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

tipaPhaseRef {tipa}

R Documentation

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.

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)