detectCycle: detectCycle

In ChemoSens/PTRMSR: Analysis of PTRMS data

detectCycle

Description

Detects breathing cycles (negative peaks with smoothing methods). A breaking cycle begins half of an inspiration, then a full expiration, then an last half of inspiration

Usage

detectCycle(
  df,
  minExpi = NULL,
  maxInspi = NULL,
  smoothMethod = "MovingAverage",
  method = "MAD",
  halfWindowSize = 5,
  timePeriod = NULL,
  SNR = 0,
  minimalDuration = 2,
  forMinExpiDivideMaxIntBy = 4,
  forMaxInspiDivideMaxIntBy = 5,
  mobileMinExpi = NULL,
  mobileMaxInspi = NULL,
  mobileK = 1
)

Arguments

df	dataframe with two columns whose colnames are 'intensity','time'
minExpi	minimal value for an expiry intensity to be detected as an expiry (blue dotted line in the plot).
maxInspi	maximal intensity of the original curve required to be considered as a breathing peak (purple dotted line in the plot)
smoothMethod	smoothing method. Among "MovingAverage" or "SavitzkyGolay". See MSnbase::smooth for more details.
method	method to estimate the noise "MAD" or "" in the spectra
halfWindowSize	required for the smoothing method. Integer corresponding to the half window size to consider.
timePeriod	vector containing the first and last value to attribue to the breathing cycle (start and end of tasting for example). Default to min(time) and max(time)
SNR	signal noise ratio (0 by default) required to be considered as a peak
minimalDuration	minimalDuration of a breathing cycle (2 by default - as a accelerated breathing frequency corresponds to 20 cycles and more by minut and a low frequency is 12 and less -)
forMinExpiDivideMaxIntBy	default to 5. When minExpi is null, it is evaluated as the ratio of the maximal intensity and forMinIntensityDivideMaxIntBy
forMaxInspiDivideMaxIntBy	default to 5. When minExpi is null, it is evaluated as the ratio of the maximal intensity and forMinIntensityDivideMaxIntBy
mobileMinExpi	default to NULL, ifelse an integer higher than 3. If not NULL, the minimal intensity required for an expiration is a mobile one, defined by an mobile average (on the number of points defined in mobileMinExpi) + mobileK * mobile standard deviations (on the same number of points)
mobileMaxInspi	default to NULL, ifelsea integer higher than 3. If not NULL, the maximal intensity required for an inspiration is a mobile one, defined by an mobile average (on the number of points defined in mobileMinExpi) - mobileK * mobile standard deviations (on the same number of points)
mobileK	default to 1. a number to be used in mobileMinExpi or mobileMaxInspi if not NULL

Value

a list containing the times corresponding to cycle limits (cycles), some plots the reversed smoothed data used for detecting peaks (gg$p2) and raw data with the cycle limits (gg$p3), a table containing information about the selected peaks: finalPeakTable and a table containing all the peaks detected before any filter (peakTable)

ChemoSens/PTRMSR documentation built on June 15, 2025, 10:40 a.m.