Read real-time SeaExplorer glider data

Reads real-time CSV files produced by a SeaExplorer glider, as detected by the presence of ".sub." in their names. Such real-time data are decimated before transmission, and thus do not represent the full data collected by the glider sensors. (Use [read.glider.seaexplorer.delayed)] instead of this, to read delayed-mode data, as downloaded from the glider after recovery.)

[read.glider.seaexplorer.delayed)]: R:read.glider.seaexplorer.delayed)

Usage

read.glider.seaexplorer.realtime(
  directory,
  yo,
  level = 1,
  progressBar = interactive,
  missingValue = 9999,
  debug
)

Arguments

directory: The directory in which the realtime SeaExplorer files are located.
yo: A numeric value (or vector) specifying the yo numbers to read. If this is not provided, read.glider.seaexplorer.delayed() will read all yo numbers for which files are present in dir.
level: Ignored by read.glider.seaexplorer.realtime and only included for similarity with read.glider.seaexplorer.delayed().
progressBar: either a logical or character value that controls whether/how to indicate the progress made in reading and interpreting the data. This can be useful, since the work can be slow. If progressBar is a logical value, then it indicates whether to show textual progress with txtProgressBar(). If progressBar is the character value "shiny", then shiny::setProgress() and shiny::incProgress() will be used, on the assumption that the call to read.glider.seaexplorer.realtime() was made within the context of a call to shiny::withProgress(). The default is to use the value returned by interactive(), i.e. to use a textual progress indicator, but only in interactive mode.
missingValue: A value that indicates missing data; all values that match this are set to NA.
debug: an integer specifying whether debugging information is to be printed during processing. If this is not provided, then the value of getOption("gliderDebug",0) is used. The printing is done by a call to gliderDebug. Setting debug=0 turns off this form of debugging, while higher values may yield more information, depending on the function. If one glider function calls another, it passes the value of debug but decreased by 1, which means that the value of debug controls not just the breadth of debugging, but also the depth.

Flag Scheme

A flag scheme is set up according to the IOOS classification system (see Table 2 of reference 1), as follows.

Name	Value	IOOS Name	Description
`pass`	1	Pass	Data has passed quality control (QC) tests
`not_evaluated`	2	Not Evaluated	Data has not been QC tested
`suspect`	3	Suspect or of High Interest	Data is considered to be of suspect or high interest
`fail`	4	Fail	Data is considered to have failed on one or more QC tests
`missing`	9	Missing Data	Data are missing; using a placeholder

Renaming of data in seaexplorer files

FIXME: are the original names the same in both "raw" and "sub" datasets?

Data in the gli files are stored in the glider item within the data slot of the returned object, renamed as follows. (Note that there is also an empty column in the seaexplorer data files, caused by a semicolon at the ends of the lines. This is read by R, but then discarded and not stored in the glider object.)

Data in the gli files are stored in the glider item within the data slot of the returned object, renamed as follows. (If the new name is listed as . that means that the old name is retained, but bear in mind that a new name will likely be assigned at some later point in the development of this package.)

OriginalName	Name	Notes
`Timestamp`	`time`	Converted to POSIXt time.
`NavState`	`navState`	-
`SecurityLevel`	`alarm`	-
`Heading`	`heading`	-
`Pitch`	`pitch`	-
`Roll`	`roll`	-
`Depth`	`pressureNav`	-
`Temperature`	`temperatureInternal`	-
`Pa`	`pressureInternal`	-
`Lat`	`latitude`	Converted to decimal degrees.
`Lon`	`longitude`	Converted to decimal degrees.
`DesiredH`	`headingDesired`	-
`BallastCmd`	`ballastCmd`	-
`BallastPos`	`ballastPos`	-
`LinCmd`	`linCmd`	-
`LinPos`	`linPos`	-
`AngCmd`	`angCmd`	-
`AngPos`	`angPos`	-
`Voltage`	`voltage`	-
`Altitude`	`altitude`	-

Data in the pld1 files are stored in the payload1 item within the data slot of the returned object, renamed as follows. Where possible, the corresponding IOOS NetCDF file variable names are also listed [see Integrated Ocean Observing System (U.S.). “NGDAC NetCDF File Format Version 2,” March 27, 2019. https://github.com/ioos/ioosngdac/wiki/NGDAC-NetCDF-File-Format-Version-2].

OriginalName	Name	IOOS name	Notes
`PLD_REALTIMECLOCK`	`time`	`time`	Converted to POSIXt time.
`NAV_RESOURCE`	`navState`	-	-
`NAV_LONGITUDE`	`longitude`	`lon`	Converted to decimal degrees.
`NAV_LATITUDE`	`latitude`	`lat`	Converted to decimal degrees.
`NAV_DEPTH`	`pressureNav`	`depth`	-
`FLBBCD_CHL_COUNT`	`chlorophyllCount`	-	-
`FLBBCD_CHL_SCALED`	`chlorophyll`	-	-
`FLBBCD_BB_700_COUNT`	`backscatterCount`	-	-
`FLBBCD_BB_700_SCALED`	`backscatter`	-	-
`FLBBCD_CDOM_COUNT`	`cdomCount`	-	-
`FLBBCD_CDOM_SCALED`	`cdom`	-	-
`GPCTD_CONDUCTIVITY`	`conductivity`	-	-
`GPCTD_TEMPERATURE`	`temperature`	`temperature`	degC
`GPCTD_PRESSURE`	`pressure`	`pressure`	dbar
`GPCTD_DOF`	`oxygenFrequency`	-	-
-	`salinity`	`salinity`	Practical Salinity (computed)

Data in the pld2 files (or others for additional payloads) are ignored in this version of the package. Please contact the authors, if you need to handle such files.

References

IOOS. “Manual for Real-Time Oceanographic Data Quality Control Flags,” May 2017. https://cdn.ioos.noaa.gov/media/2017/12/QARTOD-Data-Flags-Manual_Final_version1.1.pdf.

Author

Dan Kelley and Clark Richards

Examples

library(oceglider)
directory <- system.file("extdata/sea_explorer/realtime_raw", package = "oceglider")
g <- read.glider.seaexplorer.realtime(directory, progressBar = FALSE)
plot(g, which = "navState")

plot(g, which = "S")

plot(g, which = "T")