oce (version 1.8-1)

section-class: Class to Store Hydrographic Section Data

Description

This class stores data from oceanographic section surveys.

Slots

data

As with all oce objects, the data slot for section objects is a list containing the main data for the object.

metadata

As with all oce objects, the metadata slot for section objects is a list containing information about the data or about the object itself. Examples that are of common interest include stationId, longitude, latitude and time.

processingLog

As with all oce objects, the processingLog slot for section 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 section objects (see [[<-,section-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 section 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 [[,section-method operator, as e.g. o[["data"]] and o[["metadata"]], respectively.

The [[,section-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.

Author

Dan Kelley

Details

Sections can be read with read.section() or created with read.section() or created from CTD objects by using as.section() or by adding a ctd station to an existing section with sectionAddStation().

Sections may be sorted with sectionSort(), subsetted with subset,section-method(), smoothed with sectionSmooth(), and gridded with sectionGrid(). A "spine" may be added to a section with addSpine(). Sections may be summarized with summary,section-method() and plotted with plot,section-method().

The sample dataset section() contains data along WOCE line A03.

See Also

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

Other things related to section data: [[,section-method, [[<-,section-method, as.section(), handleFlags,section-method, initializeFlagScheme,section-method, plot,section-method, read.section(), sectionAddStation(), sectionGrid(), sectionSmooth(), sectionSort(), section, subset,section-method, summary,section-method

Examples

library(oce)
data(section)
plot(section[["station", 1]])
pairs(cbind(z=-section[["pressure"]],T=section[["temperature"]],S=section[["salinity"]]))
# T profiles for first few stations in section, at common scale
par(mfrow=c(3,3))
Tlim <- range(section[["temperature"]])
ylim <- rev(range(section[["pressure"]]))
for (stn in section[["station", 1:9]]) {
    plotProfile(stn, xtype="potential temperature", ylim=ylim, Tlim=Tlim)
}