Package: PhysioAnalysis 0.5.30

Yusuke Matsui

PhysioAnalysis: Analysis and Visualization for PhysioExperiment Objects

Provides analysis and visualization functions for physiological signal data stored in 'PhysioExperiment' objects, which extend the Bioconductor 'SummarizedExperiment' container. Methods include the fast Fourier transform ('FFT'), time-frequency decomposition, epoching, functional connectivity (coherence and phase-based measures), graph and network metrics, statistical parametric mapping, and cluster-based permutation testing. Visualization utilities cover scalp topographic maps ('topoplots'), multichannel signal displays, and network graphs. Compiled routines are provided through 'Rcpp' and 'RcppArmadillo'.

Authors:Yusuke Matsui [aut, cre]

PhysioAnalysis_0.5.30.tar.gz
PhysioAnalysis_0.5.30.zip(r-4.7-x86_64)PhysioAnalysis_0.5.30.zip(r-4.7-arm64)PhysioAnalysis_0.5.30.zip(r-4.6-x86_64)PhysioAnalysis_0.5.30.zip(r-4.6-arm64)PhysioAnalysis_0.5.30.zip(r-4.5-x86_64)
PhysioAnalysis_0.5.30.tgz(r-4.6-x86_64)PhysioAnalysis_0.5.30.tgz(r-4.6-arm64)PhysioAnalysis_0.5.30.tgz(r-4.5-x86_64)PhysioAnalysis_0.5.30.tgz(r-4.5-arm64)
PhysioAnalysis_0.5.30.tar.gz(r-4.7-arm64)PhysioAnalysis_0.5.30.tar.gz(r-4.7-x86_64)PhysioAnalysis_0.5.30.tar.gz(r-4.6-arm64)PhysioAnalysis_0.5.30.tar.gz(r-4.6-x86_64)
PhysioAnalysis_0.5.30.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioAnalysis/json (API)

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

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

openblascppopenmp

3.48 score 1 packages 118 exports 40 dependencies

Last updated from:f29df30bcb. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK243
linux-devel-x86_64OK300
source / vignettesOK247
linux-release-arm64OK244
linux-release-x86_64OK284
macos-release-arm64OK412
macos-release-x86_64OK381
macos-oldrel-arm64OK320
macos-oldrel-x86_64OK421
windows-devel-arm64OK347
windows-devel-x86_64OK298
windows-release-arm64OK345
windows-release-x86_64OK306
windows-oldrel-x86_64OK293
wasm-releaseOK123

Exports:adfTestadjacencyMatrixanovaEpochsarSpectrumarYuleWalkerautocorrelationaverageEpochsbandPowerbetweennessCentralitybinarizeNetworkblandAltmanbootstrapCIcircularLinearCorrelationcircularSummarycliffsDeltaclusteringCoefficientclusterPermutationTestcohensDcoherenceconnectivityMatrixcorrectPValuescorrelationMatrixcorrelationTestcronbachAlphacrossSpectrumdunnTesteffectSizeeigenvectorCentralityepochDataepochSlidingepochTimesetaSquaredfftSignalsfindSignificantWindowsfPCAfriedmanTestfunctionalMixedModelfunctionalRegressionglobalEfficiencygrandAveragegraphLaplacianhilbertTransformiccinstantaneousAmplitudeinstantaneousPhaseinterquartileRangeintraclassCorrelationjarqueBeraTestkendallTaukpssTestkruskalTestksNormalityTestleveneTestlinearRegressionljungBoxTestlocalEfficiencymdcmedianAbsDevmodularitymultipleRegressionnemenyiTestnetworkBasedStatisticnodeDegreeoneWayAnovapairedTTestpartialAutocorrelationpartialCorrelationpathLengthpliplotAdjacencyMatrixplotDynamicConnectivityplotERPplotMultiChannelplotNBSnetworkplotNetworkplotNetworkMetricsplotNetworkStabilityplotPSDplotSignalplotSpecparamplotSpectrogramplotSPMplotTopomapplotTopomapSeriesplvrankBiserialrayleighTestreconstructFPCAregisterCurvesscalarOnFunctionRegressionsemsignalMomentsslidingWindowConnectivitysmallWorldnessspecparamspecparamBiomarkerspectralClusteringspectralDecompositionspectrogramspmAnovaspmMANOVAspmPairedTTestspmRegressionspmSnPMspmTTesttemporalStabilitytfcethresholdNetworktrimmedMeantTestEpochstukeyHSDtwoSampleTTestwatsonWilliamsTestwaveformCMCwaveformICCwaveformReliabilitywaveletTransformwPLI

Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraydigestfarvergenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglatticelifecycleMASSMatrixMatrixGenericsmatrixStatsPhysioExperimentR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfosignalSparseArraySummarizedExperimentvctrsviridisLitewithrXVector

Spectral Analysis with PhysioAnalysis
Introduction | Setup | Creating Example Data | FFT Analysis | Interpreting the FFT Output | Power Spectral Density | Band Power Extraction | Spectrogram (Short-Time Fourier Transform) | Window Parameters | Wavelet Transform | Hilbert Transform and Instantaneous Measures | Summary | References | Session Info
Rendered fromspectral-analysis.Rmdusingknitr::rmarkdown

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

Statistical Testing with PhysioAnalysis
Introduction | Setup | Creating Epoched Test Data | Pointwise t-Tests | One-Sample t-Test | Two-Sample t-Test | Paired t-Test | One-Sided Tests | ANOVA Across Conditions | Cluster-Based Permutation Tests | How It Works | One-Sample Cluster Test | Examining the Permutation Distribution | Effect Sizes | Bootstrap Confidence Intervals | Multiple Comparison Correction | Choosing a Correction Method | Finding Significant Time Windows | Complete Workflow Example | References | Session Info
Rendered fromstatistical-testing.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
Augmented Dickey-Fuller (ADF) unit-root test statisticadfTest
Create adjacency matrix from connectivityadjacencyMatrix
ANOVA across conditionsanovaEpochs
Autoregressive (parametric) spectral densityarSpectrum
Autoregressive model fit by Yule-Walker (AR(p))arYuleWalker
Autocorrelation function (ACF)autocorrelation
Average epochsaverageEpochs
Compute band powerbandPower
Compute betweenness centralitybetweennessCentrality
Binarize networkbinarizeNetwork
Bootstrap confidence interval for ERPbootstrapCI
Cliff's delta for two independent samplescliffsDelta
Compute clustering coefficientclusteringCoefficient
Cluster-based permutation testclusterPermutationTest
Connectivity Analysis for PhysioExperimentcoherence
Compute connectivity matrix for a frequency bandconnectivityMatrix
Multiple comparison correctioncorrectPValues
Compute correlation matrix between channelscorrelationMatrix
Correlation TestcorrelationTest
Cronbach's alpha (internal-consistency reliability)cronbachAlpha
Compute cross-spectral densitycrossSpectrum
Dunn's test (post-hoc pairwise comparisons after Kruskal-Wallis)dunnTest
Compute effect size (Cohen's d / Hedges g)effectSize
Compute eigenvector centralityeigenvectorCentrality
Epoching operations for PhysioExperimentepochData
Create epochs using sliding windowepochSliding
Get epoch time vectorepochTimes
Fast Fourier transform helperfftSignals
Find significant time windowsfindSignificantWindows
Friedman rank-sum test (non-parametric repeated-measures omnibus)friedmanTest
Functional random-intercept (multilevel) model for waveformsfunctionalMixedModel
Function-on-scalar regression (coefficient curves)functionalRegression
Compute global efficiencyglobalEfficiency
Grand average across subjects/samplesgrandAverage
Compute graph LaplaciangraphLaplacian
Hilbert transform for instantaneous amplitude/phasehilbertTransform
Extract instantaneous amplitude (envelope)instantaneousAmplitude
