ctd-class: Class to Store CTD (or general hydrographic) Data

Description

Class to store hydrographic data such as measured with a CTD (conductivity, temperature, depth) instrument, or with other systems that produce similar data. Data repositories may store conductivity, temperature and depth, as in the instrument name, but it is also common to store salinity, temperature and pressure instead (or in addition). For this reason, ctd objects are required to hold salinity, temperature and pressure in their data slot, with other data being optional. Formulae are available for converting between variants of these data triplets, e.g. swSCTp can calculate salinity given conductivity, temperature and pressure, and these are used by the main functions that create ctd objects. For example, if read.ctd.sbe is used to read a Seabird file that contains only conductivity, temperature and pressure, then that function will automatically append a data item to hold salinity. as.ctd acts similarly. The result this is that all ctd objects hold salinity, temperature and pressure, which are henceforth called the three basic quantities.

Arguments

Accessing data

Data may be extracted with [[,ctd-method and inserted with [[<-,ctd-method. As noted above, [[,ctd-method returns temperature in the ITS-90 scale and pressure in dbar, regardless of the scale and unit of the data within the object. Type ?"[[,ctd-method" or ?"[[<-,ctd-method" to learn more. Depth is accessed with e.g. ctd[["depth"]], while its negative, the vertical coordinate, is accessed with e.g. ctd[["z"]]; note that these are calculated using swDepth and swZ, and that any values that may have been read in a data file are ignored. Potential temperature defined according to UNESCO-1980 is calculated with ctd[["theta"]] or ctd[["potential temperature"]]. Salinity is retrieved with ctd[["S"]] or ctd[["salinity"]]. Conservative Temperature defined according to TEOS-2010 is calculated with ctd[["CT"]] or ctd[["conservative temperature"]]. Absolute salinity is calculated with ctd[["SA"]] or

ctd[["absolute
salinity"]]

. Note that the salinity calculation requires a latitude and longitude, and if the ctd object lacks those data, the values 300E and 30N will be used as a default. The square of buoyancy frequency is retrieved with ctd[["N2"]] or swN2, density ratio with ctd[["Rrho"]] and spiciness with ctd[["spice"]].

Extracting values

Items stored in the object may be altered with e.g.

ctd[["salinity"]]
  <- rep(35,10)

. For obvious reasons, this does not work with derived quantities such as conservative temperature, etc.

Reading/creating data

A file containing CTD profile data may be read with read.ctd, and a CTD object can also be created with as.ctd. See read.ctd for references on data formats used in CTD files. Data can also be assembled into ctd objects with as.ctd. Statistical summaries are provided by summary,ctd-method, while show displays an overview. CTD objects may be plotted with plot,ctd-method, which does much of its work by calling plotProfile or plotTS, both of which can also be called by the user, to get fine control over the plots. A CTD profile can be isolated from a larger record with ctdTrim, a task made easier when plotScan is used to examine the results. Towyow data can be split up into sets of profiles (ascending or descending) with ctdFindProfiles. CTD data may be smoothed and/or cast onto specified pressure levels with ctdDecimate. As with all oce objects, low-level manipulation may be done with oceSetData and oceSetMetadata. Additionally, many of the contents of CTD objects may be altered with the [[,ctd-method scheme discussed above, and skilled users may also manipulate the contents directly.

Details

Different units and scales are permitted for the three basic quantities, and most oce functions check those units and scales before doing calculations (e.g. of seawater density), because those calculations demand certain units and scales. The way this is handled is that the accessor function [[,ctd-method returns values in standardized form. For example, a ctd object might hold temperature defined on the IPTS-68 scale, but e.g. ctd[["temperature"]] returns a value on the ITS-90 scale. (The conversion is done with T90fromT68.) Similarly, pressure may be stored in either dbars or PSI, but e.g. ctd[["pressure"]] returns a value in dbars, after multiplying by 0.689476 if the value is stored in PSI. Luckily, there is (as of early 2016) only one salinity scale in common use in data files, namely PSS-78.

The TEOS-10 notation for these quantities also works, with ctd[["SP"]], ctd[["t"]] and ctd[["p"]] returning identical values to those returned for the longer names.

After the names listed above have been checked, the remaining names in the data slot are checked using pmatch, so that e.g. ctd[["sal"]] will recover practical salinity, ctd[["sc"]] will recover scan (if it exists), etc.