read.rsk: Read a Rsk file

In oce: Analysis of Oceanographic Data

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,
  encoding = NA,
  tz = getOption("oceTz", default = "UTC"),
  tzOffsetLocation,
  patm = FALSE,
  allTables = TRUE,
  processingLog,
  debug = getOption("oceDebug")
)

Arguments

file	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.
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.)
to	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.
by	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.
encoding	ignored.
tz	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 of the ⁠~/.Rprofile⁠ file.
tzOffsetLocation	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 UTCdelta 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.
patm	controls the handling of atmospheric pressure, an important issue for RBR instruments that record absolute pressure; see “Details”.
allTables	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 analysis.
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.

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 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, but read.rsk() attempts to infer location nevertheless. The procedure involves comparing the tstamp (time-stamp) field from the hydrographic part of the dataset (which is in a database table named data) with the tstamp field in the geographical part of the dataset (in a table named geodata). (The 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 approx(), after adding 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 longitude and latitude are inserted into the metadata slot of the return value, in the form of vectors with the same length as pressure in the data slot.

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 objects to ctd objects.

Value

An rsk object.

Author(s)

Dan Kelley and Clark Richards

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.

RBR-global.com, 2020. “Ruskin User Guide.” RBR, August 18, 2020. Revision RBR#0006105revH.

See Also

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 work, e.g. as.ctd() can be used to create CTD object, so that the generic plot obeys the CTD format.

Other things related to rsk data: [[,rsk-method, [[<-,rsk-method, as.rsk(), ctdFindProfilesRBR(), plot,rsk-method, rsk-class, rskPatm(), rskToc(), rsk, subset,rsk-method, summary,rsk-method

oce documentation built on July 9, 2023, 5:18 p.m.