rapids/config.yaml

# See https://www.rapids.science/setup/configuration/#database-credentials
DATABASE_GROUP: &database_group
  MY_GROUP

# See https://www.rapids.science/setup/configuration/#timezone-of-your-study
TIMEZONE: &timezone
  America/New_York

# See https://www.rapids.science/setup/configuration/#participant-files
PIDS: [j01]

# See https://www.rapids.science/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES:
  SOURCE:
    TYPE: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
    DATABASE_GROUP: *database_group
    CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
    TIMEZONE: *timezone
  PHONE_SECTION:
    ADD: TRUE
    DEVICE_ID_COLUMN: device_id # column name
    IGNORED_DEVICE_IDS: []
  FITBIT_SECTION:
    ADD: TRUE
    DEVICE_ID_COLUMN: device_id # column name
    IGNORED_DEVICE_IDS: []

# See https://www.rapids.science/setup/configuration/#day-segments
DAY_SEGMENTS: &day_segments
  TYPE: EVENT # FREQUENCY, PERIODIC, EVENT
  FILE: "data/external/daysegments_event.csv"
  INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs

# See https://www.rapids.science/setup/configuration/#device-data-source-configuration
DEVICE_DATA:
  PHONE:
    SOURCE: 
      TYPE: DATABASE
      DATABASE_GROUP: *database_group
      DEVICE_ID_COLUMN: device_id # column name
    TIMEZONE: 
      TYPE: SINGLE # SINGLE or MULTIPLE
      VALUE: *timezone # IF TYPE=SINGLE, see docs
  FITBIT:
    SOURCE: 
      TYPE: DATABASE # DATABASE or FILES (set each FITBIT_SENSOR TABLE attribute accordingly with a table name or a file path)
      COLUMN_FORMAT: JSON # JSON or PLAIN_TEXT
      DATABASE_GROUP: *database_group
      DEVICE_ID_COLUMN: device_id # column name
    TIMEZONE: 
      TYPE: SINGLE # Fitbit only supports SINGLE timezones
      VALUE: *timezone # see docs

############## PHONE ###########################################################
################################################################################

PHONE_VALID_SENSED_BINS:
  COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
  BIN_SIZE: &bin_size 5 # (in minutes)
  # Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS. 
  # If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory.
  # You can choose any of the keys shown below, just make sure its TABLE exists in your database!
  # PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT,
  # PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION
  PHONE_SENSORS: []

PHONE_VALID_SENSED_DAYS:
  COMPUTE: False
  MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour [6] # (out of 60min/BIN_SIZE bins)
  MIN_VALID_HOURS_PER_DAY: &min_valid_hours_per_day [16] # (out of 24) MIN_HOURS_PER_DAY

# Communication SMS features config, TYPES and FEATURES keys need to match
PHONE_MESSAGES:
  TABLE: messages
  PROVIDERS:
    RAPIDS:
      COMPUTE: True
      MESSAGES_TYPES : [received, sent]
      FEATURES: 
        received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
        sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
      SRC_LANGUAGE: "r"
      SRC_FOLDER: "rapids" # inside src/features/phone_messages

# Communication call features config, TYPES and FEATURES keys need to match
PHONE_CALLS:
  TABLE: calls
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      CALL_TYPES: [missed, incoming, outgoing]
      FEATURES:
        missed:  [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
        incoming: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
        outgoing: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
      SRC_LANGUAGE: "r"
      SRC_FOLDER: "rapids" # inside src/features/phone_calls

PHONE_LOCATIONS:
  TABLE: locations
  LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED  
  FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD: 30 # minutes, only replicate location samples to the next sensed bin if the phone did not stop collecting data for more than this threshold
  FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION: 720 # minutes, only replicate location samples to consecutive sensed bins if they were logged within this threshold after a valid location row
  PROVIDERS:
    DORYAB:
      COMPUTE: False
      FEATURES: ["locationvariance","loglocationvariance","totaldistance","averagespeed","varspeed","circadianmovement","numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","meanlengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy"]
      DBSCAN_EPS: 10 # meters
      DBSCAN_MINSAMPLES: 5
      THRESHOLD_STATIC : 1 # km/h
      MAXIMUM_GAP_ALLOWED: 300
      MINUTES_DATA_USED: False
      SAMPLING_FREQUENCY: 0
      SRC_FOLDER: "doryab" # inside src/features/phone_locations
      SRC_LANGUAGE: "python"

