641 lines
33 KiB
YAML
641 lines
33 KiB
YAML
########################################################################################################################
|
|
# GLOBAL CONFIGURATION #
|
|
########################################################################################################################
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#participant-files
|
|
PIDS: [p01]
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
|
|
CREATE_PARTICIPANT_FILES:
|
|
CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
|
|
PHONE_SECTION:
|
|
ADD: True
|
|
IGNORED_DEVICE_IDS: []
|
|
FITBIT_SECTION:
|
|
ADD: True
|
|
IGNORED_DEVICE_IDS: []
|
|
EMPATICA_SECTION:
|
|
ADD: True
|
|
IGNORED_DEVICE_IDS: []
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#time-segments
|
|
TIME_SEGMENTS: &time_segments
|
|
TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT
|
|
FILE: "data/external/timesegments_periodic.csv"
|
|
INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
|
|
TIMEZONE:
|
|
TYPE: SINGLE
|
|
SINGLE:
|
|
TZCODE: America/New_York
|
|
MULTIPLE:
|
|
TZCODES_FILE: data/external/multiple_timezones_example.csv
|
|
IF_MISSING_TZCODE: STOP
|
|
DEFAULT_TZCODE: America/New_York
|
|
FITBIT:
|
|
ALLOW_MULTIPLE_TZ_PER_DEVICE: False
|
|
INFER_FROM_SMARTPHONE_TZ: False
|
|
|
|
########################################################################################################################
|
|
# PHONE #
|
|
########################################################################################################################
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
|
|
PHONE_DATA_STREAMS:
|
|
USE: aware_csv
|
|
|
|
# AVAILABLE:
|
|
aware_mysql:
|
|
DATABASE_GROUP: MY_GROUP
|
|
|
|
aware_csv:
|
|
FOLDER: data/external/aware_csv
|
|
|
|
aware_influxdb:
|
|
DATABASE_GROUP: MY_GROUP
|
|
|
|
# Sensors ------
|
|
|
|
# https://www.rapids.science/latest/features/phone-accelerometer/
|
|
PHONE_ACCELEROMETER:
|
|
CONTAINER: accelerometer
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
|
|
SRC_SCRIPT: src/features/phone_accelerometer/rapids/main.py
|
|
|
|
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_SCRIPT: src/features/phone_accelerometer/panda/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-activity-recognition/
|
|
PHONE_ACTIVITY_RECOGNITION:
|
|
CONTAINER:
|
|
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 AR 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_SCRIPT: src/features/phone_activity_recognition/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-applications-crashes/
|
|
PHONE_APPLICATIONS_CRASHES:
|
|
CONTAINER: applications_crashes
|
|
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: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
|
|
|
|
# See https://www.rapids.science/latest/features/phone-applications-foreground/
|
|
PHONE_APPLICATIONS_FOREGROUND:
|
|
CONTAINER: 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
|
|
INCLUDE_EPISODE_FEATURES: False
|
|
SINGLE_CATEGORIES: ["all", "email"]
|
|
MULTIPLE_CATEGORIES:
|
|
social: ["socialnetworks", "socialmediatools"]
|
|
entertainment: ["entertainment", "gamingknowledge", "gamingcasual", "gamingadventure", "gamingstrategy", "gamingtoolscommunity", "gamingroleplaying", "gamingaction", "gaminglogic", "gamingsports", "gamingsimulation"]
|
|
CUSTOM_CATEGORIES:
|
|
social_media: ["com.google.android.youtube", "com.snapchat.android", "com.instagram.android", "com.zhiliaoapp.musically", "com.facebook.katana"]
|
|
dating: ["com.tinder", "com.relance.happycouple", "com.kiwi.joyride"]
|
|
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:
|
|
APP_EVENTS: ["countevent", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
|
|
APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"]
|
|
IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
|
|
IGNORE_EPISODES_LONGER_THAN: 300 # in minutes, set to 0 to disable
|
|
SRC_SCRIPT: src/features/phone_applications_foreground/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-applications-notifications/
|
|
PHONE_APPLICATIONS_NOTIFICATIONS:
|
|
CONTAINER: applications_notifications
|
|
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: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
|
|
|
|
# See https://www.rapids.science/latest/features/phone-battery/
|
|
PHONE_BATTERY:
|
|
