{
  "_id": "6a1a74cf1d7bb097a09d1974",
  "Package": "PhysioExperiment",
  "Title": "Unified Analysis of Physiological Signals",
  "Version": "1.0.0",
  "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Matsui\",\nrole = c(\"aut\", \"cre\"),\nemail = \"matsui@example.com\")",
  "Description": "A comprehensive R/Bioconductor framework for physiological\nsignal analysis. Provides a unified data model\n(PhysioExperiment class extending SummarizedExperiment) for\nmulti-modal sensor signals (EEG, EMG, ECG, IMU, MoCap).\nIncludes file I/O (EDF, BDF, BrainVision, GDF, HDF5, BIDS, CSV,\nMATLAB), database integration (DuckDB), signal preprocessing\n(filtering, artifact removal, epoching), time-frequency\nanalysis, connectivity analysis, network metrics, statistical\ntesting (SPM1D, permutation tests), and publication-quality\nvisualization.",
  "biocViews": "Software, TimeCourse, Preprocessing",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/matsui-lab/PhysioExperiment",
  "BugReports": "https://github.com/matsui-lab/PhysioExperiment/issues",
  "Collate": "'PhysioExperiment-class.R' 'PhysioExperiment-accessors.R'\n'PhysioExperiment-methods.R' 'channels.R' 'events.R'\n'event-query.R' 'utils-signal.R' 'utils-na.R' 'io-readwrite.R'\n'io-edf.R' 'io-brainvision.R' 'io-gdf.R' 'io-hdf5.R'\n'io-bids.R' 'io-csv.R' 'io-matlab.R' 'db-interface.R'\n'db-schema.R' 'ops-filter.R' 'ops-filters-advanced.R'\n'ops-fft.R' 'ops-rereference.R' 'ops-artifact.R' 'ops-epoch.R'\n'ops-epoch-sliding.R' 'ops-resample.R' 'ops-timefreq.R'\n'ops-connectivity.R' 'ops-network.R' 'stats-tests.R'\n'stats-spm.R' 'vis-plot.R' 'vis-multichannel.R' 'vis-topomap.R'\n'vis-network.R' 'gui-launcher.R' 'RcppExports.R' 'zzz.R'",
  "Config/pak/sysreqs": "libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://x-biosignal.r-universe.dev",
  "Date/Publication": "2026-03-16 11:30:50 UTC",
  "RemoteUrl": "https://github.com/x-biosignal/PhysioExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "a6d6c3eca2f1f3d077f194fd0711fe10095e4290",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-28 14:47:43 UTC",
    "User": "root"
  },
  "Author": "Yusuke Matsui [aut, cre]",
  "Maintainer": "Yusuke Matsui <matsui@example.com>",
  "MD5sum": "ba944d7fe00e206ed046a14eb25bbde4",
  "_user": "x-biosignal",
  "_type": "src",
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  "_created": "2026-05-28T14:47:43.000Z",
  "_published": "2026-05-30T05:25:35.408Z",
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  "_host": "GitHub-Actions",
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    "author": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "committer": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "message": "docs: Add comprehensive README\n",
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    "name": "Yusuke Matsui",
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2026-12",
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  "_tags": [],
  "_topics": [
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    "timecourse",
    "preprocessing",
    "openblas",
    "cpp",
    "openmp"
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  "_rbuild": "4.6.0",
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    "extra/citation.json",
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    "extra/contents.json",
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    "extra/NEWS.txt",
    "extra/PhysioExperiment.html",
    "extra/readme.html",
    "extra/readme.md",
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  "_exports": [
    "addEvents",
    "adjacencyMatrix",
    "anovaEpochs",
    "applyMontage",
    "as.data.frame",
    "assaySamplingRates",
    "averageEpochs",
    "bandPower",
    "baselineCorrect",
    "betweennessCentrality",
    "binarizeNetwork",
    "bootstrapCI",
    "butterworthFilter",
    "cbindPhysio",
    "channelInfo",
    "channelInfo<-",
    "channelNames",
    "channelNames<-",
    "checkGUIDependencies",
    "checkNA",
    "classifyICAComponents",
    "cleanData",
    "clusteringCoefficient",
    "clusterPermutationTest",
    "coherence",
    "connectDatabase",
    "connectivityMatrix",