    BARNETT:
      COMPUTE: False
      FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
      ACCURACY_LIMIT: 51 # meters, drops location coordinates with an accuracy higher than this. This number means there's a 68% probability the true location is within this radius
      TIMEZONE: *timezone
      MINUTES_DATA_USED: False # Use this for quality control purposes, how many minutes of data (location coordinates gruped by minute) were used to compute features
      SRC_FOLDER: "barnett" # inside src/features/phone_locations
      SRC_LANGUAGE: "r"

PHONE_BLUETOOTH:
  TABLE: bluetooth
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
      SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
      SRC_LANGUAGE: "r"


PHONE_ACTIVITY_RECOGNITION:
  TABLE: 
    ANDROID: plugin_google_activity_recognition
    IOS: plugin_ios_activity_recognition
  EPISODE_THRESHOLD_BETWEEN_ROWS: 5 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
      ACTIVITY_CLASSES:
        STATIONARY: ["still", "tilting"]
        MOBILE: ["on_foot", "walking", "running", "on_bicycle"]
        VEHICLE: ["in_vehicle"]
      SRC_FOLDER: "rapids" # inside src/features/phone_activity_recognition
      SRC_LANGUAGE: "python"

PHONE_BATTERY:
  TABLE: battery
  EPISODE_THRESHOLD_BETWEEN_ROWS: 30 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
      SRC_FOLDER: "rapids" # inside src/features/phone_battery
      SRC_LANGUAGE: "python"

PHONE_SCREEN:
  TABLE: screen
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      REFERENCE_HOUR_FIRST_USE: 0
      IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
      IGNORE_EPISODES_LONGER_THAN: 0 # in minutes, set to 0 to disable
      FEATURES: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration", "firstuseafter"] # "episodepersensedminutes" needs to be added later
      EPISODE_TYPES: ["unlock"]
      SRC_FOLDER: "rapids" # inside src/features/phone_screen
      SRC_LANGUAGE: "python"

PHONE_LIGHT:
  TABLE: light
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
      SRC_FOLDER: "rapids" # inside src/features/phone_light
      SRC_LANGUAGE: "python"

PHONE_ACCELEROMETER:
  TABLE: accelerometer
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
      SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
      SRC_LANGUAGE: "python"
    
    PANDA:
      COMPUTE: False
      VALID_SENSED_MINUTES: False
      FEATURES:
        exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
        nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
      SRC_FOLDER: "panda" # inside src/features/phone_accelerometer
      SRC_LANGUAGE: "python"

PHONE_APPLICATIONS_FOREGROUND:
  TABLE: applications_foreground
  APPLICATION_CATEGORIES:
    CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
    CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
    UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
    SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      SINGLE_CATEGORIES: ["all", "email"]
      MULTIPLE_CATEGORIES:
        social: ["socialnetworks", "socialmediatools"]
        entertainment: ["entertainment", "gamingknowledge", "gamingcasual", "gamingadventure", "gamingstrategy", "gamingtoolscommunity", "gamingroleplaying", "gamingaction", "gaminglogic", "gamingsports", "gamingsimulation"]
      SINGLE_APPS: ["top1global", "com.facebook.moments", "com.google.android.youtube", "com.twitter.android"] # There's no entropy for single apps
      EXCLUDED_CATEGORIES: []
      EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
      FEATURES: ["count", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
      SRC_FOLDER: "rapids" # inside src/features/phone_applications_foreground
      SRC_LANGUAGE: "python"

PHONE_WIFI_VISIBLE:
  TABLE: "wifi"
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
      SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
      SRC_LANGUAGE: "r"

PHONE_WIFI_CONNECTED:
  TABLE: "sensor_wifi"
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
      SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
      SRC_LANGUAGE: "r"

PHONE_CONVERSATION:
  TABLE: 
    ANDROID: plugin_studentlife_audio_android
    IOS: plugin_studentlife_audio
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
    "sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","noisesumenergy",
    "noiseavgenergy","noisesdenergy","noiseminenergy","noisemaxenergy","voicesumenergy",
    "voiceavgenergy","voicesdenergy","voiceminenergy","voicemaxenergy","silencesensedfraction","noisesensedfraction",
    "voicesensedfraction","unknownsensedfraction","silenceexpectedfraction","noiseexpectedfraction","voiceexpectedfraction",
    "unknownexpectedfraction","countconversation"]
      RECORDING_MINUTES: 1
      PAUSED_MINUTES : 3
      SRC_FOLDER: "rapids" # inside src/features/phone_conversation
      SRC_LANGUAGE: "python"

