This class stores data from oceanographic section surveys.
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.
Slots
dataAs with all
oceobjects, thedataslot forsectionobjects is a list containing the main data for the object.metadataAs with all
oceobjects, themetadataslot forsectionobjects is a list containing information about thedataor about the object itself. Examples that are of common interest includestationId,longitude,latitudeandtime.processingLogAs with all
oceobjects, theprocessingLogslot forsectionobjects is a list with entries describing the creation and evolution of the object. The contents are updated by variousocefunctions to keep a record of processing steps. Object summaries andprocessingLogShow()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.
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(),
section,
sectionAddStation(),
sectionGrid(),
sectionSmooth(),
sectionSort(),
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)
}
