Package: PhysioExperiment 1.0.0

Yusuke Matsui

PhysioExperiment: Unified Analysis of Physiological Signals (Meta-Package)

A meta-package for the Physio ecosystem: attaching it loads and re-exports the public API of the core packages (PhysioCore data model, PhysioIO file/database I/O, PhysioPreprocess signal preprocessing, and PhysioAnalysis time-frequency/connectivity/network/statistics/visualization), so existing code that used the former monolithic 'PhysioExperiment' package keeps working. It also provides the GUI/REST launchers. Domain packages (EEG, ECG, EMG, EDA, MoCap, cross-modal, MSK-Net, OpenSim, clinical) are installed separately from the same ecosystem.

Authors:Yusuke Matsui [aut, cre]

PhysioExperiment_1.0.0.tar.gz
PhysioExperiment_1.0.0.zip(r-4.7-any)PhysioExperiment_1.0.0.zip(r-4.6-any)PhysioExperiment_1.0.0.zip(r-4.5-any)
PhysioExperiment_1.0.0.tgz(r-4.6-any)PhysioExperiment_1.0.0.tgz(r-4.5-any)
PhysioExperiment_1.0.0.tar.gz(r-4.7-any)PhysioExperiment_1.0.0.tar.gz(r-4.6-any)
PhysioExperiment_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioExperiment/json (API)

# Install 'PhysioExperiment' in R:

install.packages('PhysioExperiment', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

software timecourse preprocessing

2.70 score 209 exports 53 dependencies

Last updated from:267b251d48. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel	NOTE	279
source / vignettes	OK	272
linux-release	NOTE	279
macos-release	NOTE	218
macos-oldrel	NOTE	185
windows-devel	NOTE	231
windows-release	NOTE	223
windows-oldrel	NOTE	213
wasm-release	OK	136

Exports:addEvents adjacencyMatrix AnalysisResult anovaEpochs appendProvenance applyMontage applyPipeline assaySamplingRates availableOperations availableReaders availableWriters averageEpochs bandPower baselineCorrect betweennessCentrality binarizeNetwork biomarkerValue blandAltman bootstrapCI butterworthFilter cbindPhysio channelInfo channelInfo<-channelNames channelNames<-checkGUIDependencies checkNA classifyICAComponents cleanData clusteringCoefficient clusterPermutationTest cohensD coherence connectDatabase connectivityMatrix correctPValues correlationMatrix createPipeline crossSpectrum dbStats decimate defaultAssay deleteExperiment deprecate_physio detectArtifacts detectBadChannels detrendSignal detrendSignals disconnectDatabase dropChannels duration effectSize eigenvectorCentrality epochData epochSliding epochTimes etaSquared eventQuery extractWindow fftSignals fillEdgeNA filterSignals filterType filterValue findSignificantWindows firFilter getChannelsByType getCurrentReference getElectrodePositions getEvents getOperation getReader getReference getWriter globalEfficiency grandAverage graphLaplacian handleNA hasNA hilbertTransform icaDecompose icaRemove icc initPhysioSchema instantaneousAmplitude instantaneousPhase interpolate interpolateBadChannels isAverageReferenced isHDF5Backed launchGUI listBIDSSessions listBIDSSubjects loadExperiment localEfficiency logStep mapClinicalCodes mdc modularity naSummary nChannels nEvents nodeDegree NormativeReference notchFilter pathLength percentPredicted PhysioBiomarker PhysioEvents PhysioExperiment physioPalette pickChannels pli plotAdjacencyMatrix plotDynamicConnectivity plotERP plotMultiChannel plotNetwork plotNetworkMetrics plotNetworkStability plotPSD plotSignal plotSpectrogram plotSPM plotTopomap plotTopomapSeries plv provenance provenance<-queryExperiments rbindPhysio readBDF readBIDS readBrainVision readClinicalMetadataCSV readCSV readEDF readElectrodePositionsCSV readEventsCSV readGDF readMAT readPhysio readPhysioHDF5 realizeHDF5 registerExperiment registerOperation registerReader registerWriter rejectBadEpochs removeBaseline removeEvents removeICAComponents renameChannels replaceNA rereference resample resolveQuery resultType resultValue runICA samplesToTime samplingRate samplingRate<-scale_color_physio scale_colour_physio scale_fill_physio sem setAssaySamplingRate setChannelTypes setChannelUnits setElectrodePositions setEvents setReference slidingWindowConnectivity smallWorldness spectralClustering spectralDecomposition spectrogram spmAnova spmPairedTTest spmTTest startAPIServer temporalStability theme_physio thresholdNetwork timeIndex timeToSamples tTestEpochs unregisterOperation unregisterReader unregisterWriter validateBIDS validateClinicalMetadata waveletTransform withProvenance wPLI writeAssayHDF5 writeBDF writeBIDS writeBrainVision writeCSV writeEDF writeElectrodePositionsCSV writeEventsCSV writeGDF writeMAT writePhysio writePhysioHDF5 zScore

Dependencies:abind Biobase BiocGenerics biocmake cli cpp11 DBI DelayedArray digest dir.expiry farver filelock generics GenomicRanges ggplot2 glue gtable h5mread HDF5Array IRanges isoband jsonlite labeling lattice lifecycle MASS Matrix MatrixGenerics matrixStats PhysioAnalysis PhysioCore PhysioIO PhysioPreprocess R6 RColorBrewer Rcpp RcppArmadillo rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors S7 scales Seqinfo signal SparseArray SummarizedExperiment vctrs viridisLite withr XVector

Getting Started with PhysioExperiment

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

Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2026-08-25
Started: 2026-08-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check GUI Dependencies	checkGUIDependencies
Launch PhysioExperiment GUI	launchGUI
Start PhysioExperiment API Server (Non-blocking)	startAPIServer

Usage by other packages (reverse dependencies)