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