Process Positions from a Folder — process

Convience function for processing GLS logger data using provided calibration values. Uses 'process_folder()' to process a folder 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()'

Usage

process_positions(
  import_directory = NULL,
  light_data_list = NULL,
  calibration_data,
  all_colony_info,
  output_directory,
  extra_metadata = NULL,
  filter_setting_list = seatrackRgls::seatrack_settings_list,
  show_filter_plots = TRUE,
  do_seasonal_calibration = NULL,
  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.
calibration_data: Data frame containing calibration data for loggers or a path pointing to the calibration data, as created by prepare_calibration().
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 processed position outputs, plots etc.
extra_metadata: Optional data frame containing extra metadata for loggers. This must have the column logger_id to join extra metadata. A year_retrieved column can also be provided to join based on a combination of logger and which session this is.
filter_setting_list: A 'GLSFilterSettingsList' object containing filter settings for loggers or a path to load one using 'read_filter_file()'. Defaults to 'seatrack_settings_list'.
show_filter_plots: A logical indicating whether to show individual filter plots for the default sun angle. Defaults to TRUE.
do_seasonal_calibration: A logical indicating whether to perform seasonal calibration. Defaults to NULL, which uses the filter_settings_list.
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 a folder containing (for each logger), processed positions, twilight estimates, plots showing the effects of filters, a folder of summary files detailing the results of filters used and maps.