Package index • actiRhythm

Reading & preparing data

Read ActiGraph counts and raw multi-brand accelerometer files, compute and calibrate raw metrics, detect non-wear, and access the bundled example data.

read.agd(): Read ActiGraph .agd File
agd.counts(): Extract Counts from .agd Data
write.agd(): Write Activity Counts to an .agd File
gt3x.to.agd(): Convert a Raw .gt3x File to an .agd File
has.inclinometer(): Check if AGD Data Has Inclinometer Information
read.actigraph.csv(): Read an ActiGraph (ActiLife) Epoch CSV
counts.from.data.frame(): Activity Counts from a Data Frame
read.raw(): Activity Counts from a Raw Accelerometer File (Any Supported Brand)
gt3x.counts(): Activity Counts from a Raw .gt3x File
axivity.counts(): Activity Counts from a Raw Axivity .cwa File
geneactiv.counts(): Activity Counts from a Raw GENEActiv .bin File
raw.metrics(): Raw-Acceleration Epoch Metrics (ENMO, MAD, z-Angle)
auto.calibrate(): Auto-Calibrate Raw Acceleration to the Unit Gravity Sphere
detect.nonwear.choi(): Choi (2011) Non-Wear Detection
detect.nonwear.troiano(): Troiano (2008) Non-Wear Detection
detect.nonwear.raw(): Non-Wear Detection from Raw Acceleration
example_agd(): Get Path to Example AGD Files
example_raw(): Synthetic Raw Acceleration Recording

Nonparametric rhythm metrics

Shape-free descriptors of the rest-activity rhythm: IS, IV, RA, L5/M10, and fragmentation, with no assumed waveform.

circadian-analysis: Circadian Rhythm Analysis
circadian.rhythm(): Circadian Rhythm Analysis
intradaily.variability.multiscale(): Multiscale Intradaily Variability (IVm)
circadian.is.multiscale(): Multi-resolution Interdaily Stability (IS)
dichotomy.index(): Dichotomy Index (I < O)
circadian.quotient(): Circadian Quotient and Relative Amplitude from a Cosinor Fit
activity.balance.index(): Activity Balance Index
rest.activity.fragmentation(): Rest-Activity Bout Fragmentation
transition.probability(): Rest-Active Transition Probabilities
state.transitions(): Rest-Activity State Transition Rates (kRA, kAR)
activity.extrema(): Generalized Least- and Most-Active Periods (MX / LX)

Cosinor models

Sinusoidal rhythm models from the single cosinor and its rhythmicity test through extended, multicomponent, population-mean, and group-comparison fits.

cosinor.analysis(): Cosinor Analysis for Circadian Rhythm
rhythmicity.test(): Cosinor Rhythmicity Test
cosinor.confidence.ellipse(): Joint Amplitude-Acrophase Confidence Ellipse (Bingham et al. 1982)
cosinor.extended(): Multi-Component Cosinor Analysis with Harmonics
cosinor.antilogistic(): Anti-Logistic (Extended) Cosinor Analysis (Marler et al. 2006)
cosinor.multicomponent(): Multicomponent Cosinor with Model Selection
population.cosinor(): Population-Mean Cosinor (Bingham)
cosinor.compare(): Compare Cosinor Rhythms Between Two Groups
consensus.rhythmicity(): Consensus Rhythmicity Across Methods

Period & spectral analysis

Estimate the free-running period and track how it drifts: Lomb-Scargle and chi-square periodograms, a bootstrap CI, a spectrogram, and ultradian power.

circadian-period: Endogenous Circadian Period Estimation (Lomb-Scargle)
circadian.period(): Estimate Endogenous Circadian Period via the Lomb-Scargle Periodogram
period.ci(): Confidence Interval for the Endogenous Circadian Period
chi.sq.periodogram(): Chi-square (Sokolove-Bushell) Periodogram
circadian.spectrogram(): Circadian Spectrogram (Period over Time)
ultradian.bandpower(): Ultradian Wavelet Band Power
residual.spectrum(): Residual Circadian Spectrum

