{
  "_id": "6ac10b78552a13804ac7ed0c",
  "Package": "PhysioCrossModal",
  "Title": "Cross-Modal Coupling Analysis for PhysioExperiment Objects",
  "Version": "0.8.4",
  "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Matsui\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mail.to.matsui@gmail.com\")",
  "Description": "Provides cross-modal coupling, connectivity, and synchrony\nanalysis between physiological signals of different modalities\n(EEG, EMG, ECG, EDA, MoCap, fNIRS, etc.). Introduces a\nMultiPhysioExperiment container class for holding multiple\nPhysioExperiment objects at different sampling rates with\ntemporal alignment. Includes spectral coherence, phase\nsynchrony (PLV, PLI, wPLI), directed coupling (Granger\ncausality), and time-domain coupling (cross-correlation)\nmethods.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Collate": "'PhysioCrossModal-package.R' 'reexports.R'\n'MultiPhysioExperiment-class.R'\n'MultiPhysioExperiment-methods.R' 'utils-spectral.R'\n'align-elastic.R' 'align-signals.R' 'coupling-spectral.R'\n'coupling-phase.R' 'granger-nonparametric.R'\n'coupling-directed.R' 'coupling-pac.R' 'coupling-frontier.R'\n'coupling-leida-metrics.R' 'coupling-timedom.R'\n'coupling-wavelet.R' 'coupling-xwt.R' 'coupling-wrapper.R'\n'coupling-matrix.R' 'stats-significance.R' 'benchmark-lodo.R'\n'crossmodal-data.R' 'vis-coupling.R' 'fusion-multiblock.R'\n'fusion-twoblock.R' 'fusion-coupled.R' 'fusion-association.R'\n'fusion-index.R' 'zzz.R'",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/x-biosignal/PhysioCrossModal,\nhttps://x-biosignal.r-universe.dev/PhysioCrossModal,\nhttps://x-biosignal.github.io/PhysioCrossModal",
  "BugReports": "https://github.com/x-biosignal/PhysioCrossModal/issues",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://x-biosignal.r-universe.dev",
  "Date/Publication": "2026-10-03 13:11:45 UTC",
  "RemoteUrl": "https://github.com/x-biosignal/PhysioCrossModal",
  "RemoteRef": "HEAD",
  "RemoteSha": "98d2b0f224738de11b607e24c889e01bfb7b82da",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 13:42:45 UTC",
    "User": "root"
  },
  "Author": "Yusuke Matsui [aut, cre]",
  "Maintainer": "Yusuke Matsui <mail.to.matsui@gmail.com>",
  "_user": "x-biosignal",
  "_type": "src",
  "_file": "PhysioCrossModal_0.8.4.tar.gz",
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  "_sha256": "853c4a2bf6d45d93d679d636a45203e0eadf1703fdb1bb2d4f25b2ed20ae155c",
  "_expires": "2027-01-11T14:04:37.000Z",
  "_created": "2026-10-03T13:42:45.000Z",
  "_published": "2026-10-03T14:04:39.915Z",
  "_jobs": [
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37126888030",
  "_status": "success",
  "_upstream": "https://github.com/x-biosignal/PhysioCrossModal",
  "_commit": {
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    "author": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "committer": "Yusuke Matsui <mail.to.matsui@gmail.com>",
    "message": "Release snapshot\n",
    "time": 1791033105
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  "_maintainer": {
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    "email": "mail.to.matsui@gmail.com",
    "login": "ymatts",
    "description": "Data scientist",
    "uuid": 5744286
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  "_distro": "resolute",
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  "_dependencies": [
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      "package": "R",
      "version": ">= 4.2",
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    {
      "package": "PhysioExperiment",
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    {
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    {
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      "package": "stats",
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  "_owner": "x-biosignal",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-40",
      "n": 1
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  "_tags": [],
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    "name": "x-biosignal",
    "followers": 1,
    "description": "Open-source R packages for biosignal analysis, biomechanics, clinical research, and rehabilitation."
