Extract information from deployment log

Usage

ss_read_log(path, path_config = NULL)

Arguments

path

File path to the Log folder.

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.

Value

Returns a list with 4 elements. deployment_dates is a data frame with two columns: start_date (the date of deployment) and end_date (date of retrieval). area_info is a data frame with five columns: county, waterbody, latitude, longitude, station, and lease. sn_table is a data frame with three columns: log_sensor (sensor name as recorded in the log), sensor_serial_number, and depth (sensor depth below the surface at low tide, from the Sensor_Depth column). string_configuration is a character string indicating how the sensor string was moored (i.e., whether the sensors float with the tide).

Details

These columns are going to change with the new logs. Deprecate this function or save it as _old for backwards compatibility.

The log must be saved in a folder called Log in .csv, .xlsx or .xls format, and must include the following columns:

Deployment_Waterbody: waterbody where string was deployed

Location_Description: the station name

Lease#: If located on an aquaculture site, the lease number (NA otherwise)

Deployment: deployment date, in the order "Ymd"

Retrieval: retrieval date, in the order "Ymd"

Logger_Latitude: The latitude at which the string was deployed

Logger_Longitude The longitude at which the string was deployed (must be a negative value)

Logger_Model The type of sensor; see below for options

Serial# The sensor serial number

Sensor_Depth: Depth at which the sensor was deployed

All other columns will be ignored.

Entries in the Logger_Model column must include the string "aquameasure", "hobo", "tidbit", or "vr2ar" (not case sensitive).

The function will stop with an Error if there is more than one eligible file (csv, .xlsx or .xls) in the Log folder.

The function will stop with an Error if there if the Logger_Longitude is a positive value.

A Warning message is printed to the console when the function does not recognize a sensor in the log.

A message is printed to the console when hobo, aquameasure, or vemco sensors are not found in the log.

A message is printed to the console if there is more than one unique entry in Deployment_Waterbody, Location_Description, Deployment, Retrieval, Logger_Latitude, or Logger_Longitude.

Author

Danielle Dempsey