosignal", "_selfowned": true, "_usedby": 22, "_updates": [ { "week": "2026-40", "n": 1 } ], "_tags": [], "_topics": [ "software", "infrastructure", "datarepresentation", "timecourse" ], "_stars": 0, "_contributors": [ { "user": "ymatts", "count": 1, "uuid": 5744286 } ], "_userbio": { "uuid": 268545536, "type": "organization", "name": "x-biosignal", "followers": 1, "description": "Open-source R packages for biosignal analysis, biomechanics, clinical research, and rehabilitation." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PhysioExperiment" }, "_devurl": "https://github.com/x-biosignal/physioexperiment", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/PhysioExperiment.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ ".fitMVAR", ".mvarSpectral", "addEvents", "addProvenance", "addSession", "addSubject", "aggregatePhysioFeatures", "aggregateTrials", "aggregateTrialWaveforms", "alignment", "alignment<-", "alignStreams", "AnalysisResult", "appendProvenance", "applyMontage", "as.data.frame", "asMSKTracker", "asMultiAssayExperiment", "assaySamplingRates", "availableOperations", "availableReaders", "availableWriters", "biomarkerValue", "blandAltman", "cbindPhysio", "changeScores", "channelInfo", "channelInfo<-", "channelNames", "channelNames<-", "checkNA", "circularLinearCorrelation", "circularSummary", "cohensD", "cohortData", "cohortData<-", "cohortDesign", "cohortTrials", "commonClock", "defaultAssay", "deprecate_physio", "design", "design<-", "detectGaps", "dropChannels", "duration", "elapsedBetweenTrials", "estimandOf", "estimateOf", "etaSquared", "eventQuery", "experiments", "experiments<-", "extractTrialFeatures", "extractWindow", "fillEdgeNA", "filterType", "filterValue", "fPCA", "getChannelsByType", "getElectrodePositions", "getEvents", "getOperation", "getReader", "getReference", "getWriter", "groups", "handleNA", "harmonize", "harmonizeChannels", "harmonizeMontage", "harmonizeReference", "harmonizeReport", "hasMeasuredTimes", "hasNA", "icc", "is.PhysioBiomarker", "logStep", "mdc", "migrateContainer", "modalities", "MultiPhysioExperiment", "MultiRatePhysioExperiment", "mvarFit", "mvarOrderSelect", "mvarTransfer", "naSummary", "nChannels", "nEvents", "nModalities", "normativeLookup", "NormativeReference", "nStreams", "nSubjects", "percentPredicted", "physioBiomarker", "PhysioBiomarker", "PhysioCohort", "PhysioEvents", "PhysioExperiment", "PhysioLongitudinal", "physioPalette", "pickChannels", "provenance", "provenance<-", "provenanceHash", "provenanceOf", "rayleighTest", "rbindPhysio", "readPhysioRDS", "reconstructFPCA", "recordActivity", "recordingMap", "recordingMap<-", "recordings", "registerCurves", "registerOperation", "registerReader", "registerWriter", "removeEvents", "renameChannels", "replaceNA", "resampleToCommon", "resolveQuery", "resultType", "resultValue", "samplesToTime", "samplingRate", "samplingRate<-", "samplingRates", "scale_color_physio", "scale_colour_physio", "scale_fill_physio", "sem", "session", "sessions", "sessions<-", "setAssaySamplingRate", "setChannelTypes", "setChannelUnits", "setElectrodePositions", "setEvents", "setReference", "show", "streamCoverage", "streamNames", "streamRates", "streams", "streams<-", "streamTimeIndex", "subject", "subjectData", "subjectData<-", "subjectIds", "subjects", "subjects<-", "subjectTrials", "subsetCohort", "summary", "theme_physio", "timeIndex", "timeToSamples", "timeWindow", "trial", "trialCoverage", "trialIntervals", "trialIntervals<-", "trials", "trials<-", "trialSet", "uncertaintyOf", "unregisterOperation", "unregisterReader", "unregisterWriter", "updateObject", "watsonWilliamsTest", "waveformCMC", "waveformICC", "waveformReliability", "withProvenance", "wpliEstimate", "zScore" ], "_help": [ { "page": "sub-MultiPhysioExperiment-ANY-ANY-ANY-method", "title": "Subset a MultiPhysioExperiment by time and stream", "topics": [ "[,MultiPhysioExperiment,ANY,ANY,ANY-method" ] }, { "page": "sub-PhysioExperiment-ANY-ANY-ANY-method", "title": "Subset PhysioExperiment by time indices", "topics": [ "[,PhysioExperiment,ANY,ANY,ANY-method" ] }, { "page": "addEvents", "title": "Add events to a PhysioExperiment object", "topics": [ "addEvents" ] }, { "page": "addProvenance", "title": "Append a provenance step, capturing an optional seed", "topics": [ "addProvenance" ] }, { "page": "addSession", "title": "Add a session to a PhysioLongitudinal", "topics": [ "addSession" ] }, { "page": "addSubject", "title": "Add a subject to a PhysioCohort", "topics": [ "addSubject" ] }, { "page": "aggregatePhysioFeatures", "title": "Aggregate features through trial, session, subject and cohort levels", "topics": [ "aggregatePhysioFeatures" ] }, { "page": "aggregateTrials", "title": "Aggregate per-trial features, choosing what counts as a trial", "topics": [ "aggregateTrials" ] }, { "page": "aggregateTrialWaveforms", "title": "Align and average trial waveforms through the experimental hierarchy", "topics": [ "aggregateTrialWaveforms" ] }, { "page": "alignStreams", "title": "Align all streams to the reference rate", "topics": [ "alignStreams" ] }, { "page": "AnalysisResult", "title": "Construct an AnalysisResult", "topics": [ "AnalysisResult" ] }, { "page": "AnalysisResult-accessors", "title": "Accessors for analysis results", "topics": [ "AnalysisResult-accessors", "biomarkerValue", "biomarkerValue,PhysioBiomarker-method", "resultType", "resultType,AnalysisResult-method", "resultValue", "resultValue,AnalysisResult-method", "resultValue,PhysioBiomarker-method" ] }, { "page": "AnalysisResult-carrier", "title": "Estimand / uncertainty carrier accessors", "topics": [ "AnalysisResult-carrier", "estimandOf", "estimandOf,AnalysisResult-method", "estimateOf", "estimateOf,AnalysisResult-method", "provenanceOf", "provenanceOf,AnalysisResult-method", "uncertaintyOf", "uncertaintyOf,AnalysisResult-method" ] }, { "page": "AnalysisResult-class", "title": "AnalysisResult: a uniform container for ecosystem analysis outputs", "topics": [ "AnalysisResult-class", "show,AnalysisResult-method" ] }, { "page": "appendProvenance", "title": "Append a provenance activity", "topics": [ "appendProvenance" ] }, { "page": "applyMontage", "title": "Apply standard montage", "topics": [ "applyMontage" ] }, { "page": "as.data.frame-PhysioExperiment-method", "title": "Coerce to data.frame", "topics": [ "as.data.frame,PhysioExperiment-method" ] }, { "page": "as.data.frame.PhysioBiomarker", "title": "Coerce a PhysioBiomarker to a one-row data.frame", "topics": [ "as.data.frame.PhysioBiomarker" ] }, { "page": "asMSKTracker", "title": "Bridge a longitudinal container to a PhysioMSKNet tracker", "topics": [ "asMSKTracker" ] }, { "page": "asMultiAssayExperiment", "title": "Coerce a PhysioLongitudinal to a MultiAssayExperiment", "topics": [ "asMultiAssayExperiment" ] }, { "page": "assaySamplingRates", "title": "Per-assay sampling rates", "topics": [ "assaySamplingRates" ] }, { "page": "blandAltman", "title": "Bland-Altman Analysis for Method Agreement", "topics": [ "blandAltman" ] }, { "page": "cbindPhysio", "title": "Combine PhysioExperiment objects by channels", "topics": [ "cbindPhysio" ] }, { "page": "changeScores", "title": "Per-visit change scores across a longitudinal container", "topics": [ "changeScores" ] }, { "page": "channelInfo", "title": "Channel information management for PhysioExperiment", "topics": [ "channelInfo" ] }, { "page": "channelInfo-set", "title": "Set channel information", "topics": [ "channelInfo<-" ] }, { "page": "channelNames", "title": "Get channel names/labels", "topics": [ "channelNames" ] }, { "page": "channelNames-set", "title": "Set channel names/labels", "topics": [ "channelNames<-" ] }, { "page": "checkNA", "title": "Check for NA values in assay data", "topics": [ "checkNA" ] }, { "page": "circularLinearCorrelation", "title": "Mardia's circular-linear correlation", "topics": [ "circularLinearCorrelation" ] }, { "page": "circularSummary", "title": "Circular mean direction and spread", "topics": [ "circularSummary" ] }, { "page": "cohensD", "title": "Cohen's d Effect Size", "topics": [ "cohensD" ] }, { "page": "cohortData", "title": "Subject-level