### 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](https://github.com/onnela-lab/beiwe) 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](https://github.com/onnela-lab/beiwe) 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](https://github.com/onnela-lab/beiwe) 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