Read a HOBOware details file and parse into a nested list.
Details
The HOBOware details file contains data on the sensor, the deployment,
and the calibration process.
Indentation level is used to indicate the hierarchy in the
data. parse_hoboware_details() parses the file into a list that
captures that structure.
The approach taken is a little bit of kludge but seems to be working for
the files produced by the DO and Conductivity loggers.
parse_hoboware_details() first edits the details text so that it can be
parsed as YAML into an R nested list.
The resulting list is then cleaned by eliminating spaces and weird
characters from the list item names (but not values) and dropping some
redundant nesting.
Note
The sample numbers in the details files include commas (e.g 1,283 ) that
trip up the YAML conversion. These are eliminated in a targeted
fashion - dropping commas between digits only on lines with
"Max:", "Min:", "Avg:", "Std Dev:" or "Samples:".
With other output files this might need to be expanded to cover more of
the file, but given that commas could potential delineate items in
a list a surgical approach was used.
With conductivity details files some of the values are separated from the
field names with "=" instead of ":", used in most of the file.
To process these items correctly all " = "
are replaced with ": " before parsing as YAML. This might create
unintended consequences in some fields or with other HOBOware output,
but it does not adversely affect any of the fields extracted by this package,
in get_do_details() or get_cond_details().
parse_hoboware_details() is primarily intended for internal package use
Examples
file <- system.file(
"extdata/2023/RB1/2023-06-09/Calibrated/DO_RB1_2023-06-09_Details.txt",
package = "BuzzardsBay")
hwd <- parse_hoboware_details(file)
str(hwd, max.level = 2)
#> List of 8
#> $ Series_DO_conc_mg_per_L :List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 11
#> ..$ Series_Statistics:List of 7
#> $ Series_Temp_C :List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 8
#> ..$ Series_Statistics:List of 7
#> $ Series_DO_Adj_Conc_mg_per_L:List of 4
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 11
#> ..$ Series_Statistics :List of 7
#> ..$ Dissolved_Oxygen_Assistant_Parameters:List of 24
#> $ Series_DO_Percent_pct :List of 4
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 11
#> ..$ Series_Statistics :List of 7
#> ..$ Dissolved_Oxygen_Assistant_Parameters:List of 24
#> $ Series_Salinity_ppt :List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 8
#> ..$ Series_Statistics:List of 7
#> $ Event_Type_Coupler_Attached:List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 6
#> ..$ Series_Statistics:List of 3
#> $ Event_Type_Stopped :List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 6
#> ..$ Series_Statistics:List of 3
#> $ Event_Type_End_Of_File :List of 3
#> ..$ Devices :List of 1
#> ..$ Deployment_Info :List of 6
#> ..$ Series_Statistics:List of 3
# These are of particular interest
hwd$Series_DO_Adj_Conc_mg_per_L$Dissolved_Oxygen_Assistant_Parameters |>
yaml::as.yaml() |>
cat()
#> Performing_Field_Calibration: .na
#> Using_start_cal_point: .na
#> Start_time: 06/02/23 11:10:00 AM GMT-04:00
#> Start_DO_conc: 7.37
#> Start_temperature_C: 22.0
#> Start_salinity_ppt: 28.47
#> Start_meter_per_titration_value_mg_per_L: 6.41
#> Start_salinity_correction: 0.8475
#> Using_end_cal_point: .na
#> End_time: 06/09/23 12:40:00 PM GMT-04:00
#> End_DO_conc: 9.12
#> End_temperature_C: 18.1
#> End_salinity_ppt: 28.47
#> End_meter_per_titration_value_mg_per_L: 7.62
#> End_salinity_correction: 0.8382
#> Adjust_for_Salinity_selected: .na
#> Salinity_datafile: Y:\BAYWATCHERS\HOBO dataloggers\RB1\Deployments_RBH\2023\6_9_2023\Calibrated
#> Data\RB1_SpecCon_6_9_2023_AH.txt
#> Overlap_mode: Option 1
#> Barometric_Pressure_selected: .na
#> Pressure_value_atm: 1.0
#> Elevation_m: 0.0
#> Reporting_data_between_selected_points_only: .na
#> Start: Field cal reference start
#> End: Field cal reference end