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@ -3,38 +3,36 @@
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########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
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PIDS: ['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107']
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PIDS: [p01]
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# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
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CREATE_PARTICIPANT_FILES:
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USERNAMES_CSV: "data/external/main_study_usernames.csv"
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CSV_FILE_PATH: "data/external/main_study_participants.csv" # see docs for required format
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CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
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PHONE_SECTION:
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ADD: True
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IGNORED_DEVICE_IDS: []
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FITBIT_SECTION:
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ADD: False
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ADD: True
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IGNORED_DEVICE_IDS: []
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EMPATICA_SECTION:
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ADD: False
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ADD: True
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IGNORED_DEVICE_IDS: []
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# See https://www.rapids.science/latest/setup/configuration/#time-segments
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TIME_SEGMENTS: &time_segments
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TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT
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FILE: "data/external/timesegments_daily.csv"
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INCLUDE_PAST_PERIODIC_SEGMENTS: TRUE # Only relevant if TYPE=PERIODIC, see docs
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FILE: "data/external/timesegments_periodic.csv"
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INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs
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# See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
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TIMEZONE:
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TYPE: MULTIPLE
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TYPE: SINGLE
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SINGLE:
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TZCODE: Europe/Ljubljana
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TZCODE: America/New_York
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MULTIPLE:
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TZ_FILE: data/external/timezone.csv
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TZCODES_FILE: data/external/multiple_timezones.csv
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IF_MISSING_TZCODE: USE_DEFAULT
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DEFAULT_TZCODE: Europe/Ljubljana
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TZCODES_FILE: data/external/multiple_timezones_example.csv
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IF_MISSING_TZCODE: STOP
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DEFAULT_TZCODE: America/New_York
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FITBIT:
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ALLOW_MULTIPLE_TZ_PER_DEVICE: False
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INFER_FROM_SMARTPHONE_TZ: False
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@ -45,15 +43,12 @@ TIMEZONE:
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# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
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PHONE_DATA_STREAMS:
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USE: aware_postgresql
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USE: aware_csv
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# AVAILABLE:
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aware_mysql:
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DATABASE_GROUP: MY_GROUP
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aware_postgresql:
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DATABASE_GROUP: PSQL_STRAW
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aware_csv:
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FOLDER: data/external/aware_csv
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@ -82,12 +77,12 @@ PHONE_ACCELEROMETER:
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# See https://www.rapids.science/latest/features/phone-activity-recognition/
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PHONE_ACTIVITY_RECOGNITION:
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CONTAINER:
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ANDROID: google_ar
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ANDROID: plugin_google_activity_recognition
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IOS: plugin_ios_activity_recognition
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EPISODE_THRESHOLD_BETWEEN_ROWS: 5 # minutes. Max time difference for two consecutive rows to be considered within the same AR episode.
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
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ACTIVITY_CLASSES:
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STATIONARY: ["still", "tilting"]
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@ -107,17 +102,16 @@ PHONE_APPLICATIONS_CRASHES:
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# See https://www.rapids.science/latest/features/phone-applications-foreground/
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PHONE_APPLICATIONS_FOREGROUND:
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CONTAINER: applications
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CONTAINER: applications_foreground
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APPLICATION_CATEGORIES:
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CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
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CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
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PACKAGE_NAMES_HASHED: True
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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
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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
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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INCLUDE_EPISODE_FEATURES: True
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COMPUTE: False
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INCLUDE_EPISODE_FEATURES: False
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SINGLE_CATEGORIES: ["all", "email"]
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MULTIPLE_CATEGORIES:
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social: ["socialnetworks", "socialmediatools"]
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@ -127,7 +121,7 @@ PHONE_APPLICATIONS_FOREGROUND:
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dating: ["com.tinder", "com.relance.happycouple", "com.kiwi.joyride"]
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SINGLE_APPS: ["top1global", "com.facebook.moments", "com.google.android.youtube", "com.twitter.android"] # There's no entropy for single apps
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EXCLUDED_CATEGORIES: []
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EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"] # TODO list system apps?
