read.rsk {oce} | R Documentation |
Read an RBR rsk or txt file, e.g. as produced by an RBR logger, producing an
object of class rsk
.
read.rsk(file, from=1, to, by=1, type, tz=getOption("oceTz", default="UTC"), patm=FALSE, processingLog, debug=getOption("oceDebug"))
file |
a connection or a character string giving the name of the file to
load. Note that |
from |
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 about the |
to |
an indication of the last datum to be read, in the same
format as |
by |
an indication of the stride length to use while walking
through the file. If this is an integer, then |
type |
optional file type, presently can be |
tz |
time zone. The value |
patm |
controls the handling of atmospheric pressure, an important issue for RBR instruments that record absolute pressure; see “Details”. |
processingLog |
if provided, the action item to be stored in the log. (Typically only provided for internal calls; the default that it provides is better for normal calls by a user.) |
debug |
a flag that can be set to |
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 hex
or 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 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 “Examples”).
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 patm
is FALSE
(the default), then
pressure read from the data file is stored in the data
slot of return
value, and the metadata
item pressureType
is set to the string
"absolute"
. (2) If patm
is 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-class
objects to
ctd-class
objects.
An object of rsk-class
.
Dan Kelley and Clark Richards
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.
The documentation for rsk-class
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 work, e.g. as.ctd
can be used to create CTD object,
so that the generic plot obeys the CTD format.