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

Description

This class stores 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. Since as.ctd() does the same with salinity, the result this is that all ctd objects hold salinity, temperature and pressure, which are henceforth called the three basic quantities.

Arguments

Slots

data: As with all oce objects, the data slot for ctd objects is a list containing the main data for the object. The key items stored in this slot are: salinity, temperature, and pressure, although in many instances there are quite a few additional items.

metadata

As with all oce objects, the metadata slot for ctd objects is a list containing information about the data or about the object itself. An example of the former might be the location at which a ctd measurement was made, stored in longitude and latitude, and of the latter might be filename, the name of the data source.

processingLog

As with all oce objects, the processingLog slot for ctd objects is a list with entries describing the creation and evolution of the object. The contents are updated by various oce functions to keep a record of processing steps. Object summaries and processingLogShow() both display the log.

Modifying slot contents

Although the [[<- operator may permit modification of the contents of '>ctd objects (see [[<-,ctd-method), it is better to use oceSetData() and oceSetMetadata(), because those functions save an entry in the processingLog that describes the change.

Retrieving slot contents

The full contents of the data and metadata slots of a '>ctd object may be retrieved in the standard R way using slot(). For example slot(o,"data") returns the data slot of an object named o, and similarly slot(o,"metadata") returns the metadata slot.

The slots may also be obtained with the [[,ctd-method operator, as e.g. o[["data"]] and o[["metadata"]], respectively.

The [[,ctd-method operator can also be used to retrieve items from within the data and metadata slots. For example, o[["temperature"]] can be used to retrieve temperature from an object containing that quantity. The rule is that a named quantity is sought first within the object's metadata slot, with the data slot being checked only if metadata does not contain the item. This [[ method can also be used to get certain derived quantities, if the object contains sufficient information to calculate them. For example, an object that holds (practical) salinity, temperature and pressure, along with longitude and latitude, has sufficient information to compute Absolute Salinity, and so o[["SA"]] will yield the calculated Absolute Salinity.

It is also possible to find items more directly, using oceGetData() and oceGetMetadata(), but neither of these functions can retrieve derived items.

Reading/creating <code>ctd</code> objects

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, and sufficiently skilled users may even manipulate the contents directly.

Data sources

Archived CTD (and other) data may be found on servers such as

https://cchdo.ucsd.edu/

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 dividing 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.

Examples

Run this code

# NOT RUN {
# 1. Create a ctd object with fake data.
a <- as.ctd(salinity=35+1:3/10, temperature=10-1:3/10, pressure=1:3)
summary(a)

# 2. Fix a typo in a station latitude (fake! it's actually okay)
data(ctd)
ctd <- oceSetMetadata(ctd, "latitude", ctd[["latitude"]]-0.001,
                     "fix latitude typo in log book")

# }

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