Circadian Rest-Activity Rhythm Analysis

Documentation for package ‘actiRhythm’ version 0.1.0

Help Pages

-- 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