read.rsk: Read a Rsk file

Description

Read an RBR rsk or txt file, e.g. as produced by an RBR logger, producing an object of class rsk.

Usage

read.rsk(file, from = 1, to, by = 1, type, tz = getOption("oceTz", default  = "UTC"), patm = FALSE, processingLog, debug = getOption("oceDebug"))

Arguments

file

a connection or a character string giving the name of the 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.

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 tz argument.)

an indication of the last datum to be read, in the same format as from. If 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.

type

optional file type, presently can be rsk or 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.

time zone. The value oceTz is set at package setup.

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. This is 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 TRUE to turn on debugging.

Value

An object of rsk-class.

Details

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.

References

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.