rythm_analysis_by_window: Helper function to analyze the period of a time series

In edpclau/circadian-dynamics: Period and Rythm Analysis of Timeseries Data

Helper function to analyze the period of a time series

Description

Helper function which takes the output from process_timeseries and runs: autocorrelation, lomb-scargle periodogram, and COSINOR analysis.

Usage

multivariate_rythm_analysis(df = NULL, sampling_rate = NULL, auto_correlation = TRUE, lomb_scargle = TRUE,
from = NULL, to = NULL, ofac = 1, multipeak_period = TRUE, peak_of_interest = Inf,
datetime = NULL, window = NULL, values = NULL)

Arguments

df	The output from multivariate_process_timeseries
sampling_rate	A character string indicating the sampling rate of the data. Examples: '30 minutes', '1 hour', '4 seconds', '100 days'.
autocorrelation	Logical. If TRUE (default) runs an autocorrelation on each window of the data. If FALSE, does not run.
lomb_scargle	Logical. If TRUE (default) runs the Lomb-Scargle Periodogram on each window on the data. If FALSE, does not run.
from	An optional numeric indicating from which period or frequency to start looking for peaks. Must be in hours. Default = 18.
to	An optional numeric indicating up to which period or frequency to start looking for peaks. Must be in hours. Default = 30.
ofac	[lomb::lsp()] The oversampling factor. Must be an integer>=1. Larger values of ofac lead to finer scanning of frequencies but may be time-consuming for large datasets and/or large frequency ranges (from...to).
datetime	optional if a data.frame is supplied. A list of multiple POSIXct vectors corresponding to each mearument variable.
window	optional if a data.frame is supplied. A list of multiple window vectors corresponding to each mearument variable.
values	optional if a data.frame is supplied. A list of multiple value vectors corresponding to each mearument variable.

Value

A names list of data.frames with the combined output of [acf_by_window()], [lsp_by_window()], and [cosinor_lm()].

Examples

analysis <- rythm_analysis(df = processed_data, sampling_rate = "30 min", auto_correlation = TRUE,
lomb_scargle = TRUE, from = 36, to = 48, multipeak_period = TRUE)

edpclau/circadian-dynamics documentation built on Aug. 25, 2023, 12:18 p.m.