Fractal & nonlinear dynamics

Long-range correlation and complexity of the activity series.

circadian-fractal: Fractal and Complexity Metrics for Activity Time Series
fractal.dfa(): Detrended Fluctuation Analysis (DFA)
mfdfa(): Multifractal Detrended Fluctuation Analysis (MF-DFA)
multiscale.entropy(): Multiscale Sample Entropy (MSE)

Decomposition & time-frequency

Data-adaptive decompositions of the recording into trend, rhythm, and noise.

circadian.wavelet(): Continuous Wavelet Transform of the Activity Rhythm
wavelet.coi(): Wavelet Cone of Influence
circadian.emd(): Empirical Mode Decomposition of the Activity Rhythm
hilbert.huang(): Hilbert-Huang Instantaneous Phase and Frequency
circadian.ssa(): Singular Spectrum Analysis of an Activity Series
circadian.flm(): Functional Linear Model of the 24-Hour Activity Profile
curve.registration(): Curve Registration of Daily Activity Profiles

Sleep & rest detection

Epoch sleep/wake scoring, rest-period and sleep-period-time detection, and locomotor inactivity during sleep.

sleep.cole.kripke(): Cole-Kripke Sleep/Wake Scoring
sleep.sadeh(): Sadeh Sleep/Wake Scoring
sleep.changepoints(): Change-Point Detection of Sleep and Wake Onsets
rest.periods(): Consolidated Rest-Period Detection (Roenneberg / MASDA)
rest.crespo(): Crespo Rest/Activity Period Detection
rest.hmm(): State-Space (Hidden Markov) Rest-Activity Model
rest.spt(): Sleep-Period-Time Window from the z-Angle (HDCZA)
sib.vanhees(): Sustained-Inactivity-Bout Sleep Scoring from the z-Angle
sleep.from.spt(): Sleep Parameters from SPT and Sustained-Inactivity Bouts
lids(): Locomotor Inactivity During Sleep (LIDS)

Phase, onset & regularity

Sleep timing, regularity, and day-to-day phase stability.

sleep.regularity.index(): Calculate Sleep Regularity Index (SRI) - Exported Version
sri.matrix(): Sleep Regularity Index (SRI) - Phillips (2017) Epoch-of-Day x Day Matrix
social.jet.lag(): Calculate Social Jet Lag
composite.phase.deviation(): Composite Phase Deviation (Fischer & Roenneberg, 2016)
phase.concentration(): Phase Concentration Tests
activity.onset.offset(): Activity Onset and Offset (Relative-Difference Phase Markers)
circadian.onset.ci(): Confidence Intervals for L5/M10 Onset Timing

Batch & reporting workflow

Run the pipeline over many recordings and export full analyses.

circadian.batch(): Batch Circadian Analysis of Multiple AGD Files
circadian.daily(): Per-Day Nonparametric Metrics
circadian.raw(): Circadian Analysis Directly from Raw Acceleration
circadian.workbook(): Export a Full Circadian Analysis to an Excel Workbook
save.circadian.plot(): Save a actiRhythm Plot to a File

Plotting & theme

ggplot2 plots and the package theme/palette.

