Few changes during addition to file structure.
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Subproject commit 98e6207ecc23a23b1f621a11f28eb87cbfb7f9da
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88
config.yaml
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config.yaml
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@ -3,7 +3,7 @@
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########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
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PIDS: [p02] #p01, p02, p03]
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PIDS: [p031] #p01, p02, p03]
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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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@ -51,7 +51,7 @@ PHONE_DATA_STREAMS:
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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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@ -80,12 +80,12 @@ 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: plugin_google_activity_recognition
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ANDROID: google_ar
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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: False
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COMPUTE: True
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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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@ -105,16 +105,17 @@ 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_foreground
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CONTAINER: applications
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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: False
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INCLUDE_EPISODE_FEATURES: False
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COMPUTE: True
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INCLUDE_EPISODE_FEATURES: True
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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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@ -124,7 +125,7 @@ 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"]
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EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"] # TODO list system apps?
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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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@ -134,7 +135,7 @@ 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: applications_notifications
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CONTAINER: 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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@ -148,7 +149,7 @@ 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: False
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COMPUTE: True
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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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@ -157,12 +158,12 @@ PHONE_BLUETOOTH:
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CONTAINER: bluetooth
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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: False
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COMPUTE: True
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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 +184,7 @@ PHONE_CALLS:
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CONTAINER: call
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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FEATURES_TYPE: EPISODES # EVENTS or EPISODES
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CALL_TYPES: [missed, incoming, outgoing]
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FEATURES:
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@ -193,7 +194,7 @@ 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:
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PHONE_CONVERSATION: # TODO Adapt for speech
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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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@ -212,14 +213,34 @@ PHONE_CONVERSATION:
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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: []
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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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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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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PHONE_ESM:
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CONTAINER: esm
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PROVIDERS:
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STRAW:
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COMPUTE: False
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SCALES: ["PANAS_positive_affect", "PANAS_negative_affect", "JCQ_job_demand", "JCQ_job_control", "JCQ_supervisor_support", "JCQ_coworker_support"]
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FEATURES: [mean]
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SRC_SCRIPT: src/features/phone_esm/straw/main.py
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# See https://www.rapids.science/latest/features/phone-keyboard/
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PHONE_KEYBOARD:
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CONTAINER: keyboard
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@ -231,10 +252,10 @@ 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
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CONTAINER: light_sensor
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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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@ -248,7 +269,7 @@ PHONE_LOCATIONS:
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PROVIDERS:
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DORYAB:
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COMPUTE: False
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COMPUTE: True
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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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@ -263,7 +284,7 @@ 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: False
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COMPUTE: True
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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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@ -278,10 +299,10 @@ 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: messages
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CONTAINER: sms
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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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@ -293,7 +314,7 @@ PHONE_SCREEN:
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CONTAINER: screen
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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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CONTAINER: wifi
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PROVIDERS:
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RAPIDS:
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COMPUTE: False
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COMPUTE: True
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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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########################################################################################################################
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# FITBIT #
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########################################################################################################################
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FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
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SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
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CR:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ["totalMagnitudeBand", "absoluteMeanBand", "varianceBand"] # Acc features
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WINDOWS:
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COMPUTE: True
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WINDOW_LENGTH: 15 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
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STANDARDIZE_FEATURES: False
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STANDARDIZE_FEATURES: True
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SRC_SCRIPT: src/features/empatica_accelerometer/cr/main.py
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@ -512,14 +534,14 @@ EMPATICA_TEMPERATURE:
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FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"]
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SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py
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CR:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ["maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean", "longestStrikeBelowMean",
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"stdDev", "median", "meanChange", "sumSquared", "squareSumOfComponent", "sumOfSquareComponents"]
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WINDOWS:
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COMPUTE: True
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WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows']
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STANDARDIZE_FEATURES: False
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STANDARDIZE_FEATURES: True
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SRC_SCRIPT: src/features/empatica_temperature/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-electrodermal-activity/
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COMPUTE: True
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WINDOW_LENGTH: 60 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', count_windows, eda_num_peaks_non_zero]
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STANDARDIZE_FEATURES: False
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STANDARDIZE_FEATURES: True
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IMPUTE_NANS: False
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SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py
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FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"]
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SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py
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CR:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features
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'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features
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WINDOWS:
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COMPUTE: True
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WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
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STANDARDIZE_FEATURES: False
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STANDARDIZE_FEATURES: True
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SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-inter-beat-interval/
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FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"]
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SRC_SCRIPT: src/features/empatica_inter_beat_interval/dbdp/main.py
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CR:
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COMPUTE: False
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COMPUTE: True
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FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features
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'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features
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PATCH_WITH_BVP: True
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COMPUTE: True
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WINDOW_LENGTH: 300 # specify window length in seconds
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SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'nlargest', 'nsmallest', 'count_windows', 'hrv_num_windows_non_nan']
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STANDARDIZE_FEATURES: False
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STANDARDIZE_FEATURES: True
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SRC_SCRIPT: src/features/empatica_inter_beat_interval/cr/main.py
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# See https://www.rapids.science/latest/features/empatica-tags/
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