    "correctPValues",
    "correlationMatrix",
    "crossSpectrum",
    "dbStats",
    "decimate",
    "defaultAssay",
    "deleteExperiment",
    "detectArtifacts",
    "detectBadChannels",
    "detrendSignal",
    "disconnectDatabase",
    "dropChannels",
    "duration",
    "effectSize",
    "eigenvectorCentrality",
    "epochData",
    "epochSliding",
    "epochTimes",
    "eventQuery",
    "extractWindow",
    "fftSignals",
    "fillEdgeNA",
    "filterSignals",
    "filterType",
    "filterValue",
    "findSignificantWindows",
    "firFilter",
    "getChannelsByType",
    "getCurrentReference",
    "getElectrodePositions",
    "getEvents",
    "getReference",
    "globalEfficiency",
    "grandAverage",
    "graphLaplacian",
    "handleNA",
    "hasNA",
    "hilbertTransform",
    "icaDecompose",
    "icaRemove",
    "initPhysioSchema",
    "instantaneousAmplitude",
    "instantaneousPhase",
    "interpolate",
    "interpolateBadChannels",
    "isAverageReferenced",
    "isHDF5Backed",
    "launchGUI",
    "listBIDSSessions",
    "listBIDSSubjects",
    "loadExperiment",
    "localEfficiency",
    "modularity",
    "naSummary",
    "nChannels",
    "nEvents",
    "nodeDegree",
    "notchFilter",
    "pathLength",
    "PhysioEvents",
    "PhysioExperiment",
    "pickChannels",
    "pli",
    "plotAdjacencyMatrix",
    "plotDynamicConnectivity",
    "plotERP",
    "plotMultiChannel",
    "plotNetwork",
    "plotNetworkMetrics",
    "plotNetworkStability",
    "plotPSD",
    "plotSignal",
    "plotSpectrogram",
    "plotSPM",
    "plotTopomap",
    "plotTopomapSeries",
    "plv",
    "queryExperiments",
    "rbindPhysio",
    "readBDF",
    "readBIDS",
    "readBrainVision",
    "readCSV",
    "readEDF",
    "readElectrodePositionsCSV",
    "readEventsCSV",
    "readGDF",
    "readMAT",
    "readPhysio",
    "readPhysioHDF5",
    "realizeHDF5",
    "registerExperiment",
    "rejectBadEpochs",
    "removeEvents",
    "renameChannels",
    "replaceNA",
    "rereference",
    "resample",
    "resolveQuery",
    "samplesToTime",
    "samplingRate",
    "samplingRate<-",
    "setAssaySamplingRate",
    "setChannelTypes",
    "setChannelUnits",
    "setElectrodePositions",
    "setEvents",
    "setReference",
    "show",
    "slidingWindowConnectivity",
    "smallWorldness",
    "spectralClustering",
    "spectralDecomposition",
    "spectrogram",
    "spmAnova",
    "spmPairedTTest",
    "spmTTest",
    "startAPIServer",
    "summary",
    "temporalStability",
    "thresholdNetwork",
    "timeIndex",
    "timeToSamples",
    "tTestEpochs",
    "validateBIDS",
    "waveletTransform",
    "wPLI",
    "writeAssayHDF5",
    "writeBDF",
    "writeBIDS",
    "writeBrainVision",
    "writeCSV",
    "writeEDF",
    "writeElectrodePositionsCSV",
    "writeEventsCSV",
    "writeGDF",
    "writeMAT",
    "writePhysio",
    "writePhysioHDF5"
  ],
  "_help": [
    {
      "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": "adjacencyMatrix",
      "title": "Network Analysis for PhysioExperiment",
      "topics": [
        "adjacencyMatrix"
      ]
    },
    {
      "page": "anovaEpochs",
      "title": "ANOVA across conditions",
      "topics": [
        "anovaEpochs"
      ]
    },
    {
      "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": "assaySamplingRates",
      "title": "Get sampling rates for all assays",
      "topics": [
        "assaySamplingRates"
      ]
    },
    {
      "page": "averageEpochs",
      "title": "Average epochs",
      "topics": [
        "averageEpochs"
      ]
    },
    {
      "page": "bandPower",
      "title": "Compute band power",
      "topics": [
        "bandPower"
      ]
    },
    {
      "page": "baselineCorrect",
      "title": "Baseline correction",
      "topics": [
        "baselineCorrect"
      ]
    },
    {
      "page": "betweennessCentrality",
      "title": "Compute betweenness centrality",
      "topics": [
        "betweennessCentrality"
      ]
    },
    {
      "page": "binarizeNetwork",
      "title": "Binarize network",
      "topics": [
        "binarizeNetwork"
      ]
    },
    {
      "page": "bootstrapCI",
      "title": "Bootstrap confidence interval for ERP",
