Survey

process_survey:

Create a cleaned and scored copy of all survey CSVs in data_dir saved in out_dir by survey ID

• -d, --data_dir:
  Path to root directory where data is stored

• -o, --out_dir:
  Path to directory into which data will be saved

• -k, --key_path:
  Path to Excel file containing survey scoring rules

• --subject_ids (optional):
  List of subject IDs to process. If nothing is provided, all subjects in data_dir will be used

• --survey_ids (optional):
  List of survey IDs to process. If nothing is provided, all surveys in data_dir will be used

• --skip_dirs (optional):
  List of directory names to skip when looking for data. Only use the dir name, not the full path

• --use_zips (optional):
  Flag to process CSVs in zip files within data_dir. Defaults to False

• --only_redcap (optional):
  Flag to only process redcap data. Mutually exclusive with only_beiwe. Defaults to False

• --only_beiwe (optional):
  Flag to only process beiwe data. Mutually exclusive with only_redcap. Defaults to False

aggregate_survey:

Take all data processed by process_survey and create a summary Excel doc saved to out_dir. First tab is a data summary, second tab is a basic statistics summary, remaining tabs contain detailed scoring for each individual survey

• -d, --data_dir:
  Path to root directory where data is stored

• -o, --out_dir:
  Path to directory into which data will be saved

• -k, --key_path:
  Path to Excel file containing survey scoring rules

• --out_name (optional):
  Name of output file. Defaults to "SURVEY_SUMMARY"

Acoustic

aggregate_acoustic:

Collects acoustic data in data_dir (processed externally in SPA) into a summary sheet in out_dir.

• -d, --data_dir:
  Path to root directory where data is stored

• -o, --out_dir:
  Path to directory into which data will be saved

• --subject_ids (optional):
  Subjects whose data should be analyzed. If nothing is provided, all subjects in data_dir will be used

• --out_name (optional):
  Name of the summary file. Defaults to "ACOUSTIC_SUMMARY"

GPS

process_gps:

Runs forest.jasmine’s GPS analysis with some user interaction and additional helpful info printed

• -d, --data_dir:
  Path to root directory where data is stored

• -o, --out_dir:
  Path to directory into which data will be saved

• --subject_ids (optional):
  Subjects whose data should be analyzed. If nothing is provided, all subjects in data_dir will be used

• --quality_thresh (optional):
  Data quality threshold. Defaults to 0.05

aggregate_gps:

Collects data from process_gps in data_dir into a summary sheet in out_dir

• -d, --data_dir:
  Path to root directory where data is stored

• -o, --out_dir:
  Path to directory into which data will be saved

• --out_name (optional):
  Name of the summary file. Defaults to "GPS_SUMMARY"

Other

combine_summaries:

Combines summary sheets into single sheet

• -o, --out_dir:
  Path to directory into which data will be saved

• --acoustic_path (optional):
  Path to acoustic summary file. Defaults to “”

• --gps_path (optional):
  Path to gps summary file. Defaults to “”

• --survey_path (optional):
  Path to survey summary file. Defaults to “”

• --out_name (optional):
  Name of output file. Defaults to "COMBINED_SUMMARY"

Quality Check

make_key:

Builds and saves a keyring file used as a key to download data from Beiwe servers

• --username:
  Beiwe username

• --beiwe_pw:
  Beiwe password

• --access_key:
  Public access key obtained from Beiwe server

• --secret_key:
  Secret access key obtained from Beiwe server

• --out_path:
  Path to directory into which key will be saved

• --beiwe_code_path
  Path to this cloned repository

• --file_pw,
  Password with which to encrypt the file

• --url, Url to Beiwe server. Defaults to: https://studies.beiwe.org

download_and_check:

Runs download_beiwe_data and quality_check for all subject ids provided

• --keyring_path:
  Path to keyring file generated by make_key

• --keyring_pw:
  Password for the keyring file

• --study_id:
  Beiwe study ID

• --out_dir:
  Path to directory into which data will be saved

• --beiwe_ids:
  Beiwe subject IDs’ data to download

• --beiwe_code_path:
  Path to this cloned repository

• --time_start:
  Earliest date at which to download data. Formatted YYYY-MM-DD. If not supplied, earliest collected data will be used for all subjects

• --time_end:
  Latest date at which to download data. Formatted YYYY-MM-DD. If not supplied, current date will be used for all subjects

• --data_streams:
  Data streams to download. Defaults to [“gps”, “survey_timings”, “survey_answers”, “audio_recordings”]

• --survey_key_path:
  Path to Excel file containing survey scoring rules

• --skip_gps_stats:
  Flag to skip running GPS processing, as this can sometimes be time-intensive

download_beiwe_data:

Downloads data from Beiwe server into specified directory

• --keyring_path:
  Path to keyring file generated by make_key

• --keyring_pw:
  Password for the keyring file

• --study_id:
  Beiwe study ID

• --out_dir:
  Path to directory into which data will be saved

• --beiwe_ids:
  Beiwe subject IDs’ data to download

• --beiwe_code_path:
  Path to this cloned repository

• --time_start:
  Earliest date at which to download data. Formatted YYYY-MM-DD. If not supplied, earliest collected data will be used for all subjects

• --time_end:
  Latest date at which to download data. Formatted YYYY-MM-DD. If not supplied, current date will be used for all subjects

• --data_streams:
  Data streams to download. Defaults to [“gps”, “survey_timings”, “survey_answers”, “audio_recordings”]

run_quality_check:

Runs a quality check on the data in data_dir on subject_id and outputs the results to data_dir/subject_id_processed/

• --data_dir:
  Path to root directory where data is stored

• --subject_id:
  Beiwe ID of subject’s data to check

• --survey_key_path:
  Path to Excel file containing survey scoring rules

• --skip_gps_stats:
  Flag to skip running GPS processing, as this can sometimes be time-intensive