metadata table of a PhysioCohort", "topics": [ "cohortData", "cohortData,PhysioCohort-method", "cohortData<-", "cohortData<-,PhysioCohort-method" ] }, { "page": "cohortDesign", "title": "Long design table of a cohort (subjects x sessions)", "topics": [ "cohortDesign" ] }, { "page": "cohortTrials", "title": "Every trial in a cohort", "topics": [ "cohortTrials" ] }, { "page": "commonClock", "title": "The shared clock", "topics": [ "commonClock" ] }, { "page": "defaultAssay", "title": "Retrieve the default assay name", "topics": [ "defaultAssay" ] }, { "page": "deprecate_physio", "title": "Emit a Physio-ecosystem deprecation warning or error", "concept": [ "lifecycle" ], "topics": [ "deprecate_physio" ] }, { "page": "design", "title": "The design schema of a PhysioLongitudinal", "topics": [ "design,PhysioLongitudinal-method", "design<-,PhysioLongitudinal-method" ] }, { "page": "detectGaps", "title": "Gaps in a series of sample times", "topics": [ "detectGaps" ] }, { "page": "dim-PhysioExperiment-method", "title": "Dim method for PhysioExperiment", "topics": [ "dim,PhysioExperiment-method" ] }, { "page": "dropChannels", "title": "Drop channels", "topics": [ "dropChannels" ] }, { "page": "duration", "title": "Get signal duration", "topics": [ "duration" ] }, { "page": "elapsedBetweenTrials", "title": "Elapsed time between two trials", "topics": [ "elapsedBetweenTrials" ] }, { "page": "etaSquared", "title": "Eta-Squared Effect Size", "topics": [ "etaSquared" ] }, { "page": "eventQuery", "title": "Create an EventQuery from a PhysioExperiment", "topics": [ "eventQuery" ] }, { "page": "EventQuery-class", "title": "EventQuery class for composable event filtering", "topics": [ "EventQuery-class" ] }, { "page": "extractTrialFeatures", "title": "Extract scalar trial features across sessions and participants", "topics": [ "extractTrialFeatures" ] }, { "page": "extractWindow", "title": "Extract time window", "topics": [ "extractWindow" ] }, { "page": "fillEdgeNA", "title": "Fill NA values at edges", "topics": [ "fillEdgeNA" ] }, { "page": "filterType", "title": "Filter events by type", "topics": [ "filterType" ] }, { "page": "filterValue", "title": "Filter events by value", "topics": [ "filterValue" ] }, { "page": "format.PhysioBiomarker", "title": "Format a PhysioBiomarker as a compact string", "topics": [ "format.PhysioBiomarker" ] }, { "page": "fPCA", "title": "Functional Data Analysis (FDA) for Biomechanics", "topics": [ "fPCA" ] }, { "page": "getChannelsByType", "title": "Get channels by type", "topics": [ "getChannelsByType" ] }, { "page": "getElectrodePositions", "title": "Get electrode positions", "topics": [ "getElectrodePositions" ] }, { "page": "getEvents", "title": "Get events from a PhysioExperiment object", "topics": [ "getEvents" ] }, { "page": "getReference", "title": "Get reference electrode", "topics": [ "getReference" ] }, { "page": "handleNA", "title": "Handle NA values in signal data", "topics": [ "handleNA" ] }, { "page": "harmonize", "title": "Harmonize channels, reference and montage across sessions", "topics": [ "harmonize" ] }, { "page": "harmonizeChannels", "title": "Harmonize channels across sessions", "topics": [ "harmonizeChannels" ] }, { "page": "harmonizeMontage", "title": "Harmonize the montage across sessions", "topics": [ "harmonizeMontage" ] }, { "page": "harmonizeReference", "title": "Harmonize the reference across sessions", "topics": [ "harmonizeReference" ] }, { "page": "harmonizeReport", "title": "Report the channels dropped / renamed per session by harmonization", "topics": [ "harmonizeReport" ] }, { "page": "hasMeasuredTimes", "title": "Does a stream carry measured sample times?", "topics": [ "hasMeasuredTimes" ] }, { "page": "hasNA", "title": "Check if data contains any NA values", "topics": [ "hasNA" ] }, { "page": "icc", "title": "Intraclass Correlation Coefficient (ICC)", "topics": [ "icc" ] }, { "page": "is.PhysioBiomarker", "title": "Test whether an object is a PhysioBiomarker", "topics": [ "is.PhysioBiomarker" ] }, { "page": "length-PhysioExperiment-method", "title": "Length