      "topics": [
        "bootstrapCI"
      ]
    },
    {
      "page": "butterworthFilter",
      "title": "Advanced signal filtering functions",
      "topics": [
        "butterworthFilter"
      ]
    },
    {
      "page": "cbindPhysio",
      "title": "Combine PhysioExperiment objects by channels",
      "topics": [
        "cbindPhysio"
      ]
    },
    {
      "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": "checkGUIDependencies",
      "title": "Check GUI Dependencies",
      "topics": [
        "checkGUIDependencies"
      ]
    },
    {
      "page": "checkNA",
      "title": "Check for NA values in assay data",
      "topics": [
        "checkNA"
      ]
    },
    {
      "page": "classifyICAComponents",
      "title": "Classify ICA components as brain or artifact",
      "topics": [
        "classifyICAComponents"
      ]
    },
    {
      "page": "cleanData",
      "title": "Clean data using an artifact removal pipeline",
      "topics": [
        "cleanData"
      ]
    },
    {
      "page": "clusteringCoefficient",
      "title": "Compute clustering coefficient",
      "topics": [
        "clusteringCoefficient"
      ]
    },
    {
      "page": "clusterPermutationTest",
      "title": "Cluster-based permutation test",
      "topics": [
        "clusterPermutationTest"
      ]
    },
    {
      "page": "coherence",
      "title": "Connectivity Analysis for PhysioExperiment",
      "topics": [
        "coherence"
      ]
    },
    {
      "page": "connectDatabase",
      "title": "Lightweight database interface",
      "topics": [
        "connectDatabase",
        "disconnectDatabase"
      ]
    },
    {
      "page": "connectivityMatrix",
      "title": "Compute connectivity matrix for a frequency band",
      "topics": [
        "connectivityMatrix"
      ]
    },
    {
      "page": "correctPValues",
      "title": "Multiple comparison correction",
      "topics": [
        "correctPValues"
      ]
    },
    {
      "page": "correlationMatrix",
      "title": "Compute correlation matrix between channels",
      "topics": [
        "correlationMatrix"
      ]
    },
    {
      "page": "crossSpectrum",
      "title": "Compute cross-spectral density",
      "topics": [
        "crossSpectrum"
      ]
    },
    {
      "page": "dbStats",
      "title": "Get database statistics",
      "topics": [
        "dbStats"
      ]
    },
    {
      "page": "decimate",
      "title": "Decimate signal",
      "topics": [
        "decimate"
      ]
    },
    {
      "page": "defaultAssay",
      "title": "Retrieve the default assay name",
      "topics": [
        "defaultAssay"
      ]
    },
    {
      "page": "deleteExperiment",
      "title": "Delete experiment from database",
      "topics": [
        "deleteExperiment"
      ]
    },
    {
      "page": "detectArtifacts",
      "title": "Detect artifacts in continuous data",
      "topics": [
        "detectArtifacts"
      ]
    },
    {
      "page": "detectBadChannels",
      "title": "Detect bad channels",
      "topics": [
        "detectBadChannels"
      ]
    },
    {
      "page": "detrendSignal",
      "title": "Detrend signal",
      "topics": [
        "detrendSignal"
      ]
    },
    {
      "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": "effectSize",
      "title": "Compute effect size (Cohen's d)",
      "topics": [
        "effectSize"
      ]
    },
    {
      "page": "eigenvectorCentrality",
      "title": "Compute eigenvector centrality",
      "topics": [
        "eigenvectorCentrality"
      ]
    },
    {
      "page": "epochData",
      "title": "Epoching operations for PhysioExperiment",
      "topics": [
        "epochData"
      ]
    },
    {
      "page": "epochSliding",
      "title": "Create epochs using sliding window",
      "topics": [
        "epochSliding"
      ]
    },
    {
      "page": "epochTimes",
      "title": "Get epoch time vector",
      "topics": [
        "epochTimes"
      ]
    },
    {
      "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": "extractWindow",
      "title": "Extract time window",
      "topics": [
        "extractWindow"
      ]
