vignettes/built_in_vartables.Rmd
built_in_vartables.RmdThis vignette discusses two built-in variable-table files. These may
be used as patterns by users wishing to create their own tables. Note
that the package requires that the files be in proper YAML format, which
can be checked by using yaml::yaml.load_file("file.yml"),
where "file.yml" is the trial file. This function will
report an error if the contents are not in proper YAML format.
adp
This table is stored in a file that may be accessed with
system.file("extdata", "adp.yml", package="ocencdf")and the contents are as follows.
type:
comment: A varTable for adp data.
date: '2022-06-28'
name: adp
version: 1
units:
1/m:
name: m-1
dbar:
name: decibar
degree * C:
name: degree_Celcius
degree * E:
name: degree_east
degree * N:
name: degree_north
m / s:
name: meters_per_second
values:
missing_value: 99999.0
variables:
v:
name: v
standard_name: velocity
pressure:
name: pressure
long_name: Sea water pressure, equals 0 at sea-level
standard_name: sea_water_pressure
salinity:
name: PSAL
long_name: Practical Salinity
standard_name: sea_water_salinity
temperature:
name: TEMP
long_name: Sea temperature in-situ ITS-90 scale
standard_name: sea_water_temperature
adv
This table is stored in a file that may be accessed with
system.file("extdata", "adv.yml", package="ocencdf")and the contents are as follows.
type:
comment: A varTable for adv data.
date: '2022-06-28'
name: adv
version: 1
units:
1/m:
name: m-1
dbar:
name: decibar
degree * C:
name: degree_Celcius
degree * E:
name: degree_east
degree * N:
name: degree_north
m / s:
name: meters_per_second
values:
missing_value: 99999.0
variables:
v:
name: v
standard_name: velocity
pressure:
name: pressure
long_name: Sea water pressure, equals 0 at sea-level
standard_name: sea_water_pressure
pitchSlow:
name: pitchSlow
long_name: Pitch in degrees
standard_name: pitch
salinity:
name: PSAL
long_name: Practical Salinity
standard_name: sea_water_salinity
temperature:
name: TEMP
long_name: Sea temperature in-situ ITS-90 scale
standard_name: sea_water_temperature
argo
This table, patterned on naming conventions in the Argo ocean float program, is stored in a file that may be accessed with
system.file("extdata", "argo.yml", package="ocencdf")and the contents are as follows.
type:
comment: See Section 3.3 of “Argo User’s Manual.” Pdf. Ifremer, July 5, 2022. https://doi.org/10.13155/29825.
date: '2022-06-10'
name: argo
version: 3
units:
1/m:
name: m-1
day:
name: days
dbar:
name: decibar
degree * C:
name: degree_Celcius
degree * E:
name: degree_east
degree * N:
name: degree_north
mu * mol *quanta/m^2/s:
name: microMoleQuanta/m^2/sec
mu * mol/kg:
name: micromole/kg
ntu:
name: ntu
values:
missing_value: 99999.0
variables:
backscattering:
name: BBMP
chlorophyll-A:
name: CHLA
standard_name: mass_concentration_of_chlorophyll_a_in_sea_water
conductivity:
name: CNDC
standard_name: sea_water_electrical_conductivity
downwelling_par:
name: DOWNWELLING_PAR
standard_name: downwelling_photosynthetic_photon_flux_in_sea_water
latitude:
name: LATITUDE
standard_name: latitude
longitude:
name: LONGITUDE
standard_name: longitude
nitrate:
name: NITRATE
standard_name: moles_of_nitrate_per_unit_mass_in_sea_water
oxygen:
name: DOXY
standard_name: moles_of_oxygen_per_unit_mass_in_sea_water
oxygenMolar:
name: MOLAR_DOXY
standard_name: mole_concentration_of_dissolved_molecular_oxygen_in_sea_water
pH:
name: PH_IN_SITU_TOTAL
standard_name: sea_water_ph_reported_on_total_scale
pressure:
name: PRES
long_name: Sea water pressure, equals 0 at sea-level
standard_name: sea_water_pressure
salinity:
name: PSAL
long_name: Practical Salinity
standard_name: sea_water_salinity
temperature:
name: TEMP
long_name: Sea temperature in-situ ITS-90 scale
standard_name: sea_water_temperature
temperatureOxygen:
name: TEMP_DOXY
standard_name: temperature_of_sensor_for_oxygen_in_sea_water
turbidity:
name: TURBIDITY
standard_name: sea_water_turbidity
up_radiance:
name: UP_RADIANCE
standard_name: upwelling_radiance_in_sea_water whp
This table, patterned on naming conventions in the World Hydrographic Program, is stored in a file that may be accessed with
system.file("extdata", "whp.yml", package="ocencdf")and the contents are as follows.
type:
date: '2022-06-04'
name: whp
version: 1
units:
1/m:
name: m-1
dbar:
name: decibar
degree * C:
name: degree_Celcius
mu * mol/kg:
name: micromole/kg
values:
missing_value: 99999.0
variables:
ammonium:
name: NH4
CFC-12:
name: CFC12
fluorescence:
name: FLUOR
nitrate:
name: NITRAT
nitrite:
name: NITRIT
NO2+NO3:
name: nitrite+nitrate
number:
name: NUMBER
oxygen:
name: CTDOXY
oxygenBottle:
name: OXYGEN
phosphate:
name: PHSPHT
pHTemperature:
name: PH_TMP
pHTotal:
name: PH_TOT
pressure:
name: CTDPRS
salinity:
name: CTDSAL
salinityBottle:
name: SALNTY
SF6:
name: SF6
silicate:
name: SILCAT
temperature:
name: CTDTMP
totalAlkalinity:
name: ALKALI
totalCarbon:
name: TCARBN
transmission:
name: TRANS