method for PhysioExperiment", "topics": [ "length,PhysioExperiment-method" ] }, { "page": "logStep", "title": "Record an analysis step in the provenance log", "topics": [ "logStep" ] }, { "page": "mdc", "title": "Minimal Detectable Change (MDC)", "topics": [ "mdc" ] }, { "page": "migrateContainer", "title": "Convert a pre-unification multimodal container", "topics": [ "migrateContainer", "updateObject,MultiPhysioExperiment-method" ] }, { "page": "multiphysio-legacy-accessors", "title": "Legacy accessors for the multimodal container", "topics": [ "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" ] }, { "page": "MultiPhysioExperiment", "title": "Construct a MultiPhysioExperiment", "topics": [ "MultiPhysioExperiment", "MultiRatePhysioExperiment" ] }, { "page": "MultiPhysioExperiment-class", "title": "Multimodal container for PhysioExperiment streams", "topics": [ "MultiPhysioExperiment-class" ] }, { "page": "MultiPhysioExperiment-methods", "title": "Display, size and stream-extraction methods for MultiPhysioExperiment", "topics": [ "dim,MultiPhysioExperiment-method", "length,MultiPhysioExperiment-method", "MultiPhysioExperiment-methods", "names,MultiPhysioExperiment-method", "show,MultiPhysioExperiment-method", "[[,MultiPhysioExperiment,ANY,ANY-method" ] }, { "page": "MultiRatePhysioExperiment-class", "title": "Legacy multi-rate container", "topics": [ "MultiRatePhysioExperiment-class" ] }, { "page": "mvarFit", "title": "Fit an MVAR model (user-facing)", "topics": [ "mvarFit" ] }, { "page": "mvarOrderSelect", "title": "MVAR model-order selection by AIC / BIC", "topics": [ "mvarOrderSelect" ] }, { "page": "mvarTransfer", "title": "MVAR transfer function and spectra (user-facing)", "topics": [ "mvarTransfer" ] }, { "page": "naSummary", "title": "Get NA summary for all assays", "topics": [ "naSummary" ] }, { "page": "nChannels", "title": "Get number of channels", "topics": [ "nChannels" ] }, { "page": "nEvents", "title": "Get number of events", "topics": [ "nEvents" ] }, { "page": "normativeLookup", "title": "Look up normative values for a biomarker", "topics": [ "normativeLookup" ] }, { "page": "NormativeReference", "title": "Construct a NormativeReference", "topics": [ "NormativeReference" ] }, { "page": "NormativeReference-class", "title": "NormativeReference: stratified normative values for a metric", "topics": [ "NormativeReference-class", "show,NormativeReference-method" ] }, { "page": "NormativeReference-compare", "title": "Normative comparisons for an observed value", "topics": [ "NormativeReference-compare", "percentPredicted", "percentPredicted,NormativeReference-method", "zScore", "zScore,NormativeReference-method" ] }, { "page": "nStreams", "title": "Number of streams", "topics": [ "nStreams" ] }, { "page": "physioBiomarker-constructor", "title": "Construct a reliability-characterised biomarker", "topics": [ "physioBiomarker" ] }, { "page": "PhysioBiomarker", "title": "Construct a PhysioBiomarker", "topics": [ "PhysioBiomarker" ] }, { "page": "PhysioBiomarker-class", "title": "PhysioBiomarker: a single computed biomarker with metadata", "topics": [ "PhysioBiomarker-class", "show,PhysioBiomarker-method" ] }, { "page": "PhysioCohort", "title": "Construct a PhysioCohort", "topics": [ "PhysioCohort" ] }, { "page": "PhysioCohort-class", "title": "Multi-subject cohort / study container", "topics": [ "PhysioCohort-class" ] }, { "page": "PhysioCohort-methods", "title": "Size, subsetting and display for PhysioCohort", "topics": [ "length,PhysioCohort-method", "PhysioCohort-methods", "show,PhysioCohort-method", "[,PhysioCohort,ANY,ANY,ANY-method" ] }, { "page": "PhysioEvents", "title": "Create a PhysioEvents object", "topics": [ "PhysioEvents" ] }, { "page": "PhysioEvents-class", "title": "Event management for PhysioExperiment", "topics": [ "PhysioEvents-class" ] }, { "page": "PhysioExperiment", "title": "Construct a PhysioExperiment object", "topics": [ "PhysioExperiment" ] }, { "page": "PhysioExperiment-class", "title": "PhysioExperiment class definition", "topics": [ "PhysioExperiment-class" ] }, { "page": "PhysioLongitudinal", "title": "Construct a PhysioLongitudinal container", "topics": [ "PhysioLongitudinal" ] }, { "page": "PhysioLongitudinal-class", "title": "Longitudinal subject/session container", "topics": [ "PhysioLongitudinal-class" ] }, { "page": "PhysioLongitudinal-methods", "title": "Display, size and subsetting for PhysioLongitudinal", "topics": [ "length,PhysioLongitudinal-method", "PhysioLongitudinal-methods", "show,PhysioLongitudinal-method", "[,PhysioLongitudinal,ANY,ANY,ANY-method" ] }, { "page": "physioPalette", "title": "Colorblind-safe palettes (qualitative, sequential, diverging)", "topics": [ "physioPalette" ] }, { "page": "pickChannels", "title": "Pick specific channels", "topics": [ "pickChannels" ] }, { "page": "print.fpca_result", "title": "Print fPCA result", "topics": [ "print.fpca_result" ] }, { "page": "provenance", "title": "Provenance / audit trail for PhysioExperiment objects", "topics": [ "provenance", "provenance,MultiPhysioExperiment-method", "provenance,PhysioCohort-method", "provenance,PhysioExperiment-method", "provenance,PhysioLongitudinal-method", "provenance<-", "provenance<-,PhysioExperiment-method" ] }, { "page": "provenanceHash", "title": "Deterministic hash of the provenance audit trail", "topics": [ "provenanceHash" ] }, { "page": "rayleighTest", "title": "Rayleigh test for a preferred direction", "topics": [ "rayleighTest" ] }, { "page": "rbindPhysio", "title": "Combine PhysioExperiment objects by time", "topics": [ "rbindPhysio" ] }, { "page": "readPhysioRDS", "title": "Read a saved object, migrating a pre-unification container", "topics": [ "readPhysioRDS" ] }, { "page": "reconstructFPCA", "title": "Reconstruct waveforms from fPCA", "topics": [ "reconstructFPCA" ] }, { "page": "recordActivity", "title": "Record a PROV activity around an operation", "topics": [ "recordActivity" ] }, { "page": "recordingMap", "title": "How trials map onto recordings", "topics": [ "recordingMap", "recordingMap<-" ] }, { "page": "recordings", "title": "The recordings held by a trial set", "topics": [ "recordings" ] }, { "page": "registerCurves", "title": "Curve registration (time warping)", "topics": [ "registerCurves" ] }, { "page": "registerOperation", "title": "Register and dispatch named operations", "concept": [ "plugin-api" ], "topics": [ "availableOperations", "getOperation", "registerOperation", "unregisterOperation" ] }, { "page": "registerReader", "title": "Register and dispatch file readers", "concept": [ "plugin-api" ], "topics": [ "availableReaders", "getReader", "registerReader", "unregisterReader" ] }, { "page": "registerWriter", "title": "Register and dispatch file writers", "concept": [ "plugin-api" ], "topics": [ "availableWriters", "getWriter", "registerWriter", "unregisterWriter" ] }, { "page": "removeEvents", "title": "Remove events from a PhysioExperiment object", "topics": [ "removeEvents" ] }, { "page": "renameChannels", "title": "Rename channels", "topics": [ "renameChannels" ] }, { "page": "replaceNA", "title": "Replace NA values in assay", "topics": [ "replaceNA" ] }, { "page": "resampleToCommon", "title": "Resample all streams onto a single common-rate view", "topics": [ "resampleToCommon" ] }, { "page": "resolveQuery", "title": "Resolve an EventQuery to get filtered events", "topics": [ "resolveQuery" ] }, { "page": "samplesToTime", "title": "Convert sample indices to times", "topics": [ "samplesToTime" ] }, { "page": "samplingRate", "title": "Accessors for PhysioExperiment", "topics": [ "samplingRate", "samplingRate,PhysioExperiment-method", "samplingRate<-", "samplingRate<-,PhysioExperiment-method" ] }, { "page": "scale_color_physio", "title": "Colorblind-safe discrete colour / fill scales for ggplot2", "topics": [ "scale_color_physio", "scale_colour_physio", "scale_fill_physio" ] }, { "page": "sem", "title": "Standard Error of Measurement (SEM)", "topics": [ "sem" ] }, { "page": "session", "title": "Retrieve a single session by visit label or id", "topics": [ "session" ] }, { "page": "sessions", "title": "Access