    },
    {
      "page": "fftSignals",
      "title": "Fast Fourier transform helper",
      "topics": [
        "fftSignals"
      ]
    },
    {
      "page": "fillEdgeNA",
      "title": "Fill NA values at edges",
      "topics": [
        "fillEdgeNA"
      ]
    },
    {
      "page": "filterSignals",
      "title": "Moving average filter",
      "topics": [
        "filterSignals"
      ]
    },
    {
      "page": "filterType",
      "title": "Filter events by type",
      "topics": [
        "filterType"
      ]
    },
    {
      "page": "filterValue",
      "title": "Filter events by value",
      "topics": [
        "filterValue"
      ]
    },
    {
      "page": "findSignificantWindows",
      "title": "Find significant time windows",
      "topics": [
        "findSignificantWindows"
      ]
    },
    {
      "page": "firFilter",
      "title": "FIR filter",
      "topics": [
        "firFilter"
      ]
    },
    {
      "page": "getChannelsByType",
      "title": "Get channels by type",
      "topics": [
        "getChannelsByType"
      ]
    },
    {
      "page": "getCurrentReference",
      "title": "Get current reference",
      "topics": [
        "getCurrentReference"
      ]
    },
    {
      "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": "globalEfficiency",
      "title": "Compute global efficiency",
      "topics": [
        "globalEfficiency"
      ]
    },
    {
      "page": "grandAverage",
      "title": "Grand average across subjects/samples",
      "topics": [
        "grandAverage"
      ]
    },
    {
      "page": "graphLaplacian",
      "title": "Compute graph Laplacian",
      "topics": [
        "graphLaplacian"
      ]
    },
    {
      "page": "handleNA",
      "title": "Handle NA values in signal data",
      "topics": [
        "handleNA"
      ]
    },
    {
      "page": "hasNA",
      "title": "Check if data contains any NA values",
      "topics": [
        "hasNA"
      ]
    },
    {
      "page": "hilbertTransform",
      "title": "Hilbert transform for instantaneous amplitude/phase",
      "topics": [
        "hilbertTransform"
      ]
    },
    {
      "page": "icaDecompose",
      "title": "ICA and Artifact Removal for PhysioExperiment",
      "topics": [
        "icaDecompose"
      ]
    },
    {
      "page": "icaRemove",
      "title": "Remove ICA components",
      "topics": [
        "icaRemove"
      ]
    },
    {
      "page": "initPhysioSchema",
      "title": "DuckDB Schema Management for PhysioExperiment",
      "topics": [
        "initPhysioSchema"
      ]
    },
    {
      "page": "instantaneousAmplitude",
      "title": "Extract instantaneous amplitude (envelope)",
      "topics": [
        "instantaneousAmplitude"
      ]
    },
    {
      "page": "instantaneousPhase",
      "title": "Extract instantaneous phase",
      "topics": [
        "instantaneousPhase"
      ]
    },
    {
      "page": "interpolate",
      "title": "Interpolate signal",
      "topics": [
        "interpolate"
      ]
    },
    {
      "page": "interpolateBadChannels",
      "title": "Interpolate bad channels",
      "topics": [
        "interpolateBadChannels"
      ]
    },
    {
      "page": "isAverageReferenced",
      "title": "Check if data is average referenced",
      "topics": [
        "isAverageReferenced"
      ]
    },
    {
      "page": "isHDF5Backed",
      "title": "S4 Methods for PhysioExperiment",
      "topics": [
        "isHDF5Backed"
      ]
    },
    {
      "page": "launchGUI",
      "title": "Launch PhysioExperiment GUI",
      "topics": [
        "launchGUI"
      ]
    },
    {
      "page": "length-PhysioExperiment-method",
      "title": "Length method for PhysioExperiment",
      "topics": [
        "length,PhysioExperiment-method"
      ]
    },
    {
      "page": "listBIDSSessions",
      "title": "List sessions for a subject in BIDS dataset",
      "topics": [
        "listBIDSSessions"
      ]
    },
    {
      "page": "listBIDSSubjects",
      "title": "List subjects in a BIDS dataset",
      "topics": [
        "listBIDSSubjects"
      ]
    },
    {
      "page": "loadExperiment",
      "title": "Load experiment from database",
