# Circadian Rest-Activity Rhythm Analysis

## Documentation for package ‘actiRhythm’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A B C D E F G H I L M P R S T U W

## -- A --

actiRhythm_colors | actiRhythm Color Generator
activity.balance.index | Activity Balance Index
activity.extrema | Generalized Least- and Most-Active Periods (MX / LX)
activity.onset.offset | Activity Onset and Offset (Relative-Difference Phase Markers)
agd.counts | Extract Counts from .agd Data
auto.calibrate | Auto-Calibrate Raw Acceleration to the Unit Gravity Sphere
axivity.counts | Activity Counts from a Raw Axivity .cwa File

## -- B --

backend_info | Backend Information

## -- C --

chi.sq.periodogram | Chi-square (Sokolove-Bushell) Periodogram
circadian-analysis | Circadian Rhythm Analysis
circadian-fractal | Fractal and Complexity Metrics for Activity Time Series
circadian-period | Endogenous Circadian Period Estimation (Lomb-Scargle)
circadian-plots | Circadian Rhythm Visualizations
circadian.batch | Batch Circadian Analysis of Multiple AGD Files
circadian.daily | Per-Day Nonparametric Metrics
circadian.emd | Empirical Mode Decomposition of the Activity Rhythm
circadian.flm | Functional Linear Model of the 24-Hour Activity Profile
circadian.is.multiscale | Multi-resolution Interdaily Stability (IS)
circadian.onset.ci | Confidence Intervals for L5/M10 Onset Timing
circadian.period | Estimate Endogenous Circadian Period via the Lomb-Scargle Periodogram
circadian.quotient | Circadian Quotient and Relative Amplitude from a Cosinor Fit
circadian.raw | Circadian Analysis Directly from Raw Acceleration
circadian.rhythm | Circadian Rhythm Analysis
circadian.spectrogram | Circadian Spectrogram (Period over Time)
circadian.ssa | Singular Spectrum Analysis of an Activity Series
circadian.wavelet | Continuous Wavelet Transform of the Activity Rhythm
circadian.workbook | Export a Full Circadian Analysis to an Excel Workbook
circadian_cpp | Complete Circadian Analysis
composite.phase.deviation | Composite Phase Deviation (Fischer & Roenneberg, 2016)
consensus.rhythmicity | Consensus Rhythmicity Across Methods
cosinor.analysis | Cosinor Analysis for Circadian Rhythm
cosinor.antilogistic | Anti-Logistic (Extended) Cosinor Analysis (Marler et al. 2006)
cosinor.compare | Compare Cosinor Rhythms Between Two Groups
cosinor.confidence.ellipse | Joint Amplitude-Acrophase Confidence Ellipse (Bingham et al. 1982)
cosinor.extended | Multi-Component Cosinor Analysis with Harmonics
cosinor.multicomponent | Multicomponent Cosinor with Model Selection
counts.from.data.frame | Activity Counts from a Data Frame
cpp_available | Check C++ Availability
curve.registration | Curve Registration of Daily Activity Profiles

## -- D --

detect.nonwear.choi | Choi (2011) Non-Wear Detection
detect.nonwear.raw | Non-Wear Detection from Raw Acceleration
detect.nonwear.troiano | Troiano (2008) Non-Wear Detection
dichotomy.index | Dichotomy Index (I < O)

## -- E --

example_agd | Get Path to Example AGD Files
example_raw | Synthetic Raw Acceleration Recording

## -- F --

fractal.dfa | Detrended Fluctuation Analysis (DFA)

## -- G --

geneactiv.counts | Activity Counts from a Raw GENEActiv .bin File
gt3x.counts | Activity Counts from a Raw .gt3x File
gt3x.to.agd | Convert a Raw .gt3x File to an .agd File

## -- H --

has.inclinometer | Check if AGD Data Has Inclinometer Information
hilbert.huang | Hilbert-Huang Instantaneous Phase and Frequency

## -- I --

intradaily.variability.multiscale | Multiscale Intradaily Variability (IVm)
IS_cpp | Interdaily Stability (IS)
IV_cpp | Intradaily Variability (IV)

## -- L --

L5M10_cpp | Calculate L5/M10 Circadian Metrics
lids | Locomotor Inactivity During Sleep (LIDS)

## -- M --

mfdfa | Multifractal Detrended Fluctuation Analysis (MF-DFA)
multiscale.entropy | Multiscale Sample Entropy (MSE)

## -- P --

period.ci | Confidence Interval for the Endogenous Circadian Period
phase.concentration | Phase Concentration Tests
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
population.cosinor | Population-Mean Cosinor (Bingham)
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

## -- R --

raw.metrics | Raw-Acceleration Epoch Metrics (ENMO, MAD, z-Angle)
read.actigraph.csv | Read an ActiGraph (ActiLife) Epoch CSV
read.agd | Read ActiGraph .agd File
read.raw | Activity Counts from a Raw Accelerometer File (Any Supported Brand)
residual.spectrum | Residual Circadian Spectrum
rest.activity.fragmentation | Rest-Activity Bout Fragmentation
rest.crespo | Crespo Rest/Activity Period Detection
rest.hmm | State-Space (Hidden Markov) Rest-Activity Model
rest.periods | Consolidated Rest-Period Detection (Roenneberg / MASDA)
rest.spt | Sleep-Period-Time Window from the z-Angle (HDCZA)
rhythmicity.test | Cosinor Rhythmicity Test
rolling_mean | Rolling Mean
rolling_sd | Rolling Standard Deviation
rolling_sum | Rolling Sum

## -- S --

save.circadian.plot | Save a actiRhythm Plot to a File
scale_color_actiRhythm | ggplot2 Scale for actiRhythm Colors
scale_fill_actiRhythm | ggplot2 Fill Scale for actiRhythm Colors
set_actiRhythm_theme | Set actiRhythm Theme as Default
sib.vanhees | Sustained-Inactivity-Bout Sleep Scoring from the z-Angle
sleep.changepoints | Change-Point Detection of Sleep and Wake Onsets
sleep.cole.kripke | Cole-Kripke Sleep/Wake Scoring
sleep.from.spt | Sleep Parameters from SPT and Sustained-Inactivity Bouts
sleep.regularity.index | Calculate Sleep Regularity Index (SRI) - Exported Version
sleep.sadeh | Sadeh Sleep/Wake Scoring
social.jet.lag | Calculate Social Jet Lag
sri.matrix | Sleep Regularity Index (SRI) - Phillips (2017) Epoch-of-Day x Day Matrix
state.transitions | Rest-Activity State Transition Rates (kRA, kAR)

## -- T --

theme_actiRhythm | actiRhythm ggplot2 Theme
transition.probability | Rest-Active Transition Probabilities

## -- U --

ultradian.bandpower | Ultradian Wavelet Band Power

## -- W --

wavelet.coi | Wavelet Cone of Influence
write.agd | Write Activity Counts to an .agd File