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,
  calibration_data,
  all_colony_info,
  output_directory,
  extra_metadata = NULL,
  filter_setting_list = seatrackRgls::seatrack_settings_list
)

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
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'.

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.