############## FITBIT ##########################################################
################################################################################

FITBIT_HEARTRATE_SUMMARY:
  TABLE: heartrate_summary
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["maxrestinghr", "minrestinghr", "avgrestinghr", "medianrestinghr", "moderestinghr", "stdrestinghr", "diffmaxmoderestinghr", "diffminmoderestinghr", "entropyrestinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["sumcaloriesoutofrange", "maxcaloriesoutofrange", "mincaloriesoutofrange", "avgcaloriesoutofrange", "mediancaloriesoutofrange", "stdcaloriesoutofrange", "entropycaloriesoutofrange", "sumcaloriesfatburn", "maxcaloriesfatburn", "mincaloriesfatburn", "avgcaloriesfatburn", "mediancaloriesfatburn", "stdcaloriesfatburn", "entropycaloriesfatburn", "sumcaloriescardio", "maxcaloriescardio", "mincaloriescardio", "avgcaloriescardio", "mediancaloriescardio", "stdcaloriescardio", "entropycaloriescardio", "sumcaloriespeak", "maxcaloriespeak", "mincaloriespeak", "avgcaloriespeak", "mediancaloriespeak", "stdcaloriespeak", "entropycaloriespeak"]
      SRC_FOLDER: "rapids" # inside src/features/fitbit_heartrate_summary
      SRC_LANGUAGE: "python"

FITBIT_HEARTRATE_INTRADAY:
  TABLE: heartrate_intraday
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
      SRC_FOLDER: "rapids" # inside src/features/fitbit_heartrate_intraday
      SRC_LANGUAGE: "python"

FITBIT_STEPS_SUMMARY:
  TABLE: steps_summary
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: ["maxsumsteps", "minsumsteps", "avgsumsteps", "mediansumsteps", "stdsumsteps"]
      SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_summary
      SRC_LANGUAGE: "python"

FITBIT_STEPS_INTRADAY:
  TABLE: steps_intraday
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES:
        STEPS: ["sum", "max", "min", "avg", "std"]
        SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
        ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
      THRESHOLD_ACTIVE_BOUT: 10 # steps
      INCLUDE_ZERO_STEP_ROWS: False
      SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_intraday
      SRC_LANGUAGE: "python"

FITBIT_SLEEP:
  TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
  TABLE:
    JSON: fitbit_sleep
    CSV:
      SUMMARY: sleep_summary
      INTRADAY: sleep_intraday
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      SLEEP_TYPES: ["main", "nap", "all"]
      SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]

FITBIT_CALORIES:
  TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
  TABLE:
    JSON: fitbit_calories
    CSV:
      SUMMARY: calories_summary
      INTRADAY: calories_intraday
  PROVIDERS:
    RAPIDS:
      COMPUTE: False
      FEATURES: []

### Visualizations #############################################################
################################################################################

HEATMAP_FEATURES_CORRELATIONS:
  PLOT: False
  MIN_ROWS_RATIO: 0.5
  MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
  MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
  PHONE_FEATURES: [accelerometer, activity_recognition, applications_foreground, battery, calls_incoming, calls_missed, calls_outgoing, conversation, light, location_doryab, messages_received, messages_sent, screen]
  FITBIT_FEATURES: [fitbit_heartrate, fitbit_step, fitbit_sleep]
  CORR_THRESHOLD: 0.1
  CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}

HISTOGRAM_VALID_SENSED_HOURS:
  PLOT: False
  MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
  MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour

HEATMAP_DAYS_BY_SENSORS:
  PLOT: False
  MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
  MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
  EXPECTED_NUM_OF_DAYS: -1
  DB_TABLES: [accelerometer, applications_foreground, battery, bluetooth, calls, light, locations, messages, screen, wifi, sensor_wifi, plugin_google_activity_recognition, plugin_ios_activity_recognition, plugin_studentlife_audio_android, plugin_studentlife_audio]

HEATMAP_SENSED_BINS:
  PLOT: False
  BIN_SIZE: *bin_size

OVERALL_COMPLIANCE_HEATMAP:
  PLOT: False
  ONLY_SHOW_VALID_DAYS: False
  EXPECTED_NUM_OF_DAYS: -1
  BIN_SIZE: *bin_size
  MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
  MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour