read.odf: Read an odf File

Description

ODF (Ocean Data Format) is a format developed at the Bedford Institute of Oceanography and also used at other Canadian Department of Fisheries and Oceans (DFO) facilities (see references 1 and 2). It can hold various types of time-series data, which includes a variety of instrument types. Thus, read.odf() is used by read.ctd.odf for CTD data, etc.

Usage

read.odf(
  file,
  columns = NULL,
  header = "list",
  exclude = NULL,
  encoding = "latin1",
  debug = getOption("oceDebug")
)

Value

An oce object.

Arguments

file: the file containing the data.
columns: An optional list that can be used to convert unrecognized data names to resultant variable names. For example, columns=list(salinity=list(name="salt", unit=list(unit=expression(), scale="PSS-78")) states that a short-name of "salt" represents salinity, and that the unit is as indicated. This is passed to cnvName2oceName() or ODFNames2oceNames(), as appropriate, and takes precedence over the lookup table in that function.
header: An indication of whether, or how, to store the entire ODF file header in the metadata slot of the returned object. There are three choices for the header argument. (1) If it is NULL, then the ODF header is not stored in the metadata slot (although some of its contents are). (2) If it is "character", the header is stored within the metadata as a vector named header, comprising a character string for each line of the header within the ODF file. (3) If it is "list", then the metadata slot of the returned object will contain a list named header that has lists as its entries. (The sub-lists are in the form of key-value pairs.) The naming of list entries is patterned on that in the ODF header, except that unduplicateNames() is used to transform repeated names by adding numerical suffices. Note: on June 6, 2019, the default value of header was changed from NULL to "list"; in addition, the resultant list was made to contain every single item in the ODF header, with unduplicateNames() being used to append integers to distinguish between repeated names in the ODF format.
exclude: either a character value holding a regular expression that is used with grep() to remove lines from the header before processing, or NULL (the default), meaning not to exclude any such lines. The purpose of this argument is to solve problems with some files, which can have thousands of lines that indicate details that are may be of little value in processing. For example, some files have thousands of lines that would be excluded by using exclude="PROCESS='Nulled the .* value" in the function call.
encoding: a character value that indicates the encoding to be used for this data file, if it is textual. The default value for most functions is "latin1", which seems to be suitable for files containing text written in English and French.
debug: 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 one function calls another, it usually reduces the value of debug first, so that a user can often obtain deeper debugging by specifying higher debug values.

Metadata conventions

Some metadata items may be specific to certain instruments, and certain research groups. It can be important for analysts to be aware of the conventions used in datasets that are under study. For example, as of June 2018, adp objects created at the Bedford Institute of Oceanography may have a metadata item named depthOffBottom (called DEPTH_OFF_BOTTOM in ODF files), which is not typically present in ctd files. This item illustrates the renaming convention, from the CAMEL_CASE used in ODF files to the snakeCase used in oce. Bearing this conversion in mind, users should not find it difficult to understand the meaning of items that read.odf() stores within the metadata slot. Users should bear in mind that the whole ODF header is saved as a list by calling the function with header="list", after which e.g. str(rval[["header"]]) or View(rval[["header"]]) can be used to isolate any information of interest (but bear in mind that suffices are used to disambiguate sibling items of identical name in the ODF header).

Handling of temperature scales

read.odf() stores temperature data directly as read from the file, which might mean the IPTS-68 scale. These values should not be used to calculate other seawater quantities, because formulae are generally based in ITS90 temperatures. To avoid problems, the accessor function converts to the modern scale, e.g. x[["temperature"]] yields temperature in the ITS90 scale, whether temperatures in the original file were reported on that scale or the older IPTS-68 scale.

Caution

Lacking detailed documentation of the ODF file format, the read.odf() and read.ctd.odf() functions were crafted based on inspection of data files, and so some guesses had to be made.

The PARAMETER_HEADER chunks describing quality-control flags are a case in point. These contain NAME components that refer to other PARAMETER_HEADER chunks that hold measured data. However, those references are not always matched well with the data names, and even if they do match, the cross-reference syntax used by the Bedford Institute of Oceanography differs from that used by l’Institut Maurice-Lamontagne. To simplify coding, it was assumed that each quality-control sequence applies to the data sequence immediately preceding it. (This assumption is made in other analysis systems.)

It is also prudent to pay attention to the units decoding, which read.odf() handles by calling unitFromString(). Be on the lookout for incorrect temperature scales, which are sometimes reported with nonstandard strings in ODF files. Also, note that you may see warnings about conductivity ratios, which some ODF files incorrectly suggest have dimensions.

Author

Dan Kelley, with help from Chantelle Layton

Details

Note that some elements of the metadata are particular to ODF objects, e.g. depthMin, depthMax and sounding, which are inferred from ODF items named MIN_DEPTH, MAX_DEPTH and SOUNDING, respectively. In addition, the more common metadata item waterDepth, which is used in ctd objects to refer to the total water depth, is set to sounding if that is finite, or to maxDepth otherwise.

The function ODFNames2oceNames() is used to translate data names from the ODF file to standard oce names.

References

For sources that describe the ODF format, see the documentation for the odf class.

Examples

Run this code

library(oce)
#
# 1. Read a CTD cast made on the Scotian Shelf. Note that the file's metadata
# states that conductivity is in S/m, but it is really conductivity ratio,
# so we must alter the unit before converting to a CTD object. Note that
# read.odf() on this data file produces a warning suggesting that the user
# repair the unit, using the method outlined here.
odf <- read.odf(system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF.gz", package = "oce"))
ctd <- as.ctd(odf) # so we can e.g. extract potential temperature
ctd[["conductivityUnit"]] <- list(unit = expression(), scale = "")
#
# 2. Make a CTD, and plot (with span to show NS)
plot(ctd, span = 500)
#
# 3. Highlight bad data on TS diagram. (Note that the eos
# is specified, because we will extract practical-salinity and
# UNESCO-defined potential temperatures for the added points.)
plotTS(ctd, type = "o", eos = "unesco") # use a line to show loops
bad <- ctd[["QCFlag"]] != 0
points(ctd[["salinity"]][bad], ctd[["theta"]][bad], col = "red", pch = 20)

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