Package index • seatrackRtools

Start interface

Run a shiny app to perform (some) of the functions below

Functions to set up the sea track folder and paths.

Functions to assist in running the within-seatrack GLS pipeline

gls_calibrate_all(): Calibrate all species/colony combinations found in seatrack logger data import folder
gls_calibrate_species_colony(): Prepare a seatrack species/colony combination for calibration
gls_metadata(): Get metadata from database based on GLS files in import directory
gls_prepare_calibration(): Prepare GLS calibration data using seatrack database
gls_prepare_file_upload(): Prepare a single GLS position data file for database upload
gls_prepare_folder_upload(): Prepare GLS position data for database upload
gls_process_positions(): Process GLS position data using seatrackRgls
gls_seatrack_calibration(): Handle existing GLS calibration data
gls_seatrack_colony_info(): Get all_colony_info for GLS processing

Functions to handle and process metadata sheets.

get_location_unprocessed(): Get unimported metadata
get_master_import_path(): Get the path of the master import file
handle_partner_metadata(): Add partner provided metadata to the master import file
load_all_master_import(): Load master import file for all colonies
load_master_import(): Load master import file for a given colony
load_partner_metadata(): Load partner provided metadata from an Excel file
modify_master_import_in_list(): Given a new master import, modify all master imports in a list sharing the same path
save_all_modified(): Save all modified master sheets
save_master_sheet(): Save a master sheet to an Excel file.

Functions to load logger data

end_logger_session(): Modify logger status to end a session
get_logger_from_metadata(): Find logger instances in files
get_unfinished_session(): Find a logger's unfinished session in the master startup data frame
handle_returned_loggers(): Handle restarted loggers
modify_logger_status(): Modify logger status

Functions to load and update non-responsive sheets

append_to_nonresponsive(): Append to nonresponsive list
get_raw_data_prev_session(): Get raw data from previous sessions
load_nonresponsive(): Load multiple nonresponsive logger sheets
load_nonresponsive_sheet(): Load nonresponsive logger sheet for current year
nonresponsive_from_master(): Get all nonresponsive loggers and export
save_nonresponsive(): Save multiple nonresponsive logger sheets to Excel files

Functions to load and update startup sheets

add_loggers_from_startup(): Attempt to add logger from startup sheets
get_startup_paths(): Get paths to all startup Excel files
set_comments(): Set or append comments in the master_startup data frame
set_master_startup_value(): Set a value in a specific cell of master startup

Functions to load and update encounter data

append_encounter_data(): Append encounter data to the master import metadata

Functions to import master import data into the Database

push_db_import_collection(): Push database import collection to database
push_db_import_collections(): Push multiple database import collections to database
push_deployments(): Push deployments to database
push_master_import_file_to_db(): Push master import file to database
push_retrievals(): Push retrievals to database Function to push retrievals from a master import sheet to the database. It checks the database for existing retrievals and only imports new retrievals to avoid duplicates. It also checks that the loggers being retrieved have an associated deployment in the database.
push_shutdowns(): Push shutdowns to database
push_startup(): Push startups to database

Functions to load and handle data from the field planning sheet

field_plan_check_locations(): Check and update locations in the field plan sheet
field_plan_combine_locations(): Combine duplicate locations/species in the field plan sheet
get_clean_field_plan(): Read and clean the field plan data
get_field_plan(): Read and process the field plan Excel sheet

Functions to create and export annual report appendix tables

create_appendix_table(): Create a formatted flextable for the appendix table
export_appendix_table_excel(): Export the flextable to an Excel file with formatting

get_open_session_dates(): Get open session dates Convenience function to get the open date for a set of logger sessions. If the download date is available, use that. If not, use the shutdown date. If both exist, use the later date. If neither are available, use a date far in the future to indicate the session is still open.
load_sheets_as_list(): Load specified sheets from an Excel file into a list of data frames

check_db_metadata_import(): Check existing rows in database given certain columns from a metadata dataframe
check_deployment_db(): Check existing deployments in database
check_retrieval_db(): Check existing retrievals in database
check_shutdown_db(): Check existing shutdowns in database
check_startups_db(): Check existing startups in database

Functions to assist in working with the ColonyRepr-package

prep_SEATRACK_ColonyRepr(): Extracts data from the SEATRACK DB and prepares it for the ColonyRepr functions
run_ColonyRepr(): Function to extract desired data from the SEATRACK database and fully run the colony representativeness analysis