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Prepare light position files a single logger and year combination

process_logger_year.Rd

Given a logger ID and year, this function processes all light data files for that logger/year combination, finding the appropriate light files in the specified import directory and applying calibration data, filter settings, colony info, and extra metadata as needed. These are then passed to 'process_logger_light_data()' to handle loading the light data and further processing.

Usage

process_logger_year(
  logger_id,
  year,
  import_directory,
  calibration_data,
  all_colony_info,
  filter_setting_list = seatrackRgls::seatrack_settings_list,
  extra_metadata = NULL,
  show_filter_plots = FALSE,
  export_maps = TRUE,
  plotting_dir = NULL,
  output_dir = NULL,
  calibration_mode = TRUE,
  analyzer = ""
)

Arguments

logger_id

The ID of the logger to process.

year

The year_retrieved to process for the logger.

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

A data frame containing metadata/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. In calibration mode, this dataframe can consist of a single row per logger/year combination. In calibration mode, the minimum required columns are logger_id, species, colony, date_deployed and date_retrieved. Providing logger_model is strongly advised. If not in calibration mode, the data frame is expected to be in the format output by running this function in calibration mode.

all_colony_info

A data frame containing colony information for all loggers (one row per colony). The required columns are colony, latitude, and longitude.

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'.

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.

export_maps

A logical indicating whether to export maps of the processed positions. Defaults to TRUE.

plotting_dir

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

output_dir

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

calibration_mode

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

analyzer

An optional string indicating the analyzer who provided calibration data, if this column is not provided in calibration data. Defaults to an empty string.

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 (if plottinging dir is not NULL) exports calibration plots.