Compile aquameasure, hobo, tidbit, and vemco data from a single deployment

Usage

ss_compile_deployment_data(
  path,
  path_config = NULL,
  trim = TRUE,
  ignore_sensors = NULL,
  depth_override = NULL
)

Arguments

path

File path to the log, aquameasure, hobo, tidbit, and/or vemco folders.

path_config

File path (including name and extension) of the water quality configuration table. Default is water_quality_configuration_table.xlsx in the tracking_sheets folder. Data must be stored in an xlsx file in a tab named "deployments". Columns must be Waterbody, Station_Name, and Depl_Date. One and only one row must match the waterbody, station, and deployment date recorded in the Log. Options for the configuration column are sub-surface buoy, surface buoy, attached to gear, attached to fixed structure, floating dock, unknown, and calval. Use of the "unknown" entry is discouraged. HINT: for optimal speed, make sure the table is NOT filtered in the excel file.

The path_config argument is ignored for new deployment logs that have an appropriate entry in the Configuration column.

Configurations recorded as NA will be converted to "unknown" with a Warning.

When there is no Configuration in the log and the deployment is not found in the configuration table, the configuration will berecoreded as "unknown" with a Warning.

If more than one configuration is detected in the log or the configuration table, the function will stop with an Error.

trim

Logical value indicating whether to trim the data to the dates specified in deployment_dates. (Note: four hours are added to the retrieval date to account for AST, e.g., in case the sensor was retrieved after 20:00 AST, which is 00:00 UTC the next day.) Default is trim = TRUE.

ignore_sensors

Vector of sensor serial numbers for sensors that are in the deployment log, but should NOT be compiled (e.g., data file missing).

depth_override

An optional character string indicating which depth variable to compile. In some files (e.g., Borgles Island 2018-02-28), there is only one "Seawater depth" observation, but a full deployment of "Average seawater depth" observations. In this case, force the code to compile the average seawater depth with depth_override = Average seawater depth.

Value

Returns a data frame of data from a sensor string deployment.

Details

Reads the deployment log and then calls ss_compile_aquameasure_data(), ss_compile_hobo_data(), and ss_compile_vemco_data() and returns the results in a single data frame.

aquameasure data must be in a folder named aquameasure, hobo data must be in a folder named hobo, tidbit data must be in a folder named tidbit, and vemco data must be in a folder name vemco (folder names are not case sensitive). The aquameasure, hobo, tidbit, and vemco folders must be in the same folder.

Columns with deployment details are added (e.g., county, waterbody, latitude, longitude, station, lease, string_configuration).

Author

Danielle Dempsey