the sessions of a PhysioLongitudinal", "topics": [ "sessions", "sessions,PhysioLongitudinal-method", "sessions<-", "sessions<-,PhysioLongitudinal-method" ] }, { "page": "setAssaySamplingRate", "title": "Set the sampling rate of a specific assay", "topics": [ "setAssaySamplingRate" ] }, { "page": "setChannelTypes", "title": "Set channel types", "topics": [ "setChannelTypes" ] }, { "page": "setChannelUnits", "title": "Set channel units", "topics": [ "setChannelUnits" ] }, { "page": "setElectrodePositions", "title": "Set electrode positions", "topics": [ "setElectrodePositions" ] }, { "page": "setEvents", "title": "Set events for a PhysioExperiment object", "topics": [ "setEvents" ] }, { "page": "setReference", "title": "Set reference electrode", "topics": [ "setReference" ] }, { "page": "show-PhysioEvents-method", "title": "Show method for PhysioEvents", "topics": [ "show,PhysioEvents-method" ] }, { "page": "show-PhysioExperiment-method", "title": "S4 Methods for PhysioExperiment", "topics": [ "show,PhysioExperiment-method" ] }, { "page": "streamCoverage", "title": "Coverage of a time span by a stream's samples", "topics": [ "streamCoverage" ] }, { "page": "streamNames", "title": "Names of the streams", "topics": [ "streamNames" ] }, { "page": "streamRates", "title": "Per-stream sampling rates", "topics": [ "streamRates" ] }, { "page": "streams", "title": "Access the streams of a MultiPhysioExperiment", "topics": [ "streams", "streams,MultiPhysioExperiment-method", "streams<-", "streams<-,MultiPhysioExperiment-method" ] }, { "page": "streamTimeIndex", "title": "Sample times of a stream on the shared clock", "topics": [ "streamTimeIndex" ] }, { "page": "subject", "title": "Retrieve a single subject's longitudinal record by id", "topics": [ "subject" ] }, { "page": "subjectData", "title": "Subject-level metadata", "topics": [ "subjectData", "subjectData,PhysioLongitudinal-method", "subjectData<-", "subjectData<-,PhysioLongitudinal-method" ] }, { "page": "subjectIds", "title": "Subject ids, subject count and group labels of a PhysioCohort", "topics": [ "groups", "nSubjects", "subjectIds" ] }, { "page": "subjects", "title": "Subjects of a PhysioCohort", "topics": [ "subjects", "subjects,PhysioCohort-method", "subjects<-", "subjects<-,PhysioCohort-method" ] }, { "page": "subjectTrials", "title": "Every trial of one subject, across sessions", "topics": [ "subjectTrials" ] }, { "page": "subsetCohort", "title": "Subset a PhysioCohort by group (or a predicate on colData)", "topics": [ "subsetCohort" ] }, { "page": "summary-PhysioExperiment-method", "title": "Summary statistics for PhysioExperiment", "topics": [ "summary,PhysioExperiment-method" ] }, { "page": "theme_physio", "title": "A clean, accessible ggplot2 theme for x-biosignal figures", "topics": [ "theme_physio" ] }, { "page": "timeIndex", "title": "Time index helper", "topics": [ "timeIndex" ] }, { "page": "timeToSamples", "title": "Convert event times to sample indices", "topics": [ "timeToSamples" ] }, { "page": "timeWindow", "title": "Select a time window across all streams", "topics": [ "timeWindow" ] }, { "page": "trial", "title": "Extract one trial", "topics": [ "trial" ] }, { "page": "trialCoverage", "title": "Coverage of one trial across every stream it names", "topics": [ "trialCoverage" ] }, { "page": "trialIntervals", "title": "Trial intervals on a stream", "topics": [ "trialIntervals", "trialIntervals<-" ] }, { "page": "trials", "title": "Trials recorded in a container", "topics": [ "trials", "trials<-" ] }, { "page": "trialSet", "title": "Hold several independently recorded trials together", "topics": [ "trialSet" ] }, { "page": "watsonWilliamsTest", "title": "Watson-Williams test for equal mean directions", "topics": [ "watsonWilliamsTest" ] }, { "page": "waveformCMC", "title": "Coefficient of multiple correlation for repeated waveforms (Kadaba CMC)", "topics": [ "waveformCMC" ] }, { "page": "waveformICC", "title": "Pointwise intraclass correlation across the movement cycle", "topics": [ "waveformICC" ] }, { "page": "waveformReliability", "title": "Waveform