Prepare Calibration Data from a Folder — prepare

Convience function for preparing GLS logger data for light data calibration. Uses process_folder() in calibration mode to handle a directory of light data. See 'process_folder()' for more details. Custom settings can be provided using filter_setting_list. For the creation of an empty filter settings template see create_filter_settings_file(). If export_calibration_template is TRUE, it will export an empty calibration sheet using 'calibration_to_wb()'.

Usage

prepare_calibration(
  import_directory = NULL,
  light_data_list = NULL,
  metadata,
  all_colony_info,
  output_directory,
  show_filter_plots = FALSE,
  export_calibration_template = TRUE,
  filter_setting_list = seatrackRgls::seatrack_settings_list,
  overwrite_calibration = FALSE,
  stop_on_error = FALSE
)

Arguments

import_directory: Directory containing raw light data files. These are expected to be named in the format <logger_id>_<year_retrieved>_<logger_model>, e.g. C23_2015_mk4083
light_data_list: A named list of data frames containing light data for each logger/year combination. List names are assumed to be logger serial numbers. If not provided, light data will be loaded from the import directory based on the logger ID and year.
metadata: A data frame containing calibration data for all loggers or a string providing a filepath to read this data from. This can be from an excel file, CSV file or a directory containing multiple calibration files. This dataframe can consist of a single row per logger/year combination, with the following columns logger_id, species, colony, date_deployed and date_retrieved. Providing logger_model is strongly advised. These will be automatically split into time windows, using the year_split setting (defaulting to "06-01" in all 'seatrack_settings_list'). Alternatively, custom time windows can be provided by including columns start_datetime and end_datetime, with one time window per row.
all_colony_info: A data frame containing colony information for all loggers (one row per colony). The required columns are colony, latitude, and longitude.
output_directory: Directory to save calibration templates and calibration plots. If show_filter_plots is TRUE
show_filter_plots: A logical indicating whether to show individual filter plots for the default sun angle. Defaults to FALSE.
export_calibration_template: When TRUE will export a calibration template in excel format. Otherwise returns the calibration template as an R object. Defaults to TRUE.
filter_setting_list: A 'GLSFilterSettingsList' object containing filter settings for loggers or a path to load one using read_filter_file(). Defaults to 'seatrackRgls::seatrack_settings_list'.
overwrite_calibration: A logical indicating whether to overwrite existing calibration output. Defaults to FALSE. If FALSE, if a calibration output directory already exists, the function will skip processing and return.
stop_on_error: A logical indicating whether to stop processing if an error occurs. Defaults to FALSE. If TRUE, if an error occurs during processing of a logger/year combination, the function will stop and return an error message. If FALSE, the function will continue processing remaining logger/year combinations and will print a message indicating which logger/year combinations had errors.

Details

Will export calibration plots to assist in choosing appropriate sun angles for processing GLS logger data (see vignette). Once these are decided on, final positions can be exported using process_positions()