Read a "ctd" File in ODV Format
read.ctd.odv(
file,
columns = NULL,
station = NULL,
missingValue,
deploymentType,
encoding = "latin1",
monitor = FALSE,
debug = getOption("oceDebug"),
processingLog,
...
)This function returns a ctd object.
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.
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.
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.
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.
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.
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.
Dan Kelley
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.
https://www.bodc.ac.uk/resources/delivery_formats/odv_format/ describes
the ODV format.
https://vocab.nerc.ac.uk/collection/P07/current/ may be
worth consulting for variable names.
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz,
[[,ctd-method,
[[<-,ctd-method,
as.ctd(),
cnvName2oceName(),
ctd,
ctd-class,
ctd.cnv.gz,
ctdDecimate(),
ctdFindProfiles(),
ctdFindProfilesRBR(),
ctdRaw,
ctdRepair(),
ctdTrim(),
ctd_aml.csv.gz,
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(),
read.ctd.aml(),
read.ctd.itp(),
read.ctd.odf(),
read.ctd.saiv(),
read.ctd.sbe(),
read.ctd.ssda(),
read.ctd.woce(),
read.ctd.woce.other(),
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames(),
woceUnit2oceUnit(),
write.ctd()