{ "_id": "6ab8fea399f7aa8c6aa396fb", "Package": "actiRhythm", "Type": "Package", "Title": "Circadian Rest-Activity Rhythm Analysis", "Version": "0.1.0", "Date": "2026-06-21", "Authors@R": "c(\nperson(c(\"Raymond\", \"Dacosta\"), \"Azadda\",\nemail = \"rdazadda@alaska.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(\"CEAL Team\", role = \"aut\"),\nperson(\"Stacy\", \"Rasmus\", role = \"aut\"))", "Description": "Quantifies the circadian rest-activity rhythm, the roughly\n24-hour cycle of activity and rest, from activity counts and\nraw accelerometer recordings. Analyses run on an activity-count\nvector and its timestamps, and a built-in reader loads\n'ActiGraph' '.agd' files (an 'SQLite' database) directly.\nComputes nonparametric metrics (interdaily stability (IS) and\nintradaily variability (IV) following Witting et al. (1990)\n; relative amplitude (RA),\nthe least-active 5-hour window (L5), and the most-active\n10-hour window (M10) following Van Someren et al. (1999)\n), cosinor models with a\nrhythmicity test, confidence ellipses, population-mean cosinor,\nand two-group parameter comparison (Cornelissen (2014)\n; Marler et al. (2006)\n), period estimation by Lomb-Scargle\n(Lomb (1976) ; Scargle (1982)\n) and chi-square (Sokolove and Bushell\n(1978) ) periodograms with\nbootstrap confidence intervals and a sliding-window\nspectrogram, fractal and nonlinear measures (Peng et al. (1994)\n; Kantelhardt et al. (2002)\n), the Sleep Regularity\nIndex (Phillips et al. (2017)\n), social jet lag,\nrest-activity state transitions, and locomotor inactivity\nduring sleep (Winnebeck et al. (2018)\n). It also reads raw\naccelerometer files ('ActiGraph' '.gt3x', 'Axivity' '.cwa',\n'GENEActiv' '.bin'), auto-calibrates them (van Hees et al.\n(2014) ), and derives the\nENMO, MAD, and z-angle metrics with diary-free sleep-period\ndetection (van Hees et al. (2018)\n), cross-checked against\n'GGIR'. A batch mode runs the analysis over a folder of files\nand writes a multi-sheet 'Excel' workbook.", "License": "MIT + file LICENSE", "URL": "https://github.com/rdazadda/actiRhythm,\nhttps://rdazadda.github.io/actiRhythm/", "BugReports": "https://github.com/rdazadda/actiRhythm/issues", "Language": "en-US", "RdMacros": "Rdpack", "SystemRequirements": "C++17", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Repository": "https://rdazadda.r-universe.dev", "Date/Publication": "2026-08-28 07:39:32 UTC", "RemoteUrl": "https://github.com/rdazadda/actirhythm", "RemoteRef": "HEAD", "RemoteSha": "c824a1b67e63184c4f927b88b859834e3407a0d2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-27 11:21:37 UTC", "User": "root" }, "Author": "Raymond Dacosta Azadda [aut, cre],\nCEAL Team [aut],\nStacy Rasmus [aut]", "Maintainer": "Raymond Dacosta Azadda ", "_user": "rdazadda", "_type": "src", 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[ "actiRhythm_colors" ] }, { "page": "activity.balance.index", "title": "Activity Balance Index", "topics": [ "activity.balance.index" ] }, { "page": "activity.extrema", "title": "Generalized Least- and Most-Active Periods (MX / LX)", "topics": [ "activity.extrema" ] }, { "page": "activity.onset.offset", "title": "Activity Onset and Offset (Relative-Difference Phase Markers)", "topics": [ "activity.onset.offset" ] }, { "page": "agd.counts", "title": "Extract Counts from .agd Data", "topics": [ "agd.counts" ] }, { "page": "auto.calibrate", "title": "Auto-Calibrate Raw Acceleration to the Unit Gravity Sphere", "topics": [ "auto.calibrate" ] }, { "page": "axivity.counts", "title": "Activity Counts from a Raw Axivity .cwa File", "topics": [ "axivity.counts" ] }, { "page": "backend_info", "title": "Backend Information", "topics": [ "backend_info" ] }, { "page": "chi.sq.periodogram", "title": "Chi-square (Sokolove-Bushell) Periodogram", "topics": [ "chi.sq.periodogram" ] }, { "page": "circadian_cpp", "title": "Complete Circadian Analysis", "topics": [ "circadian_cpp" ] }, { "page": "circadian-analysis", "title": "Circadian