Extract Parts of a CTD Object

Description

The [[ method works for all oce objects, i.e. objects inheriting from oce-class. The purpose, as with the related replacement method, [[<-, is to insulate users from the internal details of oce objects, by looking for items within the various storage slots of the object. Items not actually stored can also be extracted, including derived data, units of measurement, and data-quality flags.

The method uses a two-step process to try to find the requested information. First, a class-specific function is used to try to access the requested information (see “Details of the specialized ... method”). Second, if no match is found, a general function is used (see ‘Details of the general method’). If neither method can locates the requested item, NULL is returned.

Usage

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## S4 method for signature 'ctd'
x[[i, j, ...]]

Arguments

x

A ctd object, i.e. one inheriting from ctd-class.

i

Character string indicating the name of item to extract.

j

Optional additional information on the i item.

...

Optional additional information (ignored).

Details of the general method

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the value of i.

First, a check is made as to whether i names one of the standard oce slots, and returns the slot contents if so. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

Next, if i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned. This list consists of an item named unit, which is an expression, and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]], then just the expression is returned, and if it ends in " scale", then just the scale is returned.

Next, if i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag). For example, x[["salinityFlag"]] returns a vector of salinity flags if x is a ctd object.

If none of the preceding conditions are met, a check is done to see if the metadata slot contains an item with the provided name, and that is returned, if so. A direct match is required for this condition.

Finally, the data slot is checked to see if it contains an item with the name indicated by i. In this case, a partial match will work; this is accomplished by using pmatch.

If none of the above-listed conditions holds, then NULL is returned.

Details of the specialized ctd method

Some uses of [[,ctd-method involve direct retrieval of items within the data slot of the ctd object, while other uses involve calculations based on items in that data slot. For an example, all ctd objects should hold an item named temperature in the data slot, so for example x[["temperature"]] will retrieve that item. By contrast, x[["sigmaTheta"]] is taken to be a request to compute sigma[theta], and so it yields a call to swTheta(x) even if the data slot of x might happen to contain an item named theta. This can be confusing at first, but it tends to lead to fewer surprises in everyday work, for otherwise the user would be forced to check the contents of any ctd object under analysis, to determine whether that item will be looked up or computed. Nothing is lost in this scheme, since the data within the object are always accessible with oceGetData.

It should be noted that the accessor is set up to retrieve quantities in conventional units. For example, read.ctd.sbe is used on a .cnv file that stores pressure in psi, it will be stored in the same unit within the ctd object, but x[["pressure"]] will return a value that has been converted to decibars. (Users who need the pressure in PSI can use x@data$pressure.) Similarly, temperature is returned in the ITS-90 scale, with a conversion having been performed with T90fromT68, if the object holds temperature in IPTS-68. Again, temperature on the IPTS-68 scale is returned with x@data$temperature.

This preference for computed over stored quantities is accomplished by first checking for computed quantities, and then falling back to the general [[ method if no match is found.

Some quantities are optionally computed. For example, some data files (e.g. the one upon which the section dataset is based) store nitrite along with the sum of nitrite and nitrate, the latter with name `NO2+NO3`. In this case, e.g. x[["nitrate"]] will detect the setup, and subtract nitrite from the sum to yield nitrate.

Below is a list of computed quantities, or at least quantites that are typically not stored in data files. (This is a vague statement because Seabird software permits calculation of many of these and hence storage within .cnv files.)

  • CT or Conservative Temperature: Conservative Temperature, computed with gsw_CT_from_t in the gsw package.

  • depth: Depth in metres below the surface, computed with swDepth(x).

  • N2: Square of Brunt-Vaisala frequency, computed with swN2(x).

  • potential temperature: Potential temperature in the UNESCO formulation, computed with swTheta(x). This is a synonym for theta.

  • Rrho: Density ratio, computed with swRrho(x).

  • SA or Absolute Salinity: Absolute Salinity, computed with gsw_SA_from_SP in the gsw package.

  • sigmaTheta: A form of potential density anomaly, computed with swSigmaTheta(x).

  • sigma0 Equal to sigmaTheta, i.e. potential density anomaly referenced to a pressure of 0dbar, computed with swSigma0(x).

  • sigma1: Potential density anomaly referenced to a pressure of 1000dbar, computed with swSigma1(x).

  • sigma2: Potential density anomaly referenced to a pressure of 2000dbar, computed with swSigma2(x).

  • sigma3: Potential density anomaly referenced to a pressure of 3000dbar, computed with swSigma3(x).

  • sigma4: potential density anomaly referenced to a pressure of 4000dbar, computed with swSigma4(x).

  • SP: Salinity on the Practical Salinity Scale, which is salinity in the data slot.

  • spice: a variable that is in some sense orthogonal to density, calculated with swSpice(x).

  • SR: Reference Salinity computed with gsw_SR_from_SP in the gsw package.

  • Sstar: Preformed Salinity computed with gsw_SR_from_SP in the gsw package.

  • theta: potential temperature in the UNESCO formulation, computed with swTheta(x). This is a synonym for potential temperature.

  • z: Vertical coordinate in metres above the surface, computed with swZ(x).

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[<-,adv-method

Other things related to ctd data: [[<-,ctd-method, as.ctd, cnvName2oceName, ctd-class, ctdDecimate, ctdFindProfiles, ctdRaw, ctdTrim, ctd, handleFlags,ctd-method, plot,ctd-method, plotProfile, plotScan, plotTS, read.ctd.itp, read.ctd.odf, read.ctd.sbe, read.ctd.woce.other, read.ctd.woce, read.ctd, subset,ctd-method, summary,ctd-method, woceNames2oceNames, write.ctd

Examples

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data(ctd)
head(ctd[["temperature"]])

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