read.ctd.odf: Read a CTD file in ODF format

Description

Read a CTD file in ODF format

Usage

read.ctd.odf(
  file,
  columns = NULL,
  station = NULL,
  missingValue,
  deploymentType = "unknown",
  monitor = FALSE,
  exclude = NULL,
  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(). For example, if a data file named salinity as "SAL", then using

d <- read.ctd(f, columns=list(
    salinity=list(name="SAL",
                  unit=list(unit=expression(),
                  scale="PSS-78"))))

would assign the "SAL" column to the salinity entry in the data slot of the CTD object returned by the read.* function.

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.

deploymentType

character string indicating the type of deployment. Use "unknown" if this is not known, "profile" for a profile (in which the data were acquired during a downcast, while the device was lowered into the water column, perhaps also including an upcast; "moored" if the device is installed on a fixed mooring, "thermosalinograph" (or "tsg") if the device is mounted on a moving vessel, to record near-surface properties, or "towyo" if the device is repeatedly lowered and raised.

monitor

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

exclude

either a character value holding a regular expression that is used with grep() to remove lines from the header before processing, or NULL (the default), meaning not to exclude any such lines. The purpose of this argument is to solve problems with some files, which can have thousands of lines that indicate details that are may be of little value in processing. For example, some files have thousands of lines that would be excluded by using exclude="PROCESS='Nulled the .* value" in the function call.

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

a '>ctd object. 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 so widely.

Details

read.ctd.odf reads files stored in Ocean Data Format, used in some Canadian hydrographic databases.

References

The ODF format, used by the Canadian Department of Fisheries and Oceans, is described to some extent in the documentation for read.odf(). It is not clear that ODF format is handled correctly in read.ctd.odf, or the more general function read.odf(), because the format varies between some sample files the author has encountered in his research.