  },
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  "_devurl": "https://github.com/x-biosignal/physiocrossmodal",
  "_pkgdown": "https://x-biosignal.github.io/PhysioCrossModal",
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.json",
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    "extra/contents.json",
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  ],
  "_cranurl": false,
  "_exports": [
    "alignment",
    "alignment<-",
    "alignObservationBlocks",
    "alignSignals",
    "alignToRate",
    "bootstrapCI",
    "cca",
    "ciPLV",
    "coherence",
    "coherenceMatrix",
    "commonClock",
    "comodulogram",
    "coupledNMF",
    "couplingAnalysis",
    "couplingAnalysisCached",
    "couplingMatrix",
    "couplingResults",
    "couplingResults<-",
    "crossBlockFactor",
    "crossCorrelation",
    "crossSpectrum",
    "crossWaveletTransform",
    "directedTransferFunction",
    "distanceCorrelation",
    "elasticAlign",
    "experiments",
    "experiments<-",
    "fuseBlocks",
    "grangerCausality",
    "jive",
    "laggedCoherence",
    "leidaStates",
    "leidaTransitions",
    "lodoGeneralization",
    "make_coupled_signals",
    "make_directed_signals",
    "make_eeg_emg",
    "mergePhysio",
    "modalities",
    "modulationIndex",
    "multimodalGaitIndex",
    "MultiPhysioExperiment",
    "multipleFactorAnalysis",
    "multitaperCoherence",
    "mutualInformation",
    "nModalities",
    "orthogonalizedAEC",
    "pairwisePhaseConsistency",
    "partialDirectedCoherence",
    "phaseAmplitudeCoupling",
    "phaseLagIndex",
    "phaseLockingValue",
    "phaseSlopeIndex",
    "plotCoherenceSpectrum",
    "plotComodulogram",
    "plotCouplingMatrix",
    "plotCouplingTimecourse",
    "plotWaveletCoherence",
    "plsBlocks",
    "representationalSimilarity",
    "rvCoefficient",
    "samplingRates",
    "slidingCrossCorrelation",
    "srvfMean",
    "streams",
    "surrogateMatrixTest",
    "surrogateTest",
    "timeWindow",
    "transferEntropy",
    "warpApply",
    "waveletCoherence",
    "waveletPLV",
    "weightedPLI"
  ],
  "_help": [
    {
      "page": "alignObservationBlocks",
      "title": "Align feature blocks using explicit observation keys",
      "topics": [
        "alignObservationBlocks"
      ]
    },
    {
      "page": "alignSignals",
      "title": "Align multiple PhysioExperiment objects to a common sampling rate",
      "topics": [
        "alignSignals"
      ]
    },
    {
      "page": "alignToRate",
      "title": "Resample a PhysioExperiment to a target sampling rate",
      "topics": [
        "alignToRate"
      ]
    },
    {
      "page": "bootstrapCI",
      "title": "Bootstrap confidence interval for coupling",
      "topics": [
        "bootstrapCI"
      ]
    },
    {
      "page": "cca",
      "title": "Canonical correlation analysis between two modalities",
      "topics": [
        "cca"
      ]
    },
    {
      "page": "ciPLV",
      "title": "Corrected imaginary phase-locking value (ciPLV)",
      "topics": [
        "ciPLV"
      ]
    },
    {
      "page": "coherence",
      "title": "Magnitude-squared coherence between two signals",
      "topics": [
        "coherence"
      ]
    },
    {
      "page": "coherenceMatrix",
      "title": "Coherence matrix across channel pairs",
      "topics": [
        "coherenceMatrix"
      ]
    },
    {
      "page": "comodulogram",
      "title": "Comodulogram (phase-frequency by amplitude-frequency PAC)",
      "topics": [
        "comodulogram"
      ]
    },
    {
      "page": "coupledNMF",
      "title": "Coupled non-negative matrix factorization across two modalities",
      "topics": [
        "coupledNMF"
      ]
    },
    {
      "page": "couplingAnalysis",
      "title": "Unified interface for cross-modal coupling analysis",
      "topics": [
        "couplingAnalysis"
      ]
    },
    {
      "page": "couplingAnalysisCached",
      "title": "Cached coupling analysis over a MultiPhysioExperiment",
      "topics": [
        "couplingAnalysisCached"
      ]
    },
    {
      "page": "couplingMatrix",
      "title": "Generic coupling matrix across channel pairs",
      "topics": [
        "couplingMatrix"
      ]
    },
    {
      "page": "couplingResults",
      "title": "Cached coupling results for a container",
      "topics": [
        "couplingResults",
        "couplingResults,MultiPhysioExperiment-method",
        "couplingResults<-",
        "couplingResults<-,MultiPhysioExperiment-method"
      ]
    },
    {
      "page": "crossBlockFactor",
      "title": "Cross-block common-factor model",
      "topics": [
        "crossBlockFactor"
      ]
    },
    {
      "page": "crossCorrelation",
      "title": "Cross-correlation between two signals",
