Read a CTD file in ODF format
read.ctd.odf(file, columns = NULL, station = NULL, missingValue,
monitor = FALSE, debug = getOption("oceDebug"), processingLog, ...)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.
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”.
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.
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.
Boolean, set to TRUE to provide an indication of
progress. This is useful if filename is a wildcard.
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 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.
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.
read.ctd.odf reads files stored in Ocean Data Format, used in
some Canadian hydrographic databases.
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.
Other things related to ctd data: [[,ctd-method,
[[<-,ctd-method, as.ctd,
cnvName2oceName, ctd-class,
ctdDecimate, ctdFindProfiles,
ctdRaw, ctdTrim,
ctd, handleFlags,ctd-method,
initialize,ctd-method,
initializeFlagScheme,ctd-method,
oceNames2whpNames,
oceUnits2whpUnits,
plot,ctd-method, plotProfile,
plotScan, plotTS,
read.ctd.itp, read.ctd.sbe,
read.ctd.woce.other,
read.ctd.woce, read.ctd,
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames,
woceUnit2oceUnit, write.ctd
Other things related to ctd data: [[,ctd-method,
[[<-,ctd-method, as.ctd,
cnvName2oceName, ctd-class,
ctdDecimate, ctdFindProfiles,
ctdRaw, ctdTrim,
ctd, handleFlags,ctd-method,
initialize,ctd-method,
initializeFlagScheme,ctd-method,
oceNames2whpNames,
oceUnits2whpUnits,
plot,ctd-method, plotProfile,
plotScan, plotTS,
read.ctd.itp, read.ctd.sbe,
read.ctd.woce.other,
read.ctd.woce, read.ctd,
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames,
woceUnit2oceUnit, write.ctd
Other things related to odf data: ODF2oce,
ODFListFromHeader,
ODFNames2oceNames,
[[,odf-method,
[[<-,odf-method, odf-class,
plot,odf-method, read.odf,
subset,odf-method,
summary,odf-method