Package: PhysioEEG 0.2.0

Yusuke Matsui

PhysioEEG: EEG Analysis Functions for PhysioExperiment Objects

Provides comprehensive electroencephalography (EEG) analysis functions for PhysioExperiment objects. Includes preprocessing (filtering, re-referencing, bad channel detection, interpolation, epoching, artifact rejection), independent component analysis (FastICA, Infomax, JADE) with automatic artifact detection, event-related potential (ERP) component detection and measurement (N100, P300, N400, P600, MMN), source localization (eLORETA, sLORETA, LCMV beamformer), EEG microstate analysis (K-means, AAHC), sleep staging (AASM criteria, spindle/K-complex/slow-wave detection), brain-computer interface features (CSP, SSVEP, motor imagery), clinical EEG analysis (spike detection, QEEG, asymmetry indices), time-frequency analysis (Morlet wavelet, STFT, multitaper, ERSP, ITC), connectivity analysis (coherence, PLV, wPLI, Granger causality), visualization (signal traces, ERP waveforms, topographic maps, spectrograms, connectivity plots, hypnograms, source maps), and simulated data generators for testing and demonstration.

Authors:Yusuke Matsui

PhysioEEG_0.2.0.tar.gz
PhysioEEG_0.2.0.zip(r-4.7)PhysioEEG_0.2.0.zip(r-4.6)PhysioEEG_0.2.0.zip(r-4.5)
PhysioEEG_0.2.0.tgz(r-4.6-any)PhysioEEG_0.2.0.tgz(r-4.5-any)
PhysioEEG_0.2.0.tar.gz(r-4.7-any)PhysioEEG_0.2.0.tar.gz(r-4.6-any)
PhysioEEG_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PhysioEEG/json (API)

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

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

On CRAN:

Conda:

3.65 score 67 exports 18 dependencies

Last updated from:7da50375ff. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK234
source / vignettesOK219
linux-release-x86_64OK234
macos-release-arm64OK133
macos-oldrel-arm64OK161
windows-develOK190
windows-releaseOK184
windows-oldrelOK176
wasm-releaseOK117

Exports:eegArtifactRejecteegAsymmetryeegBadChannelseegBCIclassifyeegBCIfeatureseegBeamformereegCoherenceeegConnectivityMatrixeegCSPeegEpocheegERPbaselineeegERPdetecteegERPdifferenceeegERPgrandAverageeegERPlatencyeegERPmeasureeegERPtesteegERSPeegFiltereegForwardModeleegGrangerCausalityeegICAeegICAdetecteegICAmixeegICAremoveeegInterpolateeegITCeegKcomplexDetecteegMicrostateBackfiteegMicrostateseegMicrostateSequenceeegMicrostateStatseegMontageeegMorletWaveleteegMotorImageryeegMultitapereegPlotConnectivityeegPlotERPeegPlotHypnogrameegPlotICAeegPlotSignaleegPlotSourceeegPlotSpectrogrameegPlotTopomapeegPlotTopomapSerieseegPLVeegPreprocesseegQEEGeegQuickStarteegRereferenceeegSleepMetricseegSleepStageeegSlowingeegSlowWaveDetecteegSourceEstimateeegSourcePowereegSpikeDetecteegSpindleDetecteegSSVEPeegSTFTeegSuppressioneegWPLImake_eegmake_eeg_bcimake_eeg_erpmake_eeg_sleepmake_eeg_spikes

Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsPhysioCoreS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

