oce (version 0.9-22)

read.ctd.sbe: Read a Seabird CTD File

Description

Read a Seabird CTD File

Usage

read.ctd.sbe(file, columns = NULL, station = NULL, missingValue,
  monitor = FALSE, debug = getOption("oceDebug"), processingLog, ...)

Arguments

file

A connection or a character string giving the name of the file to load. For read.ctd.sbe() and read.ctd.woce(), this may be a wildcard (e.g. "*.cnv" or "*.csv") in which case the return value is a vector containing CTD objects created by reading the files from list.files with pattern set to the specified wildcard pattern.

columns

An optional list that can be used to convert unrecognized data names to resultant variable names. This is used only by read.ctd.sbe and read.ctd.odf; see “Examples”.

station

Optional character string containing an identifying name or number for the station. This can be useful if the routine cannot determine the name automatically, or if another name is preferred.

missingValue

Optional missing-value flag; data matching this value will be set to NA upon reading. If this is provided, then it overrules any missing-value flag found in the data. For Seabird (.cnv) files, there is usually no need to set missingValue, because it can be inferred from the header (typically as -9.990e-29). Set missingValue=NULL to turn off missing-value detection, even in .cnv files that contain missing-value codes in their headers. If missingValue is not specified, then an attempt is made to infer such a value from the data, by testing whether salinity and/or temperature has a minimum that is under -8 in value; this should catch common values in files, without false positives. A warning will be issued in this case, and a note inserted in the processing log of the return value.

monitor

Boolean, set to TRUE to provide an indication of progress. This is useful if filename is a wildcard.

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.

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.

...

additional arguments, passed to called routines.

Value

An object of ctd-class. The details of the contents depend on the source file. The metadata slot is particularly variable across data formats, because the meta-information provided in those formats varies widely.

Details

This function reads files stored in Seabird .cnv format. Note that these files can contain multiple sensors for a given field. For example, the file might contain a column named t090C for one temperature sensor and t190C for a second. The first will be denoted temperature in the data slot of the return value, and the second will be denoted temperature1. This means that the first sensor will be used in any future processing that accesses temperature. This is for convenience of processing, and it does not pose a limitation, because the data from the second sensor are also available as e.g. x[["temperature1"]], where x is the name of the returned value. For the details of the mapping from .cnv names to ctd names, see cnvName2oceName.

The original data names as stored in file are stored within the metadata slot as dataNamesOriginal, and are displayed with summary alongside the numerical summary. See the Appendix VI of [2] for the meanings of these names (in the "Short Name" column of the table spanning pages 161 through 172).

References

1. The Sea-Bird SBE 19plus profiler is described at http://www.seabird.com/products/spec_sheets/19plusdata.htm. Some more information is given in the Sea-Bird data-processing manaual http://www.seabird.com/document/sbe-data-processing-manual.

2. A SBE data processing manual is at http://www.seabird.com/document/sbe-data-processing-manual.

See Also

Other things related to ctd data: [[,ctd-method, [[<-,ctd-method, as.ctd, cnvName2oceName, ctd-class, ctdDecimate, ctdFindProfiles, ctdRaw, ctdTrim, ctd, handleFlags,ctd-method, oceNames2whpNames, oceUnits2whpUnits, plot,ctd-method, plotProfile, plotScan, plotTS, read.ctd.itp, read.ctd.odf, read.ctd.woce.other, read.ctd.woce, read.ctd, subset,ctd-method, summary,ctd-method, woceNames2oceNames, woceUnit2oceUnit, write.ctd

Examples

# NOT RUN {
f <- system.file("extdata", "ctd.cnv", package="oce")
## Read the file in the normal way
d <- read.ctd(f)
## Read an imaginary file, in which salinity is named 'salt'
d <- read.ctd(f, columns=list(
  salinity=list(name="salt", unit=list(expression(), scale="PSS-78"))))

# }