oce (version 0.9-20)

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, debug = getOption("oceDebug"), processingLog)

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.

debug

Logical. If TRUE, print some information that might be helpful during debugging.

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.

Value

An object of class section-class.

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.

References

Several repository sites provide section data. An example that is perhaps likely to exist for years is http://cchdo.ucsd.edu, but a search on "WOCE bottle data" should turn up other sites, if this one ceases to exist. Only the so-called exchange BOT data format can be processed by read.section() at this time.

See Also

Other things related to section data: [[,section-method, [[<-,section-method, as.section, handleFlags,section-method, plot,section-method, section-class, sectionAddStation, sectionGrid, sectionSmooth, sectionSort, section, subset,section-method, summary,section-method