      "topics": [
        "crossCorrelation"
      ]
    },
    {
      "page": "crossSpectrum",
      "title": "Cross-spectral density between two signals",
      "topics": [
        "crossSpectrum"
      ]
    },
    {
      "page": "crossWaveletTransform",
      "title": "Cross-wavelet transform (XWT) with red-noise significance",
      "topics": [
        "crossWaveletTransform"
      ]
    },
    {
      "page": "directedTransferFunction",
      "title": "Directed Transfer Function for multichannel / multimodal signals",
      "topics": [
        "directedTransferFunction"
      ]
    },
    {
      "page": "distanceCorrelation",
      "title": "Distance correlation between two modality blocks",
      "topics": [
        "distanceCorrelation"
      ]
    },
    {
      "page": "elasticAlign",
      "title": "Elastic (SRVF) alignment of two curves",
      "topics": [
        "elasticAlign"
      ]
    },
    {
      "page": "fuseBlocks",
      "title": "Feature-level fusion of modality blocks",
      "topics": [
        "fuseBlocks"
      ]
    },
    {
      "page": "grangerCausality",
      "title": "Granger Causality Between Two Signals",
      "topics": [
        "grangerCausality"
      ]
    },
    {
      "page": "jive",
      "title": "JIVE: Joint and Individual Variation Explained",
      "topics": [
        "jive"
      ]
    },
    {
      "page": "laggedCoherence",
      "title": "Lagged coherence between two signals",
      "topics": [
        "laggedCoherence"
      ]
    },
    {
      "page": "leidaStates",
      "title": "LEiDA dynamic functional-connectivity states",
      "topics": [
        "leidaStates"
      ]
    },
    {
      "page": "leidaTransitions",
      "title": "LEiDA state-transition metrics",
      "topics": [
        "leidaTransitions"
      ]
    },
    {
      "page": "lodoGeneralization",
      "title": "Leave-one-site-out generalization benchmark",
      "topics": [
        "lodoGeneralization"
      ]
    },
    {
      "page": "make_coupled_signals",
      "title": "Generate coupled sinusoidal signals",
      "topics": [
        "make_coupled_signals"
      ]
    },
    {
      "page": "make_directed_signals",
      "title": "Generate directed coupling signals",
      "topics": [
        "make_directed_signals"
      ]
    },
    {
      "page": "make_eeg_emg",
      "title": "Generate simulated EEG-EMG PhysioExperiment pair",
      "topics": [
        "make_eeg_emg"
      ]
    },
    {
      "page": "mergePhysio",
      "title": "Merge two PhysioExperiment objects by combining channels",
      "topics": [
        "mergePhysio"
      ]
    },
    {
      "page": "modulationIndex",
      "title": "Modulation-index comodulogram with surrogate inference",
      "topics": [
        "modulationIndex"
      ]
    },
    {
      "page": "multimodalGaitIndex",
      "title": "Composite multi-modal gait deviation index",
      "topics": [
        "multimodalGaitIndex"
      ]
    },
    {
      "page": "MultiPhysioExperiment-crossmodal",
      "title": "The multimodal container",
      "topics": [
        "MultiPhysioExperiment-crossmodal"
      ]
    },
    {
      "page": "MultiPhysioExperiment-crossmodal-methods",
      "title": "Methods on the multimodal container",
      "topics": [
        "MultiPhysioExperiment-crossmodal-methods"
      ]
    },
    {
      "page": "multipleFactorAnalysis",
      "title": "Multiple Factor Analysis (multi-block PCA)",
      "topics": [
        "multipleFactorAnalysis"
      ]
    },
    {
      "page": "multitaperCoherence",
      "title": "Multitaper coherence",
      "topics": [
        "multitaperCoherence"
      ]
    },
    {
      "page": "mutualInformation",
      "title": "Mutual Information (histogram estimator)",
      "topics": [
        "mutualInformation"
      ]
    },
    {
      "page": "orthogonalizedAEC",
      "title": "Orthogonalised amplitude-envelope correlation (leakage-corrected)",
      "topics": [
        "orthogonalizedAEC"
      ]
    },
    {
      "page": "pairwisePhaseConsistency",
      "title": "Pairwise phase consistency (PPC)",
      "topics": [
        "pairwisePhaseConsistency"
      ]
    },
    {
      "page": "partialDirectedCoherence",
      "title": "Partial Directed Coherence for multichannel / multimodal signals",
      "topics": [
        "partialDirectedCoherence"
      ]
    },
    {
      "page": "phaseAmplitudeCoupling",
      "title": "Phase-amplitude coupling",
      "topics": [
        "phaseAmplitudeCoupling"
      ]
    },
    {
      "page": "phaseLagIndex",
      "title": "Phase Lag Index (PLI)",
      "topics": [
        "phaseLagIndex"
      ]
    },
    {
      "page": "phaseLockingValue",
      "title": "Phase Locking Value (PLV)",
