This function, meant for internal use by the package, uses
yaml::yaml.load_file() to read YAML files that describe the
output NetCDF format created by e.g. ctd2ncdf(). Users wishing
to define such files for their own use should follow the pattern
of the source directory inst/extdata/argo.yml.
read.varTable(varTable = "argo", debug = 0)character value indicating the name of the table (see ‘Details’).
integer, 0 (the default) for quiet action apart from messages and warnings, or any larger value to see more output that describes the processing steps.
read.varTable() returns a list that specifies some information
to be stored in NetCDF files created by e.g. ctd2ncdf().
The value of varTable controls the variable-name translation
table to be used. If varTable is NULL, then a default table
is used, the choice of which depends on the function that
calls read.varTable(). Alternatively,
if varTable is a character value, then there are 3 possibilities.
If varTable is "-", then an empty variable table is returned.
If varTable ends in .yml, then it is taken as a file to be read.
Otherwise, ".yml" is appended to varTable and a file with that
name is sought in the inst/ext_data source directory.
At the moment, there are two such built-in files, named
"argo.yml" and "whp.yml".
library(ocencdf)
str(read.varTable("whp"))
#> List of 4
#> $ type :List of 3
#> ..$ date : chr "2022-06-04"
#> ..$ name : chr "whp"
#> ..$ version: int 1
#> $ units :List of 4
#> ..$ 1/m :List of 1
#> .. ..$ name: chr "m-1"
#> ..$ dbar :List of 1
#> .. ..$ name: chr "decibar"
#> ..$ degree * C :List of 1
#> .. ..$ name: chr "degree_Celcius"
#> ..$ mu * mol/kg:List of 1
#> .. ..$ name: chr "micromole/kg"
#> $ values :List of 1
#> ..$ missing_value: num 99999
#> $ variables:List of 21
#> ..$ ammonium :List of 4
#> .. ..$ name : chr "NH4"
#> .. ..$ long_name : chr "ammonium"
#> .. ..$ standard_name: chr "ammonium"
#> .. ..$ missing_value: num 99999
#> ..$ CFC-12 :List of 4
#> .. ..$ name : chr "CFC12"
#> .. ..$ long_name : chr "CFC-12"
#> .. ..$ standard_name: chr "CFC-12"
#> .. ..$ missing_value: num 99999
#> ..$ fluorescence :List of 4
#> .. ..$ name : chr "FLUOR"
#> .. ..$ long_name : chr "fluorescence"
#> .. ..$ standard_name: chr "fluorescence"
#> .. ..$ missing_value: num 99999
#> ..$ nitrate :List of 4
#> .. ..$ name : chr "NITRAT"
#> .. ..$ long_name : chr "nitrate"
#> .. ..$ standard_name: chr "nitrate"
#> .. ..$ missing_value: num 99999
#> ..$ nitrite :List of 4
#> .. ..$ name : chr "NITRIT"
#> .. ..$ long_name : chr "nitrite"
#> .. ..$ standard_name: chr "nitrite"
#> .. ..$ missing_value: num 99999
#> ..$ NO2+NO3 :List of 4
#> .. ..$ name : chr "nitrite+nitrate"
#> .. ..$ long_name : chr "NO2+NO3"
#> .. ..$ standard_name: chr "NO2+NO3"
#> .. ..$ missing_value: num 99999
#> ..$ number :List of 4
#> .. ..$ name : chr "NUMBER"
#> .. ..$ long_name : chr "number"
#> .. ..$ standard_name: chr "number"
#> .. ..$ missing_value: num 99999
#> ..$ oxygen :List of 4
#> .. ..$ name : chr "CTDOXY"
#> .. ..$ long_name : chr "oxygen"
#> .. ..$ standard_name: chr "oxygen"
#> .. ..$ missing_value: num 99999
#> ..$ oxygenBottle :List of 4
#> .. ..$ name : chr "OXYGEN"
#> .. ..$ long_name : chr "oxygenBottle"
#> .. ..$ standard_name: chr "oxygenBottle"
#> .. ..$ missing_value: num 99999
#> ..$ phosphate :List of 4
#> .. ..$ name : chr "PHSPHT"
#> .. ..$ long_name : chr "phosphate"
#> .. ..$ standard_name: chr "phosphate"
#> .. ..$ missing_value: num 99999
#> ..$ pHTemperature :List of 4
#> .. ..$ name : chr "PH_TMP"
#> .. ..$ long_name : chr "pHTemperature"
#> .. ..$ standard_name: chr "pHTemperature"
#> .. ..$ missing_value: num 99999
#> ..$ pHTotal :List of 4
#> .. ..$ name : chr "PH_TOT"
#> .. ..$ long_name : chr "pHTotal"
#> .. ..$ standard_name: chr "pHTotal"
#> .. ..$ missing_value: num 99999
#> ..$ pressure :List of 4
#> .. ..$ name : chr "CTDPRS"
#> .. ..$ long_name : chr "pressure"
#> .. ..$ standard_name: chr "pressure"
#> .. ..$ missing_value: num 99999
#> ..$ salinity :List of 4
#> .. ..$ name : chr "CTDSAL"
#> .. ..$ long_name : chr "salinity"
#> .. ..$ standard_name: chr "salinity"
#> .. ..$ missing_value: num 99999
#> ..$ salinityBottle :List of 4
#> .. ..$ name : chr "SALNTY"
#> .. ..$ long_name : chr "salinityBottle"
#> .. ..$ standard_name: chr "salinityBottle"
#> .. ..$ missing_value: num 99999
#> ..$ SF6 :List of 4
#> .. ..$ name : chr "SF6"
#> .. ..$ long_name : chr "SF6"
#> .. ..$ standard_name: chr "SF6"
#> .. ..$ missing_value: num 99999
#> ..$ silicate :List of 4
#> .. ..$ name : chr "SILCAT"
#> .. ..$ long_name : chr "silicate"
#> .. ..$ standard_name: chr "silicate"
#> .. ..$ missing_value: num 99999
#> ..$ temperature :List of 4
#> .. ..$ name : chr "CTDTMP"
#> .. ..$ long_name : chr "temperature"
#> .. ..$ standard_name: chr "temperature"
#> .. ..$ missing_value: num 99999
#> ..$ totalAlkalinity:List of 4
#> .. ..$ name : chr "ALKALI"
#> .. ..$ long_name : chr "totalAlkalinity"
#> .. ..$ standard_name: chr "totalAlkalinity"
#> .. ..$ missing_value: num 99999
#> ..$ totalCarbon :List of 4
#> .. ..$ name : chr "TCARBN"
#> .. ..$ long_name : chr "totalCarbon"
#> .. ..$ standard_name: chr "totalCarbon"
#> .. ..$ missing_value: num 99999
#> ..$ transmission :List of 4
#> .. ..$ name : chr "TRANS"
#> .. ..$ long_name : chr "transmission"
#> .. ..$ standard_name: chr "transmission"
#> .. ..$ missing_value: num 99999