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  "Package": "PhysioMSKNet",
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  "Title": "Musculoskeletal Network Analysis for Physiological Data",
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  "Author": "Yusuke Matsui",
  "Maintainer": "Yusuke Matsui <matsui@nagoya-u.jp>",
  "Description": "Network science analysis of the human musculoskeletal\nsystem. Implements hypergraph representations of muscle-bone\nconnections, physical simulation via damped harmonic\noscillators, perturbation-based impact scoring, community\ndetection, and clinical outcome prediction. Based on Murphy et\nal. (2018) <doi:10.1371/journal.pbio.2002811>.",
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    "loadMSKData",
    "loadMuscleMetadata",
    "loadValidationData",
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    "mocapNetworkKinematics",
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    "mskAnnotate",
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    "mskCloseness",
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    "mskCommunityProfile",
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    "mskCompensationNetwork",
    "mskCompensationRiskScore",
    "mskCompensationSummary",
    "mskConsensusPartition",
    "mskCoordinationQualityScore",
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    "mskDetectRecoveryPlateau",
    "mskDetectResponderStatus",
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    "mskFunctionalMilestones",
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    "MSKHypergraph",
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    "mskImpactRecoveryModel",
    "mskImpactScore",
    "mskImpactScoreAll",
    "mskInjuryRiskProfile",
    "mskKGSummary",
    "mskLongitudinalTracker",
    "mskMinimalDetectableChange",
    "mskModularity",
    "mskNetworkMetrics",
    "mskNeuralAdaptationIndex",
    "mskNullEnsemble",
    "mskNullHypergraph",
    "mskOutcomeConfidenceInterval",
    "mskOutcomeReport",
    "mskOutcomeSummary",
    "mskPathwayQuery",
    "mskPredictFunctionalOutcome",
    "mskReassess",
    "mskRecoveryTimeline",
    "mskRecoveryTrajectoryFit",
    "mskRehabProtocol",
    "mskReproducePaper",
    "mskRobustRegression",
    "mskShortestPaths",
    "mskSimulate",
    "mskSynergyChangeIndex",
    "mskZRand",
    "neuromechCorticomuscularCoupling",
    "neuromechDirectionalCoupling",
    "neuromechElectromechanicalDelay",
    "neuromechIntegratedVulnerability",
    "neuromechJointTorque",
    "neuromechMotorDriveTopography",
    "neuromechMuscleSynergy",
    "neuromechSummary",
    "opensimCompareModels",
    "opensimForceToImpact",
    "opensimNetworkAnalysis",
    "opensimToMSKHypergraph",
    "plotCommunityStructure",
    "plotDegreeDistribution",
    "plotHomunculus",
    "plotImpactVsDegree",
    "plotImpactVsRecovery",
    "plotMSKNetwork",
    "projectBoneGraph",
    "projectMuscleGraph",
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      "page": "degreeDistribution",
      "title": "Degree Distribution",
      "topics": [
        "degreeDistribution"
      ]
    },
    {
      "page": "emgCommunityCompare",
      "title": "Compare EMG and MSK Communities",
      "topics": [
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      ]
    },
    {
      "page": "emgMSKEnrichment",
      "title": "EMG Activation Enrichment by MSK Community",
      "topics": [
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      ]
    },
    {
      "page": "emgStructuralCoherence",
      "title": "Compare EMG Coherence with MSK Structural Connectivity",
      "topics": [
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      ]
    },
    {
      "page": "emgToMSKMapping",
      "title": "Map EMG Channels to MSK Muscles",
      "topics": [
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      ]
    },
    {
      "page": "hyperedgeDegree",
      "title": "Hyperedge (Muscle) Degree",
      "topics": [
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      ]
    },
    {
      "page": "imuCommunityDynamics",
      "title": "IMU-based Community Dynamics",
      "topics": [
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      ]
    },
    {
      "page": "imuImpactPrediction",
      "title": "IMU-based Impact Prediction",
      "topics": [
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      ]
    },
    {
      "page": "imuNetworkKinematics",
      "title": "IMU-based Network Kinematics Analysis",
      "topics": [
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    },
    {
      "page": "imuToMSKMapping",
      "title": "Map IMU Sensor Placements to MSK Bones",
      "topics": [
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      ]
    },
    {
      "page": "loadIncidenceMatrix",
      "title": "Load Incidence Matrix",
      "topics": [
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      ]
    },
    {
      "page": "loadMSKData",
      "title": "Load MSK Network Data",
      "topics": [
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    },
    {
      "page": "loadMuscleMetadata",
      "title": "Load Muscle Metadata",
      "topics": [
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      ]
    },
    {
      "page": "loadValidationData",
      "title": "Load Validation Data",
      "topics": [
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      ]
