This is a provisional function, written to handle a particular file created in Spring of 2023 by MUN researchers, as part of an OTN project. Please consult the “Slocum Gliders” vignette for more information about this file.
Usage
read.glider.slocum.netcdf(
file,
readAll = FALSE,
nameMap = list(salinity = "glider_record/sci_rbrctd_salinity_00", SA =
"absolute_salinity", temperature = "glider_record/sci_rbrctd_temperature_00", CT =
"conservative_temperature", pressure = "glider_record/sci_rbrctd_seapressure_00",
time = "glider_record/sci_rbrctd_timestamp", conductivity =
"glider_record/sci_rbrctd_conductivity_00", latitude = "glider_record/m_gps_lat",
longitude = "glider_record/m_gps_lon", profileLat = "profile_lat", profileLon =
"profile_lon", density = "density", oxygen = "oxygen_concentration",
u = "u", v
= "v", vxi = "glider_record/m_initial_water_vx", vyi =
"glider_record/m_initial_water_vy", vy = "glider_record/m_water_vy", vx =
"glider_record/m_water_vx", id = "profile_id"),
debug = 0
)Arguments
- file
Name of a netcdf file.
- readAll
logical value indicating whether to read all the data columns in the file. The default, FALSE, means to only read columns that appear in
nameMap. Using FALSE can yield significant decreases in processing time and memory usage. For the 2 Gb test file used during the coding of this function (which, admittedly, seems to have a great deal of duplication or near-duplication of data), settingreadAllto FALSE drops the reading time from 12 s to 1.5s, and the size of the resultant value from 2.0Gb to 0.28 Gb.- nameMap
either a character value or a list. In the first case, the only permitted possibility is
nameMap="?", which instructsread.glider.slocum.netcdf()to return a vector of variable names as determined by scanning the file. Examining this list can be a useful first step in the exploration of data file. Once the variables are known, it makes sense to use the list form ofnameMap, perhaps starting with the default value.- debug
an integer controlling how much information is printed during processing. If this is 0, then only errors and warnings will be printed. If it is 1, then the function entry and exit are signalled, and a line is printed for each variable read.
Value
A glider object, i.e. one inheriting from glider. (This class inherits from oce::oce in the oce package.)
Details
Since different files might use different naming conventions for data,
it is helpful to establish a mapping between names in the file and the
names that are to be stored in the return object. This is what the
nameMap argument is for. The file may contain information that
will guide the user as to which of various possibilities to use,
although reference to other documents, on consultation with the
data provider may be required. Again, see the “Slocum Gliders”
vignette for more on this topic.
See also
Other functions to read glider data:
read.glider.netcdf(),
read.glider.netcdf.ioos(),
read.glider.seaexplorer.delayed(),
read.glider.seaexplorer.realtime(),
read.glider.slocum.csv()
Other functions to read netcdf glider data:
read.glider.netcdf(),
read.glider.netcdf.ioos()