ggplot2 visualizations for the circadian / chronobiology metrics produced by actiRhythm. These functions are thin plotting wrappers around the existing analytic engines and add no new fitting logic:
plot_periodogramdraws the Lomb-Scargle periodogram and highlights the endogenous period estimated bycircadian.period.plot_extended_cosinoroverlays the Marler extended (anti-logistic) cosinor fit fromcosinor.antilogisticand the ordinary cosinor fromcosinor.analysison the averaged 24-hour activity profile.plot_dfadraws the detrended-fluctuation log-log scaling plot fromfractal.dfa.
Every function returns a ggplot object, never errors on degenerate or
insufficient input (it returns an annotated empty plot instead), and falls
back to ggplot2::theme_minimal() when the package theme helpers are
unavailable.
References
Lomb NR (1976). “Least-squares frequency analysis of unequally spaced data.” Astrophysics and Space Science, 39(2), 447–462. doi:10.1007/BF00648343 .
Scargle JD (1982). “Studies in astronomical time series analysis. II. Statistical aspects of spectral analysis of unevenly spaced data.” The Astrophysical Journal, 263, 835–853. doi:10.1086/160554 .
Marler MR, Gehrman P, Martin JL, Ancoli-Israel S (2006). “The sigmoidally transformed cosine curve: a mathematical model for circadian rhythms with symmetric non-sinusoidal shapes.” Statistics in Medicine, 25(22), 3893–3904. doi:10.1002/sim.2466 .
Peng CK, Buldyrev SV, Havlin S, Simons M, Stanley HE, Goldberger AL (1994). “Mosaic organization of DNA nucleotides.” Physical Review E, 49(2), 1685–1689. doi:10.1103/PhysRevE.49.1685 .