    },
    {
      "page": "mocapCommunityDynamics",
      "title": "Within vs Between Community Movement Synchrony",
      "topics": [
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      ]
    },
    {
      "page": "mocapImpactPrediction",
      "title": "Kinematic Stress-based Impact Prediction",
      "topics": [
        "mocapImpactPrediction"
      ]
    },
    {
      "page": "mocapNetworkKinematics",
      "title": "Compute Kinematic Coupling vs MSK Structure",
      "topics": [
        "mocapNetworkKinematics"
      ]
    },
    {
      "page": "mocapToMSKMapping",
      "title": "Map MoCap Segments to MSK Bones",
      "topics": [
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      ]
    },
    {
      "page": "mskAdaptProtocol",
      "title": "Adapt Rehabilitation Protocol Based on Reassessment",
      "topics": [
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      ]
    },
    {
      "page": "mskAnnotate",
      "title": "Annotate MSK Hypergraph with Knowledge Graph Data",
      "topics": [
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      ]
    },
    {
      "page": "mskBetweenness",
      "title": "Betweenness Centrality via BFS",
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    },
    {
      "page": "mskClinicalEvidence",
      "title": "Map Injured Muscles to Clinical Codes and Evidence",
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    },
    {
      "page": "mskClinicalPredictor",
      "title": "Clinical Prediction from MSK Network Topology",
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    },
    {
      "page": "mskCloseness",
      "title": "Closeness Centrality",
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    },
    {
      "page": "mskCommunityDetect",
      "title": "Community Detection on MSK Network",
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      ]
    },
    {
      "page": "mskCommunityProfile",
      "title": "Profile a MSK Community's Functional Characteristics",
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      ]
    },
    {
      "page": "mskCompensationEvolution",
      "title": "Track Compensation Pattern Evolution Over Time",
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    },
    {
      "page": "mskCompensationNetwork",
      "title": "Build Compensation Network",
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      ]
    },
    {
      "page": "mskCompensationRiskScore",
      "title": "Compensation Risk Score",
      "topics": [
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      ]
    },
    {
      "page": "mskCompensationSummary",
      "title": "Comprehensive Compensation Analysis Summary",
      "topics": [
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      ]
    },
    {
      "page": "mskConsensusPartition",
      "title": "Consensus Partition",
      "topics": [
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      ]
    },
    {
      "page": "mskCoordinationQualityScore",
      "title": "Compute Coordination Quality Score",
      "topics": [
        "mskCoordinationQualityScore"
      ]
    },
    {
      "page": "mskDetectCompensation",
      "title": "Detect Compensatory Activation Patterns",
      "topics": [
        "mskDetectCompensation"
      ]
    },
    {
      "page": "mskDetectRecoveryPlateau",
      "title": "Detect Recovery Plateau in Longitudinal Data",
      "topics": [
        "mskDetectRecoveryPlateau"
      ]
    },
    {
      "page": "mskDetectResponderStatus",
      "title": "Classify Muscles as Responders, Non-Responders, or Deteriorated",
      "topics": [
        "mskDetectResponderStatus"
      ]
    },
    {
      "page": "mskEnrichKG",
      "title": "Functional Enrichment of Muscles via Knowledge Graph",
      "topics": [
        "mskEnrichKG"
      ]
    },
    {
      "page": "mskFunctionalMilestones",
      "title": "Generate Functional Milestones for Rehabilitation",
      "topics": [
        "mskFunctionalMilestones"
      ]
    },
    {
      "page": "mskHomuncCorrelation",
      "title": "Homunculus Correlation Analysis",
      "topics": [
        "mskHomuncCorrelation"
      ]
    },
    {
      "page": "MSKHypergraph",
      "title": "Create MSK Hypergraph Object",
      "topics": [
        "MSKHypergraph"
      ]
    },
    {
      "page": "mskImpactDeviation",
      "title": "Compute Impact Deviation",
      "topics": [
        "mskImpactDeviation"
      ]
    },
    {
      "page": "mskImpactRecoveryModel",
      "title": "Impact-Recovery Prediction Model",
      "topics": [
        "mskImpactRecoveryModel"
      ]
    },
    {
      "page": "mskImpactScore",
      "title": "Compute Impact Score for One Muscle",
      "topics": [
        "mskImpactScore"
      ]
    },
    {
      "page": "mskImpactScoreAll",
      "title": "Compute Impact Scores for All Muscles",
      "topics": [
        "mskImpactScoreAll"
      ]
    },
    {
      "page": "mskInjuryRiskProfile",
      "title": "Patient-specific Injury Risk Profile",
      "topics": [
        "mskInjuryRiskProfile"
      ]
    },
    {
      "page": "mskKGSummary",
      "title": "KG-Enriched Summary of MSK Network",
      "topics": [
        "mskKGSummary"
      ]
    },
    {
      "page": "mskLongitudinalTracker",
      "title": "Track Longitudinal MSK Metrics Across Timepoints",
      "topics": [
        "mskLongitudinalTracker"
      ]
    },
    {
