oce (version 1.0-1)

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. 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.

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 that will save an entry in the processingLog to describe the change.

Retrieving slot contents

The full contents of the data and metadata slots of a ctd object named ctd may be retrieved in the standard R way. For example, slot(ctd, "data") and slot(ctd, "metadata") return the data and metadata slots, respectively. The [[,ctd-method operator can also be used to access slots, with ctd[["data"]] and ctd[["metadata"]], respectively. Furthermore, [[,ctd-method can be used to retrieve named items (and potentially some derived items) within the metadata and data slots, the former taking precedence over the latter in the lookup. It is also possible to find items more directly, using oceGetData and oceGetMetadata, but this cannot 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 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.

See Also

Other things related to ctd data: [[,ctd-method, [[<-,ctd-method, as.ctd, cnvName2oceName, ctdDecimate, ctdFindProfiles, ctdRaw, ctdTrim, ctd, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames, oceUnits2whpUnits, plot,ctd-method, plotProfile, plotScan, plotTS, read.ctd.itp, read.ctd.odf, read.ctd.sbe, read.ctd.woce.other, read.ctd.woce, read.ctd, setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames, woceUnit2oceUnit, write.ctd

Other classes provided by oce: adp-class, adv-class, argo-class, bremen-class, cm-class, coastline-class, lisst-class, lobo-class, met-class, oce-class, odf-class, rsk-class, sealevel-class, section-class, topo-class, windrose-class

Examples

# 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")

# }