ptrvReport: Returns a report for a given dataset
In ChemoSens/PTRMSR: Analysis of PTRMS data

ptrvReport

R Documentation

Returns a report for a given dataset

Description

Returns a report for a given dataset

Usage

ptrvReport(
  dataset,
  selecIons = "evolving",
  listIons = NULL,
  referenceBreath,
  smoothMethod = "MovingAverage",
  methodDetectStart = "startPeakProportion",
  noisePeriodIBT = c(0, 30),
  noisePeriodSig = c(0, 30),
  noisePeriodDS = c(0, 30),
  proportionOfMax = 0.3,
  halfWindowSize = 12,
  startPeriod = c(20, 60),
  detectingStart = FALSE,
  minimalDuration = 2,
  minExpi = NULL,
  maxInspi = NULL,
  forMinExpiDivideMaxIntBy = 4,
  forMaxInspiDivideMaxIntBy = 5
)

Arguments

`dataset`	whose names are timeCol, Ion1,... ,Ionp.
`selecIons`	if "evolving", the selected ions are the ones found as significant in ptrvSignificantSNRIons with noisePeriodSig and max method.If "namely", only the ions present in listIons are selected
`listIons`	list of ions to be presented in the report
`referenceBreath`	name of the ion taken as reference for breathing
`smoothMethod`	NULL, "SavitzkyGolay" or "MovingAverage"
`methodDetectStart`	method to detect start (see ptrvDetectStart). If numeric, the
`noisePeriodIBT`	noise period used during intensity by time calculation
`noisePeriodSig`	noise period used during significant ions calculation
`noisePeriodDS`	noise period used during the start detection
`proportionOfMax`	Number between 0 and 1. If method startPeakProportion is chosen and length(starts)==1, the starting time will be the first time that the intensity reaches this proportion of the maximale intensity of the peak. If length(starts) > 1, the starting time will be the minimum value obtained with this method for all starts.
`halfWindowSize`	parameter used to determine the smooth for the peak-picking used in break detection
`startPeriod`	Vector of two numbers. The starting time obtained has to be in this interval.
`detectingStart`	boolean specifying wether the detect start procedure should be done (TRUE) or not (FALSE)
`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 -)
`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)
`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