Read a file that contains a series of ctd profiles that make up an
oceanographic section.
Only exchange BOT comma-separated value format is permitted at this time,
but other formats may be added later. It should also be noted that the parsing
scheme was developed after inspection of the A03 data set (see Examples). This
may cause problems if the format is not universal. For example, the header must
name the salinity column "CTDSAL"; if not, salinity values will not be
read from the file.
read.section(
file,
directory,
sectionId = "",
flags,
ship = "",
scientist = "",
institute = "",
missingValue = -999,
debug = getOption("oceDebug"),
processingLog
)A file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see ‘Details’).
A character string indicating the name of a directory that contains a set of CTD files that hold individual stations in the section.
Optional string indicating the name for the section. If not provided, the section ID is determined by examination of the file header.
Ignored, and deprecated (will be disallowed in a future version).
Name of the ship carrying out the sampling.
Name of chief scientist aboard ship.
Name of chief scientist's institute.
Numerical value used to indicate missing data.
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many oce functions. Generally, setting debug=0
turns off the printing, while higher values suggest that more information
be printed. If one function calls another, it usually reduces the value of
debug first, so that a user can often obtain deeper debugging
by specifying higher debug values.
If provided, the action item to be stored in the log. This is typically only provided for internal calls; the default that it provides is better for normal calls by a user.
WOCE datasets commonly have a column named CTDSAL for salinity inferred
from a CTD and SALNTY (not a typo) for salinity derived from bottle data.
If only one of these is present in the data file, the data will be called
salinity in the data slot of the return value. However, if both
are present, then CTDSAL is stored as salinity and SALNTY
is stored as salinityBottle.
Several repository sites provide section data. A reasonably stable example is
https://cchdo.ucsd.edu, but a search on "WOCE bottle data" should
turn up other sites, if this ceases to exist. Only
the so-called exchange BOT data format can be processed by read.section()
at this time. Data names are inferred from column headings using
woceNames2oceNames().
Other things related to section data:
[[,section-method,
[[<-,section-method,
as.section(),
handleFlags,section-method,
initializeFlagScheme,section-method,
plot,section-method,
section-class,
sectionAddStation(),
sectionGrid(),
sectionSmooth(),
sectionSort(),
section,
subset,section-method,
summary,section-method