Extract instantaneous phaseinstantaneousPhase
Interquartile Range (robust spread)interquartileRange
Intraclass correlation coefficients (ICC)intraclassCorrelation
Jarque-Bera test for normalityjarqueBeraTest
Kendall's tau-b rank correlationkendallTau
KPSS test for stationaritykpssTest
Kruskal-Wallis rank-sum test (non-parametric between-groups omnibus)kruskalTest
Kolmogorov-Smirnov Test for NormalityksNormalityTest
Levene's test for homogeneity of varianceleveneTest
Simple linear regression (ordinary least squares)linearRegression
Ljung-Box test for autocorrelation (white-noise / portmanteau test)ljungBoxTest
Compute local efficiencylocalEfficiency
Median Absolute Deviation (robust dispersion)medianAbsDev
Compute network modularitymodularity
Multiple linear regression (ordinary least squares)multipleRegression
Nemenyi post-hoc test (all pairwise comparisons after a Friedman test)nemenyiTest
Network-Based Statistic (NBS)networkBasedStatistic
Compute node degreenodeDegree
One-way ANOVA (omnibus F-test) across groupsoneWayAnova
Paired-Samples t-TestpairedTTest
Partial autocorrelation function (PACF)partialAutocorrelation
Partial correlation controlling for covariatespartialCorrelation
Compute shortest path lengthpathLength
Compute Phase Lag Index (PLI)pli
Plot adjacency matrix heatmapplotAdjacencyMatrix
Plot dynamic connectivityplotDynamicConnectivity
Plot event-related potential (ERP) waveformplotERP
Multi-channel visualization functionsplotMultiChannel
Plot a significant NBS subnetworkplotNBSnetwork
Network Visualization for PhysioExperimentplotNetwork
Plot network metricsplotNetworkMetrics
Plot network stability over timeplotNetworkStability
Plot power spectral densityplotPSD
Plot a signal channelplotSignal
Plot a specparam model fitplotSpecparam
Plot spectrogramplotSpectrogram
Plot SPM resultplotSPM
Topographic Map VisualizationplotTopomap
Plot topographic map animationplotTopomapSeries
Compute Phase Locking Value (PLV)plv
Rank-biserial correlation for two independent samplesrankBiserial
Scalar-on-function regression (functional coefficient)scalarOnFunctionRegression
Signal distribution moments (mean, SD, skewness, kurtosis)signalMoments
Sliding window connectivityslidingWindowConnectivity
Compute small-worldnesssmallWorldness
Spectral parameterization (specparam / FOOOF)print.specparam_result specparam
Aperiodic parameter as a PhysioBiomarkerspecparamBiomarker
Spectral clustering of network nodesspectralClustering
Spectral decomposition of graph LaplacianspectralDecomposition
Time-Frequency Analysis for PhysioExperimentspectrogram
SPM ANOVA (F-test)spmAnova
SPM one-way MANOVA (Hotelling's T^2 / chi-square vector field)spmMANOVA
SPM paired t-testspmPairedTTest
SPM linear-regression t-fieldspmRegression
Non-parametric (permutation) SPMspmSnPM
Statistical Parametric Mapping (SPM1D) for BiomechanicsspmTTest
Compute temporal stability of networktemporalStability
Threshold-Free Cluster Enhancement (TFCE)tfce
Threshold network by densitythresholdNetwork
Trimmed Mean (robust location)trimmedMean
Statistical Testing for PhysioExperimenttTestEpochs
Tukey HSD post-hoc test (all pairwise comparisons after one-way ANOVA)tukeyHSD
Two-Sample t-TesttwoSampleTTest
Wavelet transformwaveletTransform
Compute weighted Phase Lag Index (wPLI)wPLI