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EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
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FEATURES:
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APP_EVENTS: ["countevent", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
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APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"]
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@ -137,7 +131,7 @@ PHONE_APPLICATIONS_FOREGROUND:
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# See https://www.rapids.science/latest/features/phone-applications-notifications/
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PHONE_APPLICATIONS_NOTIFICATIONS:
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CONTAINER: notifications
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CONTAINER: applications_notifications
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APPLICATION_CATEGORIES:
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CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
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CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
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@ -151,7 +145,7 @@ PHONE_BATTERY:
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EPISODE_THRESHOLD_BETWEEN_ROWS: 30 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
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SRC_SCRIPT: src/features/phone_battery/rapids/main.py
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@ -160,12 +154,12 @@ PHONE_BLUETOOTH:
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CONTAINER: bluetooth
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
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SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R
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DORYAB:
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COMPUTE: True
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COMPUTE: False
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FEATURES:
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ALL:
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DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
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@ -183,7 +177,7 @@ PHONE_BLUETOOTH:
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# See https://www.rapids.science/latest/features/phone-calls/
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PHONE_CALLS:
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CONTAINER: call
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CONTAINER: calls.csv
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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@ -196,7 +190,7 @@ PHONE_CALLS:
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SRC_SCRIPT: src/features/phone_calls/rapids/main.R
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# See https://www.rapids.science/latest/features/phone-conversation/
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PHONE_CONVERSATION: # TODO Adapt for speech
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PHONE_CONVERSATION:
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CONTAINER:
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ANDROID: plugin_studentlife_audio_android
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IOS: plugin_studentlife_audio
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@ -215,21 +209,10 @@ PHONE_CONVERSATION: # TODO Adapt for speech
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# See https://www.rapids.science/latest/features/phone-data-yield/
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PHONE_DATA_YIELD:
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SENSORS: [#PHONE_ACCELEROMETER,
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PHONE_ACTIVITY_RECOGNITION,
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PHONE_APPLICATIONS_FOREGROUND,
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PHONE_APPLICATIONS_NOTIFICATIONS,
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PHONE_BATTERY,
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PHONE_BLUETOOTH,
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PHONE_CALLS,
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PHONE_LIGHT,
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PHONE_LOCATIONS,
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PHONE_MESSAGES,
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PHONE_SCREEN,
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PHONE_WIFI_VISIBLE]
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SENSORS: []
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
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MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
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SRC_SCRIPT: src/features/phone_data_yield/rapids/main.R
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@ -245,10 +228,10 @@ PHONE_KEYBOARD:
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# See https://www.rapids.science/latest/features/phone-light/
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PHONE_LIGHT:
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CONTAINER: light_sensor
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CONTAINER: light
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
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SRC_SCRIPT: src/features/phone_light/rapids/main.py
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@ -262,7 +245,7 @@ PHONE_LOCATIONS:
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PROVIDERS:
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DORYAB:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["locationvariance","loglocationvariance","totaldistance","avgspeed","varspeed", "numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","avglengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy","timeathome", "homelabel"]
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DBSCAN_EPS: 100 # meters
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DBSCAN_MINSAMPLES: 5
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@ -277,7 +260,7 @@ PHONE_LOCATIONS:
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SRC_SCRIPT: src/features/phone_locations/doryab/main.py
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BARNETT:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
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IF_MULTIPLE_TIMEZONES: USE_MOST_COMMON
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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
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@ -292,10 +275,10 @@ PHONE_LOG:
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# See https://www.rapids.science/latest/features/phone-messages/
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PHONE_MESSAGES:
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CONTAINER: sms
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CONTAINER: messages
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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MESSAGES_TYPES : [received, sent]
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FEATURES:
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received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
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@ -307,7 +290,7 @@ PHONE_SCREEN:
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CONTAINER: screen
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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REFERENCE_HOUR_FIRST_USE: 0
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IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
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IGNORE_EPISODES_LONGER_THAN: 360 # in minutes, set to 0 to disable
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@ -329,7 +312,7 @@ PHONE_WIFI_VISIBLE:
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CONTAINER: wifi
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
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SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R
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@ -557,16 +540,16 @@ EMPATICA_TAGS:
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#1-histograms-of-phone-data-yield
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HISTOGRAM_PHONE_DATA_YIELD:
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PLOT: True
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PLOT: False
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#2-heatmaps-of-overall-data-yield
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HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
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PLOT: True
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PLOT: False
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TIME: RELATIVE_TIME # ABSOLUTE_TIME or RELATIVE_TIME
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#3-heatmap-of-recorded-phone-sensors
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HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
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PLOT: True
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PLOT: False
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# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#4-heatmap-of-sensor-row-count
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HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
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@ -577,7 +560,7 @@ HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
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# See https://www.rapids.science/latest/visualizations/feature-visualizations/#1-heatmap-correlation-matrix
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HEATMAP_FEATURE_CORRELATION_MATRIX:
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PLOT: True
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PLOT: False
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MIN_ROWS_RATIO: 0.5
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CORR_THRESHOLD: 0.1
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CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
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@ -590,17 +573,17 @@ HEATMAP_FEATURE_CORRELATION_MATRIX:
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ALL_CLEANING_INDIVIDUAL:
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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IMPUTE_SELECTED_EVENT_FEATURES:
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COMPUTE: True
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MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
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COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable
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COLS_VAR_THRESHOLD: True
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ROWS_NAN_THRESHOLD: 1 # set to 1 to disable
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ROWS_NAN_THRESHOLD: 0.3 # set to 1 to disable
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DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
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DATA_YIELD_RATIO_THRESHOLD: 0.3 # set to 0 to disable
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DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
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DROP_HIGHLY_CORRELATED_FEATURES:
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COMPUTE: False
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COMPUTE: True
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MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
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CORR_THRESHOLD: 0.95
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SRC_SCRIPT: src/features/all_cleaning_individual/rapids/main.R
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@ -608,32 +591,17 @@ ALL_CLEANING_INDIVIDUAL:
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ALL_CLEANING_OVERALL:
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PROVIDERS:
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RAPIDS:
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COMPUTE: True
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COMPUTE: False
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IMPUTE_SELECTED_EVENT_FEATURES:
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COMPUTE: True
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MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
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COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable
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COLS_VAR_THRESHOLD: True
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ROWS_NAN_THRESHOLD: 1 # set to 1 to disable
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ROWS_NAN_THRESHOLD: 0.3 # set to 1 to disable
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DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
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DATA_YIELD_RATIO_THRESHOLD: 0.3 # set to 0 to disable
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DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
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DROP_HIGHLY_CORRELATED_FEATURES:
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COMPUTE: False
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COMPUTE: True
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MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
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CORR_THRESHOLD: 0.95
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SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R
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########################################################################################################################
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# Analysis Workflow Example #
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########################################################################################################################
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PARAMS_FOR_ANALYSIS:
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BASELINE:
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FOLDER: data/external/baseline
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CONTAINER: [results-survey637813_final.csv, # Slovenia
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results-survey358134_final.csv, # Belgium 1
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results-survey413767_final.csv # Belgium 2
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]
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QUESTION_LIST: survey637813+question_text.csv
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FEATURES: [age, gender, startlanguage, demand, control, demand_control_ratio]
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CATEGORICAL_FEATURES: [gender]
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SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R
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