      "topics": [
        "loadExperiment"
      ]
    },
    {
      "page": "localEfficiency",
      "title": "Compute local efficiency",
      "topics": [
        "localEfficiency"
      ]
    },
    {
      "page": "modularity",
      "title": "Compute network modularity",
      "topics": [
        "modularity"
      ]
    },
    {
      "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": "nodeDegree",
      "title": "Compute node degree",
      "topics": [
        "nodeDegree"
      ]
    },
    {
      "page": "notchFilter",
      "title": "Notch filter (power line noise removal)",
      "topics": [
        "notchFilter"
      ]
    },
    {
      "page": "pathLength",
      "title": "Compute shortest path length",
      "topics": [
        "pathLength"
      ]
    },
    {
      "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": "pickChannels",
      "title": "Pick specific channels",
      "topics": [
        "pickChannels"
      ]
    },
    {
      "page": "pli",
      "title": "Compute Phase Lag Index (PLI)",
      "topics": [
        "pli"
      ]
    },
    {
      "page": "plotAdjacencyMatrix",
      "title": "Plot adjacency matrix heatmap",
      "topics": [
        "plotAdjacencyMatrix"
      ]
    },
    {
      "page": "plotDynamicConnectivity",
      "title": "Plot dynamic connectivity",
      "topics": [
        "plotDynamicConnectivity"
      ]
    },
    {
      "page": "plotERP",
      "title": "Plot event-related potential (ERP) waveform",
      "topics": [
        "plotERP"
      ]
    },
    {
      "page": "plotMultiChannel",
      "title": "Multi-channel visualization functions",
      "topics": [
        "plotMultiChannel"
      ]
    },
    {
      "page": "plotNetwork",
      "title": "Network Visualization for PhysioExperiment",
      "topics": [
        "plotNetwork"
      ]
    },
    {
      "page": "plotNetworkMetrics",
      "title": "Plot network metrics",
      "topics": [
        "plotNetworkMetrics"
      ]
    },
    {
      "page": "plotNetworkStability",
      "title": "Plot network stability over time",
      "topics": [
        "plotNetworkStability"
      ]
    },
    {
      "page": "plotPSD",
      "title": "Plot power spectral density",
      "topics": [
        "plotPSD"
      ]
    },
    {
      "page": "plotSignal",
      "title": "Plot a signal channel",
      "topics": [
        "plotSignal"
      ]
    },
    {
      "page": "plotSpectrogram",
      "title": "Plot spectrogram",
      "topics": [
        "plotSpectrogram"
      ]
    },
    {
      "page": "plotSPM",
      "title": "Plot SPM result",
      "topics": [
        "plotSPM"
      ]
    },
    {
      "page": "plotTopomap",
      "title": "Topographic Map Visualization",
      "topics": [
        "plotTopomap"
      ]
    },
    {
      "page": "plotTopomapSeries",
      "title": "Plot topographic map animation",
      "topics": [
        "plotTopomapSeries"
      ]
    },
    {
      "page": "plv",
      "title": "Compute Phase Locking Value (PLV)",
      "topics": [
        "plv"
      ]
    },
    {
      "page": "print.spm_result",
      "title": "Print SPM result",
      "topics": [
        "print.spm_result"
      ]
    },
    {
      "page": "queryExperiments",
      "title": "Query experiments from database",
      "topics": [
        "queryExperiments"
      ]
    },
    {
      "page": "rbindPhysio",
      "title": "Combine PhysioExperiment objects by time",
      "topics": [
        "rbindPhysio"
      ]
    },
    {
      "page": "readBDF",
      "title": "Read BDF (BioSemi Data Format) file",
      "topics": [
        "readBDF"
      ]
    },
    {
      "page": "readBIDS",
      "title": "BIDS Format Support for PhysioExperiment",
      "topics": [
        "readBIDS"
      ]
    },
    {
      "page": "readBrainVision",
      "title": "BrainVision File Format I/O for PhysioExperiment",
      "topics": [
        "readBrainVision"
      ]
    },
    {
      "page": "readCSV",
      "title": "CSV/TSV I/O for PhysioExperiment",
      "topics": [
        "readCSV"
      ]
    },
    {
      "page": "readEDF",
      "title": "EDF/EDF+ file I/O",
      "topics": [
