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Flag adp Data Past Water Column Boundary

Source: R/adp.R
adpFlagPastBoundary.Rd

Flag variables with the same dimension of v in an adp object that are beyond the water column boundary while retaining existing flags. Currently, this operation can only be performed on adp objects that contain bottom ranges. Commonly, handleFlags() would then be used to remove such data.

Usage

adpFlagPastBoundary(
  x = NULL,
  fields = NULL,
  df = 20,
  smoother,
  trim = 0.15,
  good = 1,
  bad = 4,
  debug = getOption("oceDebug")
)

Arguments

x

an adp object containing bottom ranges.

fields

a variable contained within x indicating which field to flag. If NULL (the default) then adpFlagPastBoundary() applies itself to all flag fields that have the same dimensionality as v in the data slot.

df

the degrees of freedom to use during the smoothing spline operation.

smoother

a function used to smooth the boundary distance. If this is not given, then smooth.spline() is called with df set equal to the value of df given by the user. If it is NULL, then no smoothing is done. If it is a function that takes 2 arguments and returns a vector of values, then that is used. For example, a user might set smoother=function(x, y) smooth.spline(x,y,nknots=length(x)/5)$y to use a smoothing spline with the indicated number of knots.

trim

a scale factor for boundary trimming (see “Details”).

good

number stored in flags to indicate good data.

bad

number stored in flags to indicate bad data.

debug

an integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many oce functions. Generally, setting debug=0 turns off the printing, while higher values suggest that more information be printed. If one function calls another, it usually reduces the value of debug first, so that a user can often obtain deeper debugging by specifying higher debug values.

Value

adpFlagPastBoundary returns an adp object with flags adjusted in the specified fields if data are beyond the water column boundary.

Details

If the object's oceCoordinate is "beam", this works by smoothing the time-dependent bottom ranges (as controlled by the smoother and perhaps the df parameters), beam-by-beam. If oceCoordinate is "enu", "xyz", or "other", smoothing is done based on a time-dependent bottom range averaged across all the beams. Once this is done, data within distance of \(1-trim\) multiplied by the bottom range are flagged as being bad. The default value of trim is 0.15, which is close to the value (0.134) of \(1-cos(angle*pi/180)\), with angle=30 as the beam angle in degrees.

See also

Other things related to adp data: [[,adp-method, [[<-,adp-method, ad2cpCodeToName(), ad2cpHeaderValue(), adp, adp-class, adpAd2cpFileTrim(), adpConvertRawToNumeric(), adpEnsembleAverage(), adpRdiFileTrim(), adp_rdi.000, applyMagneticDeclination,adp-method, as.adp(), beamName(), beamToXyz(), beamToXyzAdp(), beamToXyzAdpAD2CP(), beamToXyzAdv(), beamUnspreadAdp(), binmapAdp(), enuToOther(), enuToOtherAdp(), handleFlags,adp-method, is.ad2cp(), plot,adp-method, read.adp(), read.adp.ad2cp(), read.adp.nortek(), read.adp.rdi(), read.adp.sontek(), read.adp.sontek.serial(), read.aquadopp(), read.aquadoppHR(), read.aquadoppProfiler(), rotateAboutZ(), setFlags,adp-method, subset,adp-method, subtractBottomVelocity(), summary,adp-method, toEnu(), toEnuAdp(), velocityStatistics(), xyzToEnu(), xyzToEnuAdp(), xyzToEnuAdpAD2CP()

Author

Jaimie Harbin, Clark Richards, and Dan Kelley