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.
dataAs 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.
metadataAs 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.
processingLogAs 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.
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.
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.
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.
Archived CTD (and other) data may be found on servers such as
https://cchdo.ucsd.edu/
Dan Kelley
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.
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz,
[[,ctd-method,
[[<-,ctd-method,
as.ctd(),
cnvName2oceName(),
ctd.cnv.gz,
ctdDecimate(),
ctdFindProfilesRBR(),
ctdFindProfiles(),
ctdRaw,
ctdRepair(),
ctdTrim(),
ctd_aml.csv.gz,
ctd,
d200321-001.ctd.gz,
d201211_0011.cnv.gz,
handleFlags,ctd-method,
initialize,ctd-method,
initializeFlagScheme,ctd-method,
oceNames2whpNames(),
oceUnits2whpUnits(),
plot,ctd-method,
plotProfile(),
plotScan(),
plotTS(),
read.ctd.aml(),
read.ctd.itp(),
read.ctd.odf(),
read.ctd.odv(),
read.ctd.sbe(),
read.ctd.ssda(),
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,
xbt-class
# 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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