Read a Seabird CTD File
read.ctd.sbe(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.
SBE files can be somewhat confusing as regards the time of measurement. If
the data file contains metadata item called start_time, then
it is converted to a POSIX time object by read.ctd.sbe and stored
within the metadata slot as "startTime". Until 2018-07-05, that
value was also stored in a metadata item named "time", but this
caused confusion for data files that also have an elapsed-time column, and so
an entry named "time" is no longer stored in the metadata slot,
for those cases in which an elapsed-time column exists in the data file.
Importantly, there is a possibility for confusion in the storage
of that elapsed-time entry within the data slot, because read.ctd.sbe
renames all of the ten variants of elapsed time (see [2] for a list)
as, simply, "time" in the data slot of the returned value.
(Numerical suffices will be used if the file contains multiple elapsed-time
columns.) This imposes upon the user the burden of using summary() on
the return value, to discover the original name of the elapsed time column,
because read.ctd.sbe does not convert the 10 possible units to
a standard, but rather simply records the numerical values that are in
the data file. The most common column name is likely timeS, for
elapsed time in seconds; see [2] for the meanings of the other 9
schemes.
The user might encounter data files with a variety of scales for temperature and
salinity. Oce keeps track of these scales in the units it sets up for the stored
variables. For example, if A is a CTD object, then
A[["temperatureUnit"]]$scale is a character string that will indicate the scale.
Modern-day data will have "ITS-90" for that scale, and old data may have
"IPTS-68". The point of saving the scale in this way is so that the various
formulas that deal with water properties can account for the scale, e.g. converting
from numerical values saved on the "IPTS-68" scale to the newer scale, using
T90fromT68 before doing calculations that are expressed in
terms of the "ITS-90" scale. This is taken care of by retrieving temperatures
with the accessor function, e.g. writing A[["temperature"]] will either
retrieve the stored values (if the scale is ITS-90) or converted values (if
the scale is IPTS-68). Even though this procedure should work, users who
really care about the details of their data are well-advised to do a couple
of tests after examining the first data line of their data file in an editor.
Note that reading a file that contains IPTS-68 temperatures produces a warning.
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).
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 manual
(next item).
2. A SBE data processing manual was once at
http://www.seabird.com/document/sbe-data-processing-manual,
but as of summer 2018, this no longer seems to be provided by SeaBird.
A web search will turn up copies of the manual that have been put
online by various research groups and data-archiving agencies.
As of 2018-07-05, the latest version was named
SBEDataProcessing_7.26.4.pdf and had release date 12/08/2017,
and this was the reference version used in coding oce.
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.odf,
read.ctd.woce.other,
read.ctd.woce, read.ctd,
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames,
woceUnit2oceUnit, write.ctd
# 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"))))
# }
Run the code above in your browser using DataLab