ctd. Accessing metadata.
Metadata (contained in the S4 slot named metadata) may be retrieved
or set by name, ctd[["longitude"]] <- ctd[["longitude"]] + 1
corrects a one-degree error.
Accessing measured data.
Column data may be accessed by name, e.g. ctd[["salinity"]],
ctd[["temperature"]], ctd[["pressure"]], etc. The TEOS-10
notation for these quantities also works, with ctd[["SP"]],
ctd[["t"]] and ctd[["p"]] returning identical values to those
returned for the longer names. (FIXME: GSW "t" should be T in ITS-90, but
"temperature" will be whatever happens to be in the datafile, which could
be IPTS-68 or ITS-90. Maybe there should be methods for "ITS-90" etc. This
needs to be adjusted in code and documentation.) After these names have
been checked, the remaining names in the data slot are checked using
pmatch, so that e.g. ctd[["sal"]] will recover
practical salinity, ctd[["sc"]] will recover scan (if
it exists), etc.
Accessing derived data.
Depth is accessed with e.g. ctd[["depth"]], while its negative, the
vertical coordinate, is accessed with e.g. ctd[["z"]]; note that
these are calculated using swDepth and swZ, and
that any values that may have been read in a data file are ignored.
Potential temperature defined according to UNESCO-1980 is calculated with
ctd[["theta"]] or ctd[["potential temperature"]]. Salinity
is retrieved with ctd[["S"]] or ctd[["salinity"]].
Conservative Temperature defined according to TEOS-2010 is calculated with
ctd[["CT"]] or ctd[["conservative temperature"]]. Absolute
salinity is calculated with ctd[["SA"]] or ctd[["absolute
salinity"]]. Note that the salinity calculation requires a latitude
and longitude, and if the ctd object lacks those data, the values
300E and 30N will be used as a default.
The square of buoyancy frequency is retrieved with ctd[["N2"]] or
swN2, density ratio with ctd[["Rrho"]] and spiciness
with ctd[["spice"]].
Assigning values.
Items stored in the object may be altered with e.g.
ctd[["salinity"]] <- rep(35,10). For obvious reasons, this does not
work with derived quantities such as conservative temperature, etc.
Overview of contents.
The show method (e.g. show(ctd)) displays information about
the object.
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.
Statistical summaries are provided by summary.ctd, while
show displays an overview.
CTD objects may be plotted with plot.ctd, 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.
Low-level manipulation may be done with functions such as
ctdAddColumn and ctdUpdateHeader.
Additionally, many of the contents of CTD objects may be altered with the
[[]] scheme discussed above, and skilled uses may also manipulate
the contents directly.