Rhythm Analysis", "topics": [ "circadian-analysis" ] }, { "page": "circadian-fractal", "title": "Fractal and Complexity Metrics for Activity Time Series", "topics": [ "circadian-fractal" ] }, { "page": "circadian-period", "title": "Endogenous Circadian Period Estimation (Lomb-Scargle)", "topics": [ "circadian-period" ] }, { "page": "circadian-plots", "title": "Circadian Rhythm Visualizations", "topics": [ "circadian-plots" ] }, { "page": "circadian.batch", "title": "Batch Circadian Analysis of Multiple AGD Files", "topics": [ "circadian.batch" ] }, { "page": "circadian.daily", "title": "Per-Day Nonparametric Metrics", "topics": [ "circadian.daily" ] }, { "page": "circadian.emd", "title": "Empirical Mode Decomposition of the Activity Rhythm", "topics": [ "circadian.emd" ] }, { "page": "circadian.flm", "title": "Functional Linear Model of the 24-Hour Activity Profile", "topics": [ "circadian.flm" ] }, { "page": "circadian.is.multiscale", "title": "Multi-resolution Interdaily Stability (IS)", "topics": [ "circadian.is.multiscale" ] }, { "page": "circadian.onset.ci", "title": "Confidence Intervals for L5/M10 Onset Timing", "topics": [ "circadian.onset.ci" ] }, { "page": "circadian.period", "title": "Estimate Endogenous Circadian Period via the Lomb-Scargle Periodogram", "topics": [ "circadian.period" ] }, { "page": "circadian.quotient", "title": "Circadian Quotient and Relative Amplitude from a Cosinor Fit", "topics": [ "circadian.quotient" ] }, { "page": "circadian.raw", "title": "Circadian Analysis Directly from Raw Acceleration", "topics": [ "circadian.raw" ] }, { "page": "circadian.rhythm", "title": "Circadian Rhythm Analysis", "topics": [ "circadian.rhythm" ] }, { "page": "circadian.spectrogram", "title": "Circadian Spectrogram (Period over Time)", "topics": [ "circadian.spectrogram" ] }, { "page": "circadian.ssa", "title": "Singular Spectrum Analysis of an Activity Series", "topics": [ "circadian.ssa" ] }, { "page": "circadian.wavelet", "title": "Continuous Wavelet Transform of the Activity Rhythm", "topics": [ "circadian.wavelet" ] }, { "page": "circadian.workbook", "title": "Export a Full Circadian Analysis to an Excel Workbook", "topics": [ "circadian.workbook" ] }, { "page": "composite.phase.deviation", "title": "Composite Phase Deviation (Fischer & Roenneberg, 2016)", "topics": [ "composite.phase.deviation" ] }, { "page": "consensus.rhythmicity", "title": "Consensus Rhythmicity Across Methods", "topics": [ "consensus.rhythmicity" ] }, { "page": "cosinor.analysis", "title": "Cosinor Analysis for Circadian Rhythm", "topics": [ "cosinor.analysis" ] }, { "page": "cosinor.antilogistic", "title": "Anti-Logistic (Extended) Cosinor Analysis (Marler et al. 2006)", "topics": [ "cosinor.antilogistic" ] }, { "page": "cosinor.compare", "title": "Compare Cosinor Rhythms Between Two Groups", "topics": [ "cosinor.compare" ] }, { "page": "cosinor.confidence.ellipse", "title": "Joint Amplitude-Acrophase Confidence Ellipse (Bingham et al. 1982)", "topics": [ "cosinor.confidence.ellipse" ] }, { "page": "cosinor.extended", "title": "Multi-Component Cosinor Analysis with Harmonics", "topics": [ "cosinor.extended" ] }, { "page": "cosinor.multicomponent", "title": "Multicomponent Cosinor with Model Selection", "topics": [ "cosinor.multicomponent" ] }, { "page": "counts.from.data.frame", "title": "Activity Counts from a Data Frame", "topics": [ "counts.from.data.frame" ] }, { "page": "cpp_available", "title": "Check C++ Availability", "topics": [ "cpp_available" ] }, { "page": "curve.registration", "title": "Curve Registration of Daily Activity Profiles", "topics": [ "curve.registration" ] }, { "page": "detect.nonwear.choi", "title": "Choi (2011) Non-Wear Detection", "topics": [ "detect.nonwear.choi" ] }, { "page": "detect.nonwear.raw", "title": "Non-Wear Detection from Raw Acceleration", 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"topics": [ "has.inclinometer" ] }, { "page": "hilbert.huang", "title": "Hilbert-Huang