{ "_id": "6ac10e21552a13804ac7eda6", "Package": "PhysioEcosystem", "Title": "Unified Entry Point for the Physio Ecosystem (Meta-Package)", "Version": "1.0.1", "Authors@R": "person(given = \"Yusuke\",\nfamily = \"Matsui\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mail.to.matsui@gmail.com\")", "Description": "A meta-package for the Physio ecosystem: attaching it\nloads and re-exports the public API of the foundation and the\ncore analysis packages (PhysioExperiment shared data model,\nPhysioIO file/database I/O, PhysioPreprocess signal\npreprocessing, and PhysioAnalysis\ntime-frequency/connectivity/network/statistics/visualization),\nso existing code that used the former monolithic\n'PhysioExperiment' meta-package keeps working. It also provides\nthe GUI/REST launchers. Domain packages (EEG, ECG, EMG, EDA,\nMoCap, cross-modal, MSK-Net, OpenSim, clinical) are installed\nseparately from the same ecosystem.", "biocViews": "Software, TimeCourse, Preprocessing", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/x-biosignal/PhysioEcosystem,\nhttps://x-biosignal.r-universe.dev/PhysioEcosystem", "BugReports": "https://github.com/x-biosignal/PhysioEcosystem/issues", "Collate": "'PhysioEcosystem-package.R' 'reexports.R' 'gui-launcher.R'\n'zzz.R'", "Config/pak/sysreqs": "libssl-dev zlib1g-dev", "Repository": "https://x-biosignal.r-universe.dev", "Date/Publication": "2026-10-03 13:11:41 UTC", "RemoteUrl": "https://github.com/x-biosignal/PhysioEcosystem", "RemoteRef": "HEAD", "RemoteSha": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-03 14:09:46 UTC", "User": "root" }, "Author": "Yusuke Matsui [aut, cre]", "Maintainer": "Yusuke Matsui ", "_user": "x-biosignal", "_type": "src", "_file": "PhysioEcosystem_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/3a194560c7f679f8090c4a251e97e4e361dc5db17d52939708a708bdad7182db", "_filesize": 327465, "_sha256": "3a194560c7f679f8090c4a251e97e4e361dc5db17d52939708a708bdad7182db", "_expires": "2027-01-11T14:15:59.000Z", "_created": "2026-10-03T14:09:46.000Z", "_published": "2026-10-03T14:16:01.574Z", "_jobs": [ { "job": 111219258772, "time": 292, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11276296420" }, { "job": 111219258738, "time": 317, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11275837501" }, { "job": 111219258723, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11276111716" }, { "job": 111219258734, "time": 232, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11276346193" }, { "job": 111218604614, "time": 229, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11275966549" }, { "job": 111219258716, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11276341015" }, { "job": 111219258744, "time": 214, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11276226397" }, { "job": 111219258767, "time": 263, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11275609188" }, { "job": 111219258790, "time": 214, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11275842319" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891", "_status": "success", "_upstream": "https://github.com/x-biosignal/PhysioEcosystem", "_commit": { "id": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "author": "Yusuke Matsui ", "committer": "Yusuke Matsui ", "message": "Release snapshot\n", "time": 1791033101 }, "_maintainer": { "name": "Yusuke Matsui", "email": "mail.to.matsui@gmail.com", "login": "ymatts", "description": "Data scientist", "uuid": 5744286 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "PhysioExperiment", "version": ">= 2.0.0", "role": "Depends" }, { "package": "PhysioIO", "role": "Depends" }, { "package": "PhysioPreprocess", "role": "Depends" }, { "package": "PhysioAnalysis", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.2.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" }, { "package": "plumber", "version": ">= 1.2.0", "role": "Suggests" }, { "package": "later", "role": "Suggests" }, { "package": "callr", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "x-biosignal", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-40", "n": 1 } ], "_tags": [], "_topics": [ "software", "timecourse", "preprocessing" ], "_stars": 0, "_contributors": [ { "user": "ymatts", "count": 1, "uuid": 5744286 } ], "_userbio": { "uuid": 268545536, "type": "organization", "name": "x-biosignal", "followers": 1, "description": "Open-source R packages for biosignal analysis, biomechanics, clinical research, and rehabilitation." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PhysioEcosystem" }, "_devurl": "https://github.com/x-biosignal/physioecosystem", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/PhysioEcosystem.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_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" ], "_help": [ { "page": "checkGUIDependencies", "title": "Check GUI Dependencies", "topics": [ "checkGUIDependencies" ] }, { "page": "launchGUI", "title": "Launch PhysioExperiment GUI", "topics": [ "launchGUI" ] }, { "page": "startAPIServer", "title": "Start PhysioExperiment API Server (Non-blocking)", "topics": [ "startAPIServer" ] } ], "_readme": "https://github.com/x-biosignal/PhysioEcosystem/raw/HEAD/README.md", "_rundeps": [ "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", "PhysioExperiment", "PhysioIO", "PhysioPreprocess", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "signal", "SparseArray", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "intro.Rmd", "filename": "intro.html", "title": "Getting Started with PhysioExperiment", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-10-03 13:11:41", "modified": "2026-10-03 13:11:41", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "physioecosystem", "_universes": [ "x-biosignal", "ymatts" ], "_previous": "1.0.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-10-03T14:12:52.000Z", "distro": "resolute", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/0dd11ee96d4921e45dc05b8548fc2b80a57a0d49063f2c8479e68a1e894a72f5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-10-03T14:13:17.000Z", "distro": "resolute", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/86ae07ed789cc3d95a1d054caf52a0f2e1b1b57a09ee3c04f253dc8a2ec6fc58", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-10-03T14:12:15.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/7267dd2bea524df773566ed11e7b778ca317444dae0fd9bae235e67f4568293e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.6.1", "os": "mac", "version": "1.0.1", "date": "2026-10-03T14:12:09.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/3871e6e649a9f6ac4d54f67fa394185c0ca7524eed38a96272e17171df9073ab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-10-03T14:12:28.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/af5c87b4bbb22f31045af59fd7c6f1944f3a90fae52a9249c8ba29f44c0fda67", "status": "success", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-10-03T14:11:27.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/9c0771a9bc9afbfe353bf3b54977a7f1408e92d5a59b21856834f5b1d7ae6a4d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-10-03T14:11:16.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/1588343ba5c8288febf62c5436149204472756be775dc855b7cd05d027aee439", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-10-03T14:11:31.000Z", "commit": "3a6a8e7ebe4ec47a97e3ad2be9ba0aa63086c940", "fileid": "https://r2.ropensci.org/26e1e16d9b5f4eb54d33a662a0e5c4f7312d286cd9c03c5906a18c06c9c31108", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/x-biosignal/actions/runs/37128435891" } ] }