      "topics": [
        "phaseLockingValue"
      ]
    },
    {
      "page": "phaseSlopeIndex",
      "title": "Phase Slope Index (directed, volume-conduction robust)",
      "topics": [
        "phaseSlopeIndex"
      ]
    },
    {
      "page": "plotCoherenceSpectrum",
      "title": "Plot coherence spectrum",
      "topics": [
        "plotCoherenceSpectrum"
      ]
    },
    {
      "page": "plotComodulogram",
      "title": "Plot a comodulogram",
      "topics": [
        "plotComodulogram"
      ]
    },
    {
      "page": "plotCouplingMatrix",
      "title": "Plot a coupling matrix as a heatmap",
      "topics": [
        "plotCouplingMatrix"
      ]
    },
    {
      "page": "plotCouplingTimecourse",
      "title": "Plot time-varying coupling from sliding-window analysis",
      "topics": [
        "plotCouplingTimecourse"
      ]
    },
    {
      "page": "plotWaveletCoherence",
      "title": "Plot wavelet coherence time-frequency map",
      "topics": [
        "plotWaveletCoherence"
      ]
    },
    {
      "page": "plsBlocks",
      "title": "Two-block partial least squares (PLS-SVD)",
      "topics": [
        "plsBlocks"
      ]
    },
    {
      "page": "representationalSimilarity",
      "title": "Representational similarity across modalities (RSA)",
      "topics": [
        "representationalSimilarity"
      ]
    },
    {
      "page": "rvCoefficient",
      "title": "RV coefficient between two modality blocks",
      "topics": [
        "rvCoefficient"
      ]
    },
    {
      "page": "slidingCrossCorrelation",
      "title": "Sliding-window cross-correlation",
      "topics": [
        "slidingCrossCorrelation"
      ]
    },
    {
      "page": "srvfMean",
      "title": "Elastic (Karcher) mean of a set of curves",
      "topics": [
        "srvfMean"
      ]
    },
    {
      "page": "surrogateMatrixTest",
      "title": "Surrogate-based significance test for coupling matrices",
      "topics": [
        "surrogateMatrixTest"
      ]
    },
    {
      "page": "surrogateTest",
      "title": "Surrogate-based significance test for coupling",
      "topics": [
        "surrogateTest"
      ]
    },
    {
      "page": "transferEntropy",
      "title": "Transfer entropy (model-free directed information)",
      "topics": [
        "transferEntropy"
      ]
    },
    {
      "page": "warpApply",
      "title": "Apply a computed warping to a companion signal",
      "topics": [
        "warpApply"
      ]
    },
    {
      "page": "waveletCoherence",
      "title": "Time-frequency wavelet coherence",
      "topics": [
        "waveletCoherence"
      ]
    },
    {
      "page": "waveletPLV",
      "title": "Time-frequency wavelet PLV",
      "topics": [
        "waveletPLV"
      ]
    },
    {
      "page": "weightedPLI",
      "title": "Weighted Phase Lag Index (wPLI)",
      "topics": [
        "weightedPLI"
      ]
    }
  ],
  "_readme": "https://github.com/x-biosignal/PhysioCrossModal/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "DelayedArray",
    "digest",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "PhysioExperiment",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "coupling-analysis.Rmd",
      "filename": "coupling-analysis.html",
      "title": "Cross-Modal Coupling Analysis with PhysioCrossModal",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Creating Synthetic Data",
        "The MultiPhysioExperiment Container",
        "Signal Alignment",
        "Spectral Coherence",
        "Welch-Method Coherence",
        "Multitaper Coherence",
        "Cross-Spectral Density",
        "Phase Synchrony",
        "Phase Locking Value (PLV)",
        "Phase Lag Index (PLI)",
        "Weighted PLI (wPLI)",
        "Directed Coupling: Granger Causality",
        "Time-Domain Coupling",
        "Cross-Correlation",
        "Sliding-Window Cross-Correlation",
        "Wavelet Time-Frequency Analysis",
        "Wavelet Coherence",
        "Wavelet PLV",
        "Unified Interface: couplingAnalysis()",
        "Multi-Channel Coupling Matrices",
        "Statistical Significance Testing",
        "Surrogate Testing",
        "Bootstrap Confidence Intervals",
        "Matrix-Level Significance with Multiple Comparison Correction",
        "Complete Workflow Example",
        "Session Information"
      ],
      "created": "2026-10-03 13:11:45",
      "modified": "2026-10-03 13:11:45",
      "commits": 1
    },
    {
      "source": "multimodal-fusion.Rmd",
      "filename": "multimodal-fusion.html",
      "title": "Integrating Modalities: Multi-Modal Fusion with PhysioCrossModal",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The integration problem",
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