read.section: Read a Section File

Description

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.

Usage

read.section(
  file,
  directory,
  sectionId = "",
  flags,
  ship = "",
  scientist = "",
  institute = "",
  missingValue = -999,
  encoding = "latin1",
  debug = getOption("oceDebug"),
  processingLog
)

Value

A section object.

Arguments

file: A file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see “Details”).
directory: A character string indicating the name of a directory that contains a set of CTD files that hold individual stations in the section.
sectionId: Optional string indicating the name for the section. If not provided, the section ID is determined by examination of the file header.
flags: Ignored, and deprecated (will be disallowed in a future version).
ship: Name of the ship carrying out the sampling.
scientist: Name of chief scientist aboard ship.
institute: Name of chief scientist's institute.
missingValue: Numerical value used to indicate missing data.
encoding: a character value that indicates the encoding to be used for this data file, if it is textual. The default value for most functions is "latin1", which seems to be suitable for files containing text written in English and French.
debug: 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.
processingLog: 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.

Disambiguating salinity

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.

Author

Dan Kelley

References

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().