Instantaneous Phase and Frequency", "topics": [ "hilbert.huang" ] }, { "page": "intradaily.variability.multiscale", "title": "Multiscale Intradaily Variability (IVm)", "topics": [ "intradaily.variability.multiscale" ] }, { "page": "IS_cpp", "title": "Interdaily Stability (IS)", "topics": [ "IS_cpp" ] }, { "page": "IV_cpp", "title": "Intradaily Variability (IV)", "topics": [ "IV_cpp" ] }, { "page": "L5M10_cpp", "title": "Calculate L5/M10 Circadian Metrics", "topics": [ "L5M10_cpp" ] }, { "page": "lids", "title": "Locomotor Inactivity During Sleep (LIDS)", "topics": [ "lids" ] }, { "page": "mfdfa", "title": "Multifractal Detrended Fluctuation Analysis (MF-DFA)", "topics": [ "mfdfa" ] }, { "page": "multiscale.entropy", "title": "Multiscale Sample Entropy (MSE)", "topics": [ "multiscale.entropy" ] }, { "page": "period.ci", "title": "Confidence Interval for the Endogenous Circadian Period", "topics": [ "period.ci" ] }, { "page": "phase.concentration", "title": "Phase Concentration Tests", "topics": [ "phase.concentration" ] }, { "page": "plot_actogram", "title": "Double-Plotted Actogram", "topics": [ "plot_actogram" ] }, { "page": "plot_changepoints", "title": "Sleep / Wake Change-Point Track", "topics": [ "plot_changepoints" ] }, { "page": "plot_chisq", "title": "Plot the Chi-Square (Sokolove-Bushell) Periodogram", "topics": [ "plot_chisq" ] }, { "page": "plot_cosinor_ellipse", "title": "Cosinor Amplitude-Acrophase Confidence Ellipse", "topics": [ "plot_cosinor_ellipse" ] }, { "page": "plot_cosinor_schematic", "title": "Annotated Cosinor Parameter Schematic", "topics": [ "plot_cosinor_schematic" ] }, { "page": "plot_dfa", "title": "Plot the Detrended Fluctuation Analysis (DFA) Scaling Relationship", "topics": [ "plot_dfa" ] }, { "page": "plot_dichotomy", "title": "Dichotomy Index Plot", "topics": [ "plot_dichotomy" ] }, { "page": "plot_emd", "title": "Empirical Mode Decomposition Stack", "topics": [ "plot_emd" ] }, { "page": "plot_extended_cosinor", "title": "Plot the Extended (Marler) Cosinor Fit on the 24-Hour Activity Profile", "topics": [ "plot_extended_cosinor" ] }, { "page": "plot_lids", "title": "LIDS Ultradian Cycle Curve", "topics": [ "plot_lids" ] }, { "page": "plot_mfdfa", "title": "Multifractal DFA Spectrum", "topics": [ "plot_mfdfa" ] }, { "page": "plot_mse", "title": "Multiscale Entropy Curve", "topics": [ "plot_mse" ] }, { "page": "plot_multicomponent", "title": "Single Cosine vs Multicomponent Cosinor Fit", "topics": [ "plot_multicomponent" ] }, { "page": "plot_multiscale", "title": "Multiscale IS and IV Profiles", "topics": [ "plot_multiscale" ] }, { "page": "plot_period_ci", "title": "Bootstrap Period Confidence Interval", "topics": [ "plot_period_ci" ] }, { "page": "plot_periodogram", "title": "Plot the Lomb-Scargle Periodogram with the Endogenous Period", "topics": [ "plot_periodogram" ] }, { "page": "plot_phase_rose", "title": "Circular Phase Rose", "topics": [ "plot_phase_rose" ] }, { "page": "plot_profile", "title": "Average-Day Profile with the L5 and M10 Windows", "topics": [ "plot_profile" ] }, { "page": "plot_raw_metrics", "title": "Raw-Acceleration Epoch Metrics Profile", "topics": [ "plot_raw_metrics" ] }, { "page": "plot_rest_comparison", "title": "Rest-Detector Comparison Strip", "topics": [ "plot_rest_comparison" ] }, { "page": "plot_spt", "title": "z-Angle Sleep-Period-Time Detection", "topics": [ "plot_spt" ] }, { "page": "plot_ssa_wcor", "title": "SSA w-Correlation Matrix", "topics": [ "plot_ssa_wcor" ] }, { "page": "plot_transitions", "title": "Rest-Activity Transition Curves", "topics": [ "plot_transitions" ] }, { "page": "plot_wavelet", "title": "Wavelet Power Scalogram", "topics": [ "plot_wavelet" ] }, { "page": "plot.actiRhythm_circadian", "title": "Plot Circadian Rhythm Profile", "topics": [ "plot.actiRhythm_circadian" ] }, { "page": "population.cosinor", "title": "Population-Mean Cosinor 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