BCI Classification
Introduction | Motor Imagery Paradigm | SSVEP Paradigm | Classification Pipeline | Setup | Motor Imagery Analysis | Common Spatial Patterns (CSP) | Feature Extraction | SSVEP Detection | Classification | Performance Evaluation | Classification Accuracy | Cohen's Kappa | Information Transfer Rate (ITR) | Cross-Validation Strategies | Summary
Rendered frombci-classification.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Clinical EEG Analysis with PhysioEEG
Setup | Spike Detection | Basic Spike Detection | Parameter Tuning | Template Matching | Sensitivity Analysis | Quantitative EEG (QEEG) | Custom Band Definitions | Normative Comparison | Asymmetry Indices | Custom Electrode Pairs and Bands | Clinical Interpretation | EEG Suppression | Interpreting BSR | EEG Slowing | Peak Frequency Method | Focal vs. Generalized Slowing | Full Clinical Workflow | Clinical Interpretation Guidelines | Spike Detection Limitations | QEEG Interpretation | When to Combine with Clinical Judgment
Rendered fromclinical-eeg.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Connectivity Analysis
Introduction | Setup | Coherence Analysis | Magnitude-Squared Coherence | Imaginary Coherence | Phase Locking Value (PLV) | Weighted Phase Lag Index (wPLI) | Granger Causality | Building Connectivity Matrices | Thresholding Strategies | Visualization | Heatmap View | Circle Plot | Method Comparison | Practical Recommendations | Frequency Band Considerations | Conclusion | References
Rendered fromconnectivity-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

EEG Preprocessing Pipeline
Introduction | Setup | Filtering with eegFilter() | Highpass Filtering | Lowpass Filtering | Bandpass Filtering | Notch Filtering | FIR vs IIR Filters | Re-referencing with eegRereference() | Average Reference | Mastoid Reference | Single Channel Reference | When to Use Each Type | Bad Channel Detection and Interpolation | Detecting Bad Channels | Interpolating Bad Channels | Recommended Workflow | ICA Artifact Removal | Running ICA | Detecting Artifact Components | Removing Artifact Components | Typical Workflow | Epoching with eegEpoch() | Creating Event Markers | Extracting Epochs | Alternative Baseline Methods | Artifact Rejection with eegArtifactReject() | Threshold-Based Rejection | Gradient-Based Rejection | Joint Probability Method | When to Use Each Method | Full Pipeline with eegPreprocess() | Parameter Selection for Different Paradigms | Best Practices | Recommended Parameter Ranges | Pipeline Order Matters | Always Inspect Data Between Steps | Document Your Pipeline
Rendered frompreprocessing-pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

EEG Source Localization with PhysioEEG
Setup | Forward Model | Spherical Head Model | Simplified BEM Model | Leadfield Interpretation | Source Estimation | MNE (Minimum Norm Estimate) | sLORETA (Standardized Low-Resolution Brain Electromagnetic Tomography) | eLORETA (Exact Low-Resolution Electromagnetic Tomography) | Comparing Methods | Beamformer | LCMV Beamformer | DICS Beamformer | Source Power | Custom Frequency Bands | Visualization | Scatter Plot | Flat Map | Comparing Methods Visually | Method Comparison | Distributed Source Imaging vs. Beamforming | Choosing a Method | Best Practices | Electrode Density | SNR Considerations | Regularization | Preprocessing Recommendations
Rendered fromsource-localization.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

ERP Analysis with PhysioEEG
Simulating an Oddball Experiment | ERP Component Detection | ERP Measurement Methods | Fractional Area Latency | Difference Waves | Artifact Removal with ICA Before ERP
Rendered fromerp-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Getting Started with PhysioEEG
Creating Test Data | Independent Component Analysis (ICA) | ERP Analysis | Quantitative EEG (QEEG) | Microstate Analysis | Brain-Computer Interface (BCI) | Sleep Analysis | Clinical EEG Analysis
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Sleep EEG Analysis
Introduction | Setup and Data Preparation | Preprocessing for Sleep EEG | Recommended Filter Settings | Artifact Detection and Removal | Automatic Sleep Staging | Sleep Stage Characteristics | Interpreting Staging Output | Sleep Spindle Detection | Detection Parameters | Clinical Significance | K-Complex Detection | Detection Methodology | Clinical Applications | Slow Wave Detection and Analysis | Slow Wave Detection | SWA Dynamics Across the Night | Clinical Interpretation | Sleep Architecture Metrics | Normal Adult Sleep Architecture | Hypnogram Visualization | Clinical Interpretation and Reporting | Complete Analysis Workflow | Abnormalities to Look For | Insomnia Pattern | Sleep Apnea | Depression | Neurodegenerative Disease | Limitations of Automated Staging | Best Practices | Conclusion | References | Session Information
Rendered fromsleep-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Time-Frequency Analysis
Introduction | Setup | Morlet Wavelet Transform | Short-Time Fourier Transform | Multitaper Spectral Analysis | Event-Related Spectral Perturbation (ERSP) | Intertrial Coherence (ITC) | Visualization with eegPlotSpectrogram | Method Comparison Guide | Session Info
Rendered fromtime-frequency-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-05

