Package: PhysioCrossModal 0.8.4

Yusuke Matsui

PhysioCrossModal: Cross-Modal Coupling Analysis for PhysioExperiment Objects

Provides cross-modal coupling, connectivity, and synchrony analysis between physiological signals of different modalities (EEG, EMG, ECG, EDA, MoCap, fNIRS, etc.). Introduces a MultiPhysioExperiment container class for holding multiple PhysioExperiment objects at different sampling rates with temporal alignment. Includes spectral coherence, phase synchrony (PLV, PLI, wPLI), directed coupling (Granger causality), and time-domain coupling (cross-correlation) methods.

Authors:Yusuke Matsui [aut, cre]

PhysioCrossModal_0.8.4.tar.gz
PhysioCrossModal_0.8.4.zip(r-4.7-any)PhysioCrossModal_0.8.4.zip(r-4.6-any)PhysioCrossModal_0.8.4.zip(r-4.5-any)
PhysioCrossModal_0.8.4.tgz(r-4.6-any)PhysioCrossModal_0.8.4.tgz(r-4.5-any)
PhysioCrossModal_0.8.4.tar.gz(r-4.7-any)PhysioCrossModal_0.8.4.tar.gz(r-4.6-any)
PhysioCrossModal_0.8.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioCrossModal/json (API)

# Install 'PhysioCrossModal' in R:
install.packages('PhysioCrossModal', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/x-biosignal/physiocrossmodal/issues

Pkgdown/docs site:https://x-biosignal.github.io

On CRAN:

Conda:

3.18 score 73 exports 22 dependencies

Last updated from:98d2b0f224. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE243
source / vignettesOK242
linux-releaseNOTE291
macos-releaseNOTE391
macos-oldrelNOTE368
windows-develNOTE401
windows-releaseNOTE405
windows-oldrelNOTE350
wasm-releaseOK115

Exports:alignmentalignment<-alignObservationBlocksalignSignalsalignToRatebootstrapCIccaciPLVcoherencecoherenceMatrixcommonClockcomodulogramcoupledNMFcouplingAnalysiscouplingAnalysisCachedcouplingMatrixcouplingResultscouplingResults<-crossBlockFactorcrossCorrelationcrossSpectrumcrossWaveletTransformdirectedTransferFunctiondistanceCorrelationelasticAlignexperimentsexperiments<-fuseBlocksgrangerCausalityjivelaggedCoherenceleidaStatesleidaTransitionslodoGeneralizationmake_coupled_signalsmake_directed_signalsmake_eeg_emgmergePhysiomodalitiesmodulationIndexmultimodalGaitIndexMultiPhysioExperimentmultipleFactorAnalysismultitaperCoherencemutualInformationnModalitiesorthogonalizedAECpairwisePhaseConsistencypartialDirectedCoherencephaseAmplitudeCouplingphaseLagIndexphaseLockingValuephaseSlopeIndexplotCoherenceSpectrumplotComodulogramplotCouplingMatrixplotCouplingTimecourseplotWaveletCoherenceplsBlocksrepresentationalSimilarityrvCoefficientsamplingRatesslidingCrossCorrelationsrvfMeanstreamssurrogateMatrixTestsurrogateTesttimeWindowtransferEntropywarpApplywaveletCoherencewaveletPLVweightedPLI

Dependencies:abindBiobaseBiocGenericscliDelayedArraydigestgenericsGenomicRangesIRangeslatticelifecycleMatrixMatrixGenericsmatrixStatsPhysioExperimentrlangS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

Cross-Modal Coupling Analysis with PhysioCrossModal
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
Rendered fromcoupling-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Integrating Modalities: Multi-Modal Fusion with PhysioCrossModal
The integration problem | Shared vs modality-specific: JIVE | Covarying directions: CCA and PLS | A common latent drive: coupled NMF | Whole-block association | One index, one matrix, one latent model | Choosing a method | Correctness | See also
Rendered frommultimodal-fusion.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Introduction to PhysioCrossModal
Overview | Creating simulated EEG and EMG data | Building PhysioExperiment objects | Creating a MultiPhysioExperiment | Spectral coherence (CMC) | Visualisation | Phase Locking Value (PLV) | Granger causality | The couplingAnalysis() wrapper | Working with raw numeric vectors | Signal alignment utilities | Statistical significance testing | Surrogate testing | Bootstrap confidence intervals | Wavelet coherence | Wavelet coherence visualization | Multi-channel coupling matrices | Summary
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Readme and manuals

