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Load and process a logger/year combination's light files

process_logger_light_data.Rd

Given a set of filepaths for light data files, calibration data, filter settings, colony info and extra metadata, this function processes the light data to estimate positions and apply various filters depending on whether calibration mode is active or not.

Usage

process_logger_light_data(
  filepaths,
  logger_calibration_data,
  filter_setting_list,
  logger_colony_info,
  all_light_data = NULL,
  logger_extra_metadata = NULL,
  show_filter_plots = FALSE,
  plotting_dir = NULL,
  calibration_mode = TRUE,
  min_length = 40,
  do_seasonal_calibration = NULL,
  stop_on_error = FALSE
)

Arguments

filepaths

A vector of file paths to the light data files.

logger_calibration_data

A data frame containing calibration data for the logger. If multiple calibration windows are provided, each will be processed in sequence.

filter_setting_list

A list of filter settings for different species. Defaults to seatrack_settings_list.

logger_colony_info

A data frame containing colony information for the logger.

all_light_data

An optional data frame containing all light data for the logger. If not provided, light data will be loaded from the filepaths.

logger_extra_metadata

A data frame containing extra metadata for the logger.

show_filter_plots

A logical indicating whether to show filter plots. Defaults to FALSE.

plotting_dir

An optional directory path to save plotting outputs. Defaults to NULL.

calibration_mode

A logical indicating whether to run in calibration mode. Defaults to TRUE.

min_length

Number indicating minimum length of light data. Anything below this will fail. Defaults to 40.

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.

Value

If calibration_mode is FALSE, returns a list containing: - twilight_estimates: A data frame of twilight estimates. - posdata_export: A data frame of processed position data. - filtering: A data frame summarizing the filtering steps applied. If calibration_mode is TRUE, returns data frame of default calibration outputs and exports calibration plots.