Read an RBR rsk or txt file, e.g. as produced by an RBR logger, producing an
object of class
a connection or a character string giving the name of the RSK file to
load. Note that
file must be a character string, because connections are
not used in that case, which is instead handled with database calls.
indication of the first datum to read. This can a positive integer
to indicate sequence number, the POSIX time of the first datum, or a character
string that can be converted to a POSIX time. (For POSIX times, be careful
an indication of the last datum to be read, in the same format as
to is missing, data will be read to the end of the file.
an indication of the stride length to use while walking through the
file. If this is an integer, then
by-1 samples are skipped between each
pair of samples that is read. If this is a string representing a time interval,
in colon-separated format (HH:MM:SS or MM:SS), then this interval is divided by
the sampling interval, to get the stride length.
optional file type, presently can be
txt (for a
text export of an RBR rsk or hex file). If this argument is not provided, an
attempt will be made to infer the type from the file name and contents.
the timezone assumed for the time values stored in the
data file. Unless the user has set an alternative value in the
~/.Rprofile file, the default will be
"UTC"; see the
“Altering oce Defaults” vignette for more on the use
offset, in hours, between the CTD clock and
the clock in the controlling computer/tablet/phone (if one was used during
the sampling). This offset is required to relate location information from the
controller to hydrographic information from the CTD, using timestamps as an
index (see "A note on location information" in “Details”).
If the user supplies a value for
tzOffsetLocation, then that is used.
If not, an attempt is made to infer it from an item named
that might be present within a table named
epochs in the file. If no
value can be inferred from either of these two methods, then
tzOffsetLocation is set to zero.
controls the handling of atmospheric pressure, an important issue for RBR instruments that record absolute pressure; see “Details”.
logical value, TRUE by default, indicating whether to save
all the non-empty tables in the database (pruned of
blob columns) in the
metadata slot of the returned object. This may be useful for detailed
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.
a flag that can be set to
TRUE to turn on debugging.
An rsk object.
This can read files produced by several RBR instruments. At the moment, five
styles are understood: (1) text file produced as an export of an RBR
rsk file; (2) text file with columns for temperature and pressure
(with sampling times indicated in the header); (3) text file with four columns,
in which the date the time of day are given in the first two columns, followed
by the temperature, and pressure; (4) text file with five columns, in which
depth in the water column is given after the pressure; (5) an SQLite-based
database format. The first four options are provided mainly for historical
reasons, since RBR instruments at the date of writing commonly use the SQLite
format, though the first option is common for all instruments that produce a
hex file that can be read using Ruskin.
Options 2-4 are mostly obsolete, and will be removed from future versions.
A note on location information.
It is possible to couple RBR CTD devices with smart phones or tablets
(see RBR-global, 2020), with the location data from the latter being stored
in the output
.rsk file. The format does not seem to be documented by RBR,
read.rsk() attempts to infer location nevertheless.
The procedure involves comparing the
field from the hydrographic part of the dataset (which is in a database
data) with the
tstamp field in the geographical part of the
dataset (in a table named
geodata entries are filtered to
those for which the
origin field equals
"auto". This seems to align
with times shown for "LOCATION" data in RBR-provided viewing software.)
The connection between the two fields is done with
tzOffsetLocation (with units converted appropriately) to the
time inferred from
geodata$tstamp field, to account for the fact that phones and tablets
may be set to local time. If the procedure succeeds, then
latitude are inserted into the
metadata slot of the return value, in the
form of vectors with the same length as
pressure in the
A note on conductivity.
RBR devices record conductivity in mS/cm, and it
is this value that is stored in the object returned by
read.rsk. This can
be converted to conductivity ratio (which is what many other instruments report)
by dividing by 42.914 (see Culkin and Smith, 1980) which will be necessary in
any seawater-related function that takes conductivity ratio as an argument (see
A note on pressure.
RBR devices tend to record absolute pressure (i.e.
sea pressure plus atmospheric pressure), unlike most oceanographic instruments
that record sea pressure (or an estimate thereof). The handling of pressure
is controlled with the
patm argument, for which there are three
possibilities. (1) If
FALSE (the default), then
pressure read from the data file is stored in the
data slot of return
value, and the
pressureType is set to the string
"absolute". (2) If
TRUE, then an estimate of
atmospheric pressure is subtracted from the raw data. For data files in the
SQLite format (i.e.
*.rsk files), this estimate will be the value read
from the file, or the ``standard atmosphere'' value 10.1325 dbar, if the file
lacks this information. (3) If
patm is a numerical value (or list of
values, one for each sampling time), then `patm` is subtracted from the
raw data. In cases 2 and 3, an additional column named
`pressureOriginal` is added to the `data` slot to store the value
contained in the data file, and `pressureType` is set to a string
starting with `"sea"`. See
as.ctd() for details of how this
setup facilitates the conversion of rsk objects to
Culkin, F., and Norman D. Smith, 1980. Determination of the concentration of potassium chloride solution having the same electrical conductivity, at 15 C and infinite frequency, as standard seawater of salinity 35.0000 ppt (Chlorinity 19.37394 ppt). IEEE Journal of Oceanic Engineering, 5, pp 22-23.
RBR-global.com, 2020. “Ruskin User Guide.” RBR, August 18, 2020. Revision RBR#0006105revH.
The documentation for rsk explains the structure of
rsk objects, and also outlines other functions dealing with them. Since
RBR has a wide variety of instruments,
rsk datasets can be quite general,
and it is common to coerce
rsk objects to other forms for specialized
as.ctd() can be used to create CTD object, so that the
generic plot obeys the CTD format.