tipaPhaseRef: Use phase reference points to estimate the phase shift...

In tipa: Tau-Independent Phase Analysis for Circadian Time-Course Data

Use phase reference points to estimate the phase shift induced by a stimulus during a circadian time-course.

Description

Calculate the phase shift based on the times of a phase reference point (e.g., onset of activity), accounting for possible period changes and for the point in the circadian cycle at which the stimulus occurred. If the rhythms of the measurement are approximately sinusoidal, it is recommended to instead use tipaCosinor().

Usage

tipaPhaseRef(phaseRefTimes, stimOnset, stimDuration = 0, period = NULL)

Arguments

phaseRefTimes	Vector of times of the chosen phase reference point.
stimOnset	Time at which the stimulus started.
stimDuration	Duration of the stimulus and any transients. Data between stimOnset and stimOnset + stimDuration will be ignored.
period	Optional list with elements "pre" and "post" corresponding to the period of the oscillations prior to and subsequent to the stimulus. If not supplied, the periods for pre- and post-stimulus are calculated as the mean time between occurrences of the phase reference point within the respective epoch. Using this argument is not recommended.

Value

A list.

phaseShift	Estimated phase shift in circadian hours. Negative values indicate a delay, positive values an advance.
epochInfo	data.frame containing estimated period for each epoch.

See Also

tipaCosinor()

Examples

# Peak times of bioluminescence (in hours)
phaseRefTimes = c(-75.5, -51.5, -27.4, -3.8,
                  20.5, 42.4, 65.5, 88.0)
result = tipaPhaseRef(phaseRefTimes, stimOnset = 0)

# Data from multiple (simulated) experiments
getExtrFile = function() {
  system.file('extdata', 'phaseRefTimes.csv', package = 'tipa')}
getStimFile = function() {
  system.file('extdata', 'stimOnsets.csv', package = 'tipa')}

extrDf = read.csv(getExtrFile(), stringsAsFactors = FALSE)
stimDf = read.csv(getStimFile(), stringsAsFactors = FALSE)

resultList = lapply(stimDf$expId, function(ii) {
  phaseRefTimes = extrDf$phaseRefTime[extrDf$expId == ii]
  stimOnset = stimDf$stimOnset[stimDf$expId == ii]
  tipaPhaseRef(phaseRefTimes, stimOnset)})

phaseShifts = sapply(resultList, function(r) r$phaseShift)

tipa documentation built on Aug. 21, 2023, 5:07 p.m.