circadian-plots: Circadian Rhythm Visualizations
plot_actogram(): Double-Plotted Actogram
plot_periodogram(): Plot the Lomb-Scargle Periodogram with the Endogenous Period
plot_chisq(): Plot the Chi-Square (Sokolove-Bushell) Periodogram
plot_period_ci(): Bootstrap Period Confidence Interval
plot_dfa(): Plot the Detrended Fluctuation Analysis (DFA) Scaling Relationship
plot_mfdfa(): Multifractal DFA Spectrum
plot_mse(): Multiscale Entropy Curve
plot_extended_cosinor(): Plot the Extended (Marler) Cosinor Fit on the 24-Hour Activity Profile
plot_cosinor_ellipse(): Cosinor Amplitude-Acrophase Confidence Ellipse
plot_multicomponent(): Single Cosine vs Multicomponent Cosinor Fit
plot_cosinor_schematic(): Annotated Cosinor Parameter Schematic
plot_profile(): Average-Day Profile with the L5 and M10 Windows
plot_dichotomy(): Dichotomy Index Plot
plot_transitions(): Rest-Activity Transition Curves
plot_multiscale(): Multiscale IS and IV Profiles
plot_wavelet(): Wavelet Power Scalogram
plot_emd(): Empirical Mode Decomposition Stack
plot_ssa_wcor(): SSA w-Correlation Matrix
plot_phase_rose(): Circular Phase Rose
plot_changepoints(): Sleep / Wake Change-Point Track
plot_lids(): LIDS Ultradian Cycle Curve
plot_rest_comparison(): Rest-Detector Comparison Strip
plot_spt(): z-Angle Sleep-Period-Time Detection
plot_raw_metrics(): Raw-Acceleration Epoch Metrics Profile
theme_actiRhythm(): actiRhythm ggplot2 Theme
set_actiRhythm_theme(): Set actiRhythm Theme as Default
scale_color_actiRhythm(): ggplot2 Scale for actiRhythm Colors
scale_fill_actiRhythm(): ggplot2 Fill Scale for actiRhythm Colors
actiRhythm_colors(): actiRhythm Color Generator

C++ backend

The compiled fast path behind the nonparametric metrics, and its controls.

cpp_available(): Check C++ Availability
backend_info(): Backend Information
circadian_cpp(): Complete Circadian Analysis
IS_cpp(): Interdaily Stability (IS)
IV_cpp(): Intradaily Variability (IV)
L5M10_cpp(): Calculate L5/M10 Circadian Metrics
rolling_mean(): Rolling Mean
rolling_sd(): Rolling Standard Deviation
rolling_sum(): Rolling Sum

Print & plot methods

S3 methods dispatched automatically when you print or plot a result object.

print(<actiRhythm_circadian>): Print Method for Circadian Rhythm Results
print(<actiRhythm_cosinor>): Print method for cosinor analysis
print(<actiRhythm_cosinor_extended>): Print method for extended cosinor analysis
print(<actiRhythm_dfa>): Print Method for DFA Results
print(<actiRhythm_mse>): Print Method for Multiscale Entropy Results
plot(<actiRhythm_circadian>): Plot Circadian Rhythm Profile
plot_actogram(): Double-Plotted Actogram
plot_changepoints(): Sleep / Wake Change-Point Track
plot_chisq(): Plot the Chi-Square (Sokolove-Bushell) Periodogram
plot_cosinor_ellipse(): Cosinor Amplitude-Acrophase Confidence Ellipse
plot_cosinor_schematic(): Annotated Cosinor Parameter Schematic
plot_dfa(): Plot the Detrended Fluctuation Analysis (DFA) Scaling Relationship
plot_dichotomy(): Dichotomy Index Plot
plot_emd(): Empirical Mode Decomposition Stack
plot_extended_cosinor(): Plot the Extended (Marler) Cosinor Fit on the 24-Hour Activity Profile
plot_lids(): LIDS Ultradian Cycle Curve
plot_mfdfa(): Multifractal DFA Spectrum
plot_mse(): Multiscale Entropy Curve
plot_multicomponent(): Single Cosine vs Multicomponent Cosinor Fit
plot_multiscale(): Multiscale IS and IV Profiles
plot_periodogram(): Plot the Lomb-Scargle Periodogram with the Endogenous Period
plot_period_ci(): Bootstrap Period Confidence Interval
plot_phase_rose(): Circular Phase Rose
plot_profile(): Average-Day Profile with the L5 and M10 Windows
plot_raw_metrics(): Raw-Acceleration Epoch Metrics Profile
plot_rest_comparison(): Rest-Detector Comparison Strip
plot_spt(): z-Angle Sleep-Period-Time Detection
plot_ssa_wcor(): SSA w-Correlation Matrix
plot_transitions(): Rest-Activity Transition Curves
plot_wavelet(): Wavelet Power Scalogram