Readme and manuals

Help Manual

Help pageTopics
Reject artifacts in epoched EEG dataeegArtifactReject
Frontal Alpha AsymmetryeegAsymmetry
Detect bad EEG channelseegBadChannels
BCI ClassificationeegBCIclassify
BCI Feature ExtractioneegBCIfeatures
EEG Beamformer Source LocalizationeegBeamformer
EEG Coherence AnalysiseegCoherence
EEG Connectivity MatrixeegConnectivityMatrix
Common Spatial Pattern (CSP) AnalysiseegCSP
Epoch continuous EEG dataeegEpoch
Baseline Correct ERP DataeegERPbaseline
Detect ERP ComponentseegERPdetect
ERP Difference WaveformeegERPdifference
Compute Grand Average ERPeegERPgrandAverage
Fractional Area LatencyeegERPlatency
Measure ERP AmplitudeeegERPmeasure
Statistical Testing for ERP DifferenceseegERPtest
Event-Related Spectral Perturbation (ERSP)eegERSP
Filter EEG signalseegFilter
Construct EEG Forward Model (Leadfield Matrix)eegForwardModel
EEG Spectral Granger CausalityeegGrangerCausality
EEG Independent Component Analysis (ICA)eegICA
Detect Artifact ICA ComponentseegICAdetect
Access ICA MetadataeegICAmix
Remove ICA Components from EEGeegICAremove
Interpolate bad EEG channelseegInterpolate
Inter-Trial Coherence (ITC)eegITC
Detect K-ComplexeseegKcomplexDetect
Backfit Microstate Template Maps to EEG DataeegMicrostateBackfit
EEG Microstate SegmentationeegMicrostates
Extract Microstate Sequence as Character LabelseegMicrostateSequence
Compute Microstate StatisticseegMicrostateStats
Assign electrode montage positionseegMontage
Morlet Wavelet Transform for EEGeegMorletWavelet
Motor Imagery ERD/ERS ComputationeegMotorImagery
Multitaper Power Spectral Density for EEGeegMultitaper
Plot Connectivity Matrix or CircleeegPlotConnectivity
Plot ERP Waveform with Confidence IntervaleegPlotERP
Plot Sleep HypnogrameegPlotHypnogram
Plot ICA ComponentseegPlotICA
Plot Multi-Channel EEG Time SerieseegPlotSignal
Plot Source Localization ResultseegPlotSource
Plot Spectrogram (Time-Frequency Heatmap)eegPlotSpectrogram
Plot EEG Topographic MapeegPlotTopomap
Plot Topographic Map SerieseegPlotTopomapSeries
EEG Phase Locking Value (PLV)eegPLV
Full EEG preprocessing pipelineeegPreprocess
Quantitative EEG (QEEG) AnalysiseegQEEG
PhysioEEG Quick Start GuideeegQuickStart
Re-reference EEG dataeegRereference
Compute Sleep MetricseegSleepMetrics
Automatic Sleep StagingeegSleepStage
EEG Slowing DetectioneegSlowing
Detect Slow WaveseegSlowWaveDetect
EEG Source EstimationeegSourceEstimate
Compute Source-Space Band PowereegSourcePower
Detect Epileptic Spikes in EEG DataeegSpikeDetect
Detect Sleep SpindleseegSpindleDetect
SSVEP Frequency DetectioneegSSVEP
Short-Time Fourier Transform for EEGeegSTFT
Burst-Suppression DetectioneegSuppression
EEG Weighted Phase Lag Index (wPLI)eegWPLI
Create Simulated EEG Datamake_eeg
Create EEG with Motor Imagery / SSVEP Patterns for BCImake_eeg_bci
Create EEG with Embedded ERP Componentsmake_eeg_erp
Create EEG with Sleep Stage Characteristicsmake_eeg_sleep
Create EEG with Embedded Epileptic Spikesmake_eeg_spikes