      "page": "mskMinimalDetectableChange",
      "title": "Compute Minimal Detectable Change from Longitudinal Tracker",
      "topics": [
        "mskMinimalDetectableChange"
      ]
    },
    {
      "page": "mskModularity",
      "title": "Compute Modularity",
      "topics": [
        "mskModularity"
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    },
    {
      "page": "mskNetworkMetrics",
      "title": "MSK Network Metrics",
      "topics": [
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    },
    {
      "page": "mskNeuralAdaptationIndex",
      "title": "Compute Neural Adaptation Index Across Timepoints",
      "topics": [
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    },
    {
      "page": "mskNullEnsemble",
      "title": "Generate Null Hypergraph Ensemble",
      "topics": [
        "mskNullEnsemble"
      ]
    },
    {
      "page": "mskNullHypergraph",
      "title": "Generate Null Hypergraph",
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    },
    {
      "page": "mskOutcomeConfidenceInterval",
      "title": "Confidence Intervals for Outcome Predictions",
      "topics": [
        "mskOutcomeConfidenceInterval"
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    },
    {
      "page": "mskOutcomeReport",
      "title": "Comprehensive Outcome Report",
      "topics": [
        "mskOutcomeReport"
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    },
    {
      "page": "mskOutcomeSummary",
      "title": "MSK Outcome Summary Report",
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    },
    {
      "page": "mskPathwayQuery",
      "title": "Query Anatomical Pathway Between Entities",
      "topics": [
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    },
    {
      "page": "mskPredictFunctionalOutcome",
      "title": "Predict Functional Outcome from MSK Network Analysis",
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    },
    {
      "page": "mskReassess",
      "title": "Reassess Patient Progress",
      "topics": [
        "mskReassess"
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    },
    {
      "page": "mskRecoveryTimeline",
      "title": "Recovery Timeline with Phase Assignment",
      "topics": [
        "mskRecoveryTimeline"
      ]
    },
    {
      "page": "mskRecoveryTrajectoryFit",
      "title": "Fit Recovery Trajectory to Longitudinal Activation Data",
      "topics": [
        "mskRecoveryTrajectoryFit"
      ]
    },
    {
      "page": "mskRehabProtocol",
      "title": "Rehabilitation Protocol Based on Network Topology",
      "topics": [
        "mskRehabProtocol"
      ]
    },
    {
      "page": "mskReproducePaper",
      "title": "Reproduce Paper Results",
      "topics": [
        "mskReproducePaper"
      ]
    },
    {
      "page": "mskRobustRegression",
      "title": "Robust Regression for MSK Data",
      "topics": [
        "mskRobustRegression"
      ]
    },
    {
      "page": "mskShortestPaths",
      "title": "Shortest Path Distances",
      "topics": [
        "mskShortestPaths"
      ]
    },
    {
      "page": "mskSimulate",
      "title": "Simulate MSK Network Dynamics",
      "topics": [
        "mskSimulate"
      ]
    },
    {
      "page": "mskSynergyChangeIndex",
      "title": "Compute Synergy Change Index Between Two Timepoints",
      "topics": [
        "mskSynergyChangeIndex"
      ]
    },
    {
      "page": "mskZRand",
      "title": "Adjusted Rand Index (z-score)",
      "topics": [
        "mskZRand"
      ]
    },
    {
      "page": "neuromechCorticomuscularCoupling",
      "title": "Corticomuscular Coherence in MSK Network Context",
      "topics": [
        "neuromechCorticomuscularCoupling"
      ]
    },
    {
      "page": "neuromechDirectionalCoupling",
      "title": "Directional Cortico-Muscular Coupling",
      "topics": [
        "neuromechDirectionalCoupling"
      ]
    },
    {
      "page": "neuromechElectromechanicalDelay",
      "title": "Electromechanical Delay via Cross-Correlation",
      "topics": [
        "neuromechElectromechanicalDelay"
      ]
    },
    {
      "page": "neuromechIntegratedVulnerability",
      "title": "Integrated Neuromechanical Vulnerability",
      "topics": [
        "neuromechIntegratedVulnerability"
      ]
    },
    {
      "page": "neuromechJointTorque",
      "title": "Joint Torque Modeling in MSK Context",
      "topics": [
        "neuromechJointTorque"
      ]
    },
    {
      "page": "neuromechMotorDriveTopography",
      "title": "Motor Drive Topography",
      "topics": [
        "neuromechMotorDriveTopography"
      ]
    },
    {
      "page": "neuromechMuscleSynergy",
      "title": "Muscle Synergy Decomposition in MSK Context",
      "topics": [
        "neuromechMuscleSynergy"
      ]
    },
    {
      "page": "neuromechSummary",
      "title": "Neuromechanics Summary",
      "topics": [
        "neuromechSummary"
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    },
    {
      "page": "opensimCompareModels",
      "title": "Compare Multiple OpenSim Models",
      "topics": [
        "opensimCompareModels"
      ]
    },
    {
      "page": "opensimForceToImpact",
      "title": "OpenSim Force-weighted Impact Analysis",
      "topics": [
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    },
    {
      "page": "opensimNetworkAnalysis",
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