read.ctd.odv {oce}

Read a "ctd" File in ODV Format

Description

Read a "ctd" File in ODV Format

Usage

read.ctd.odv(
  file,
  columns = NULL,
  station = NULL,
  missingValue,
  deploymentType,
  encoding = "latin1",
  monitor = FALSE,
  debug = getOption("oceDebug"),
  processingLog,
  ...
)

Arguments

file

either a connection or a character value naming a file. 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.

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.

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.

Details

read.ctd.odv() attempts to read files stored in ODV format, used by some European data providers. This works only crudely, as of 2020-05-17. In particular, the translation from ODV parameter names to oce names is very limited. For example, only one of the dozens of possibilities for variants of phosphate is handled at the moment, and that is because this was the variant supplied in a test file sent to the author on 2020-05-16. It is unlikely that full support of ODV files will become available in read.ctd.odv(), given the lack of a comprehensive source listing ODV variable names and their meanings, and low user interest.

Value

This function returns a ctd object.

Author(s)

Dan Kelley

References

1. ⁠https://www.bodc.ac.uk/resources/delivery_formats/odv_format/⁠ describes the ODV format.

2. ⁠https://vocab.nerc.ac.uk/collection/P07/current/⁠ may be worth consulting for variable names.

See Also

Other things related to ctd data: CTD_BCD2014666_008_1_DN.ODF.gz, [[,ctd-method, [[<-,ctd-method, as.ctd(), cnvName2oceName(), ctd-class, ctd.cnv.gz, ctdDecimate(), ctdFindProfilesRBR(), ctdFindProfiles(), ctdRaw, ctdRepair(), ctdTrim(), ctd_aml.csv.gz, ctd, d200321-001.ctd.gz, d201211_0011.cnv.gz, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames(), oceUnits2whpUnits(), plot,ctd-method, plotProfile(), plotScan(), plotTS(), read.ctd.aml(), read.ctd.itp(), read.ctd.odf(), read.ctd.saiv(), read.ctd.sbe(), read.ctd.ssda(), read.ctd.woce.other(), read.ctd.woce(), read.ctd(), setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames(), woceUnit2oceUnit(), write.ctd()