        "readEDF"
      ]
    },
    {
      "page": "readElectrodePositionsCSV",
      "title": "Read electrode positions from CSV",
      "topics": [
        "readElectrodePositionsCSV"
      ]
    },
    {
      "page": "readEventsCSV",
      "title": "Read events from CSV/TSV file",
      "topics": [
        "readEventsCSV"
      ]
    },
    {
      "page": "readGDF",
      "title": "GDF (General Data Format) File I/O for PhysioExperiment",
      "topics": [
        "readGDF"
      ]
    },
    {
      "page": "readMAT",
      "title": "MATLAB .mat File I/O for PhysioExperiment",
      "topics": [
        "readMAT"
      ]
    },
    {
      "page": "readPhysioHDF5",
      "title": "Read PhysioExperiment from HDF5",
      "topics": [
        "readPhysioHDF5"
      ]
    },
    {
      "page": "realizeHDF5",
      "title": "Realize HDF5-backed data to memory",
      "topics": [
        "realizeHDF5"
      ]
    },
    {
      "page": "registerExperiment",
      "title": "Register a PhysioExperiment in the database",
      "topics": [
        "registerExperiment"
      ]
    },
    {
      "page": "rejectBadEpochs",
      "title": "Reject bad epochs",
      "topics": [
        "rejectBadEpochs"
      ]
    },
    {
      "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": "rereference",
      "title": "Re-referencing Operations for EEG Data",
      "topics": [
        "rereference"
      ]
    },
    {
      "page": "resample",
      "title": "Resampling operations for PhysioExperiment",
      "topics": [
        "resample"
      ]
    },
    {
      "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"
      ]
    },
    {
      "page": "setAssaySamplingRate",
      "title": "Set sampling rate for 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": "Show method for PhysioExperiment",
      "topics": [
        "show,PhysioExperiment-method"
      ]
    },
    {
      "page": "slidingWindowConnectivity",
      "title": "Sliding window connectivity",
      "topics": [
        "slidingWindowConnectivity"
      ]
    },
    {
      "page": "smallWorldness",
      "title": "Compute small-worldness",
      "topics": [
        "smallWorldness"
      ]
    },
    {
      "page": "spectralClustering",
      "title": "Spectral clustering of network nodes",
      "topics": [
        "spectralClustering"
      ]
    },
    {
      "page": "spectralDecomposition",
      "title": "Spectral decomposition of graph Laplacian",
      "topics": [
        "spectralDecomposition"
      ]
    },
    {
      "page": "spectrogram",
      "title": "Time-Frequency Analysis for PhysioExperiment",
      "topics": [
        "spectrogram"
      ]
    },
    {
      "page": "spmAnova",
      "title": "SPM ANOVA (F-test)",
      "topics": [
        "spmAnova"
      ]
    },
    {
      "page": "spmPairedTTest",
      "title": "SPM paired t-test",
      "topics": [
        "spmPairedTTest"
      ]
    },
    {
      "page": "spmTTest",
      "title": "Statistical Parametric Mapping (SPM1D) for Biomechanics",
      "topics": [
        "spmTTest"
      ]
    },
    {
      "page": "startAPIServer",
      "title": "Start PhysioExperiment API Server (Non-blocking)",
      "topics": [
        "startAPIServer"
      ]
    },
    {
      "page": "summary-PhysioExperiment-method",
      "title": "Summary statistics for PhysioExperiment",
      "topics": [
        "summary,PhysioExperiment-method"
      ]
    },
    {
      "page": "temporalStability",
      "title": "Compute temporal stability of network",
      "topics": [
        "temporalStability"
      ]
    },
    {
      "page": "thresholdNetwork",
      "title": "Threshold network by density",
      "topics": [
        "thresholdNetwork"
      ]
    },
    {
      "page": "timeIndex",
      "title": "Time index helper",
      "topics": [
        "timeIndex"
      ]
    },
    {
      "page": "timeToSamples",
      "title": "Convert event times to sample indices",
      "topics": [
        "timeToSamples"
      ]
    },
    {
      "page": "tTestEpochs",
      "title": "Statistical Testing for PhysioExperiment",
      "topics": [
        "tTestEpochs"
      ]
    },
    {