Help Manual

Help pageTopics
Align feature blocks using explicit observation keysalignObservationBlocks
Align multiple PhysioExperiment objects to a common sampling ratealignSignals
Resample a PhysioExperiment to a target sampling ratealignToRate
Bootstrap confidence interval for couplingbootstrapCI
Canonical correlation analysis between two modalitiescca
Corrected imaginary phase-locking value (ciPLV)ciPLV
Magnitude-squared coherence between two signalscoherence
Coherence matrix across channel pairscoherenceMatrix
Comodulogram (phase-frequency by amplitude-frequency PAC)comodulogram
Coupled non-negative matrix factorization across two modalitiescoupledNMF
Unified interface for cross-modal coupling analysiscouplingAnalysis
Cached coupling analysis over a MultiPhysioExperimentcouplingAnalysisCached
Generic coupling matrix across channel pairscouplingMatrix
Cached coupling results for a containercouplingResults couplingResults,MultiPhysioExperiment-method couplingResults<- couplingResults<-,MultiPhysioExperiment-method
Cross-block common-factor modelcrossBlockFactor
Cross-correlation between two signalscrossCorrelation
Cross-spectral density between two signalscrossSpectrum
Cross-wavelet transform (XWT) with red-noise significancecrossWaveletTransform
Directed Transfer Function for multichannel / multimodal signalsdirectedTransferFunction
Distance correlation between two modality blocksdistanceCorrelation
Elastic (SRVF) alignment of two curveselasticAlign
Feature-level fusion of modality blocksfuseBlocks
Granger Causality Between Two SignalsgrangerCausality
JIVE: Joint and Individual Variation Explainedjive
Lagged coherence between two signalslaggedCoherence
LEiDA dynamic functional-connectivity statesleidaStates
LEiDA state-transition metricsleidaTransitions
Leave-one-site-out generalization benchmarklodoGeneralization
Generate coupled sinusoidal signalsmake_coupled_signals
Generate directed coupling signalsmake_directed_signals
Generate simulated EEG-EMG PhysioExperiment pairmake_eeg_emg
Merge two PhysioExperiment objects by combining channelsmergePhysio
Modulation-index comodulogram with surrogate inferencemodulationIndex
Composite multi-modal gait deviation indexmultimodalGaitIndex
The multimodal containerMultiPhysioExperiment-crossmodal
Methods on the multimodal containerMultiPhysioExperiment-crossmodal-methods
Multiple Factor Analysis (multi-block PCA)multipleFactorAnalysis
Multitaper coherencemultitaperCoherence
Mutual Information (histogram estimator)mutualInformation
Orthogonalised amplitude-envelope correlation (leakage-corrected)orthogonalizedAEC
Pairwise phase consistency (PPC)pairwisePhaseConsistency
Partial Directed Coherence for multichannel / multimodal signalspartialDirectedCoherence
Phase-amplitude couplingphaseAmplitudeCoupling
Phase Lag Index (PLI)phaseLagIndex
Phase Locking Value (PLV)phaseLockingValue
Phase Slope Index (directed, volume-conduction robust)phaseSlopeIndex
Plot coherence spectrumplotCoherenceSpectrum
Plot a comodulogramplotComodulogram
Plot a coupling matrix as a heatmapplotCouplingMatrix
Plot time-varying coupling from sliding-window analysisplotCouplingTimecourse
Plot wavelet coherence time-frequency mapplotWaveletCoherence
Two-block partial least squares (PLS-SVD)plsBlocks
Representational similarity across modalities (RSA)representationalSimilarity
RV coefficient between two modality blocksrvCoefficient
Sliding-window cross-correlationslidingCrossCorrelation
Elastic (Karcher) mean of a set of curvessrvfMean
Surrogate-based significance test for coupling matricessurrogateMatrixTest
Surrogate-based significance test for couplingsurrogateTest
Transfer entropy (model-free directed information)transferEntropy
Apply a computed warping to a companion signalwarpApply
Time-frequency wavelet coherencewaveletCoherence
Time-frequency wavelet PLVwaveletPLV
Weighted Phase Lag Index (wPLI)weightedPLI