reliability report: CMC, ICC / SEM / MDC curves", "topics": [ "waveformReliability" ] }, { "page": "withProvenance", "title": "Carry a provenance log onto a derived object and record a step", "topics": [ "withProvenance" ] }, { "page": "wpliEstimate", "title": "Weighted phase-lag index estimator (raw and debiased)", "topics": [ "wpliEstimate" ] } ], "_readme": "https://github.com/x-biosignal/PhysioExperiment/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "DelayedArray", "digest", "generics", "GenomicRanges", "IRanges", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "event-handling.Rmd", "filename": "event-handling.html", "title": "Event Handling in PhysioExperiment", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The PhysioEvents Class", "Creating Events", "Default Values", "Inspecting Events", "Attaching Events to PhysioExperiment", "Setting Events from a Data Frame", "Retrieving Events", "Adding Events", "Removing Events", "Time and Sample Conversion", "Working with Event Windows", "Events and Time Concatenation", "Summary", "Session Info" ], "created": "2026-10-03 13:11:53", "modified": "2026-10-03 13:11:53", "commits": 1 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting Started with PhysioExperiment", "author": "Yusuke Matsui", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Creating a PhysioExperiment", "Multiple Assays", "Accessing Basic Properties", "Sampling Rate", "Dimensions and Duration", "Default Assay", "Channel Management", "Reading Channel Information", "Setting Channel Properties", "Subsetting Channels", "Reference Electrode", "Subsetting and Combining", "Time-based Subsetting", "Combining Objects", "Summary Statistics", "NA Handling", "Next Steps", "Session Info" ], "created": "2026-10-03 13:11:53", "modified": "2026-10-03 13:11:53", "commits": 1 } ], "_score": 4.819543935541869, "_indexed": true, "_nocasepkg": "physioexperiment", "_universes": [ "x-biosignal", "ymatts" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.3.1", "date": "2026-10-03T13:44:32.000Z", "distro": "resolute", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/1a6b8a28420b84ecd07f68577c390f04a3edfc914ae8d6ef987807169ffc7e8f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.6.1", "os": "linux", "version": "2.3.1", "date": "2026-10-03T13:44:35.000Z", "distro": "resolute", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/7053237718ff4939fa734648e6f802e0673cfc3c23ad939564fb97938ac476f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.5.3", "os": "mac", "version": "2.3.1", "date": "2026-10-03T13:57:01.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/bb4cf1c296aafbe3d15537249919eb72f4118b73dd9ef3fdfd9a545b50a35958", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.6.1", "os": "mac", "version": "2.3.1", "date": "2026-10-03T13:56:58.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/3c2aff0ca78e28ca2c243dc39ab8c4fd69e0d2d62f0004cbe3f8592bbb0fefa4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.6.0", "os": "wasm", "version": "2.3.1", "date": "2026-10-03T13:44:27.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/dc6083e88206fad0d254987190b9e42a7b058b693b213a98636330b28a180e2c", "status": "success", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.7.0", "os": "win", "version": "2.3.1", "date": "2026-10-03T13:43:41.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/0be7724aeac1811193df4f1e3b15ef9aa38de077f3050fece0062a73fdbde4eb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.5.3", "os": "win", "version": "2.3.1", "date": "2026-10-03T13:44:08.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/a4aa11a93ecdb6ded0782274929316d0a05aec55514ac873e14baba76a7485db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" }, { "r": "4.6.1", "os": "win", "version": "2.3.1", "date": "2026-10-03T13:43:53.000Z", "commit": "e65059e55edbd9bf0568f094cdeb97124805084c", "fileid": "https://r2.ropensci.org/4d05fd213d67f96ee4536197c2f96e4ebca1d4178cb3e44237521a000bf3793a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126851296" } ] }