      "page": "validateBIDS",
      "title": "Validate BIDS dataset structure",
      "topics": [
        "validateBIDS"
      ]
    },
    {
      "page": "waveletTransform",
      "title": "Wavelet transform",
      "topics": [
        "waveletTransform"
      ]
    },
    {
      "page": "wPLI",
      "title": "Compute weighted Phase Lag Index (wPLI)",
      "topics": [
        "wPLI"
      ]
    },
    {
      "page": "writeAssayHDF5",
      "title": "Write assay to HDF5 file",
      "topics": [
        "writeAssayHDF5"
      ]
    },
    {
      "page": "writeBDF",
      "title": "Write BDF (BioSemi Data Format) file",
      "topics": [
        "writeBDF"
      ]
    },
    {
      "page": "writeBIDS",
      "title": "Write PhysioExperiment to BIDS format",
      "topics": [
        "writeBIDS"
      ]
    },
    {
      "page": "writeBrainVision",
      "title": "Write PhysioExperiment to BrainVision format",
      "topics": [
        "writeBrainVision"
      ]
    },
    {
      "page": "writeCSV",
      "title": "Write PhysioExperiment to CSV file",
      "topics": [
        "writeCSV"
      ]
    },
    {
      "page": "writeEDF",
      "title": "Write EDF file",
      "topics": [
        "writeEDF"
      ]
    },
    {
      "page": "writeElectrodePositionsCSV",
      "title": "Write electrode positions to CSV",
      "topics": [
        "writeElectrodePositionsCSV"
      ]
    },
    {
      "page": "writeEventsCSV",
      "title": "Write events to CSV file",
      "topics": [
        "writeEventsCSV"
      ]
    },
    {
      "page": "writeGDF",
      "title": "Write PhysioExperiment to GDF format",
      "topics": [
        "writeGDF"
      ]
    },
    {
      "page": "writeMAT",
      "title": "Write PhysioExperiment to MATLAB .mat file",
      "topics": [
        "writeMAT"
      ]
    },
    {
      "page": "writePhysio",
      "title": "Basic read/write helpers",
      "topics": [
        "readPhysio",
        "writePhysio"
      ]
    },
    {
      "page": "writePhysioHDF5",
      "title": "HDF5 Backend for PhysioExperiment",
      "topics": [
        "writePhysioHDF5"
      ]
    }
  ],
  "_readme": "https://github.com/x-biosignal/PhysioExperiment/raw/HEAD/README.md",
  "_rundeps": [
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      "source": "intro.Rmd",
      "filename": "intro.html",
      "title": "Getting Started with PhysioExperiment",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Overview",
        "2. Installation",
        "3. Creating a PhysioExperiment",
        "3.1 From scratch",
        "3.2 From a CSV file",
        "3.3 Adding events",
        "4. Exploring the Object",
        "4.1 Printing and dimensions",
        "4.2 Accessing the sampling rate",
        "4.3 Channel information",
        "4.4 Assay access",
        "4.5 Subsetting",
        "5. Signal Processing",
        "5.1 Butterworth filtering",
        "5.2 Notch filter",
        "5.3 FIR filter",
        "5.4 Moving-average filter",
        "5.5 Detrending",
        "5.6 Re-referencing",
        "6. Epoching and Averaging",
        "6.1 Creating epochs",
        "6.2 Baseline correction and artifact rejection",
        "6.3 Averaging epochs",
        "7. Time-Frequency Analysis",
        "7.1 Spectrogram (STFT)",
        "7.2 Wavelet transform",
        "7.3 Band power",
        "7.4 Hilbert transform",
        "7.5 FFT",
        "8. Visualization",
        "8.1 Single-channel trace",
        "8.2 Multi-channel display",
        "8.3 Power spectral density",
        "8.4 Event-related potential (ERP)",
        "8.5 Topographic map",
        "8.6 Spectrogram",
        "9. Statistical Testing",
        "9.1 Pointwise t-test",
        "9.2 ANOVA",
        "9.3 Cluster-based permutation test",
        "9.4 Multiple comparison correction",
        "9.5 Effect size and confidence intervals",
        "9.6 Finding significant time windows",
        "10. Database Integration",
        "11. Graphical User Interface",
        "Session Information"
      ],
      "created": "2026-03-16 08:31:37",
      "modified": "2026-03-16 08:31:37",
      "commits": 1
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