CONTAINER: 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_SCRIPT: src/features/phone_battery/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-bluetooth/
|
|
PHONE_BLUETOOTH:
|
|
CONTAINER: bluetooth
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
|
SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R
|
|
|
|
DORYAB:
|
|
COMPUTE: False
|
|
FEATURES:
|
|
ALL:
|
|
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
|
|
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
OWN:
|
|
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
|
|
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
OTHERS:
|
|
DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
|
|
SCANS_MOST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
SCANS_LEAST_FREQUENT_DEVICE: ["withinsegments", "acrosssegments", "acrossdataset"]
|
|
SRC_SCRIPT: src/features/phone_bluetooth/doryab/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-calls/
|
|
PHONE_CALLS:
|
|
CONTAINER: calls.csv
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES_TYPE: EPISODES # EVENTS or EPISODES
|
|
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_SCRIPT: src/features/phone_calls/rapids/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/phone-conversation/
|
|
PHONE_CONVERSATION:
|
|
CONTAINER:
|
|
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_SCRIPT: src/features/phone_conversation/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-data-yield/
|
|
PHONE_DATA_YIELD:
|
|
SENSORS: []
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
|
|
MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
|
|
SRC_SCRIPT: src/features/phone_data_yield/rapids/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/phone-keyboard/
|
|
PHONE_KEYBOARD:
|
|
CONTAINER: keyboard
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["sessioncount","averageinterkeydelay","averagesessionlength","changeintextlengthlessthanminusone","changeintextlengthequaltominusone","changeintextlengthequaltoone","changeintextlengthmorethanone","maxtextlength","lastmessagelength","totalkeyboardtouches"]
|
|
SRC_SCRIPT: src/features/phone_keyboard/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-light/
|
|
PHONE_LIGHT:
|
|
CONTAINER: light
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
|
|
SRC_SCRIPT: src/features/phone_light/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-locations/
|
|
PHONE_LOCATIONS:
|
|
CONTAINER: locations
|
|
LOCATIONS_TO_USE: ALL_RESAMPLED # ALL, GPS, ALL_RESAMPLED, 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
|
|
ACCURACY_LIMIT: 100 # meters, drops location coordinates with an accuracy equal or higher than this. This number means there's a 68% probability the true location is within this radius
|
|
|
|
PROVIDERS:
|
|
DORYAB:
|
|
COMPUTE: False
|
|
FEATURES: ["locationvariance","loglocationvariance","totaldistance","avgspeed","varspeed", "numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","avglengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy","timeathome", "homelabel"]
|
|
DBSCAN_EPS: 100 # meters
|
|
DBSCAN_MINSAMPLES: 5
|
|
THRESHOLD_STATIC : 1 # km/h
|
|
MAXIMUM_ROW_GAP: 300 # seconds
|
|
MINUTES_DATA_USED: False
|
|
CLUSTER_ON: PARTICIPANT_DATASET # PARTICIPANT_DATASET, TIME_SEGMENT, TIME_SEGMENT_INSTANCE
|
|
INFER_HOME_LOCATION_STRATEGY: DORYAB_STRATEGY # DORYAB_STRATEGY, SUN_LI_VEGA_STRATEGY
|
|
MINIMUM_DAYS_TO_DETECT_HOME_CHANGES: 3
|
|
CLUSTERING_ALGORITHM: DBSCAN # DBSCAN, OPTICS
|
|
RADIUS_FOR_HOME: 100
|
|
SRC_SCRIPT: src/features/phone_locations/doryab/main.py
|
|
|
|
BARNETT:
|
|
COMPUTE: False
|
|
FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
|
|
IF_MULTIPLE_TIMEZONES: USE_MOST_COMMON
|
|
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_SCRIPT: src/features/phone_locations/barnett/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/phone-log/
|
|
PHONE_LOG:
|
|
CONTAINER:
|
|
ANDROID: aware_log
|
|
IOS: ios_aware_log
|
|
PROVIDERS: # None implemented yet but this sensor can be used in PHONE_DATA_YIELD
|
|
|
|
# See https://www.rapids.science/latest/features/phone-messages/
|
|
PHONE_MESSAGES:
|
|
CONTAINER: messages
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
MESSAGES_TYPES : [received, sent]
|
|
FEATURES:
|
|
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
|
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
|
SRC_SCRIPT: src/features/phone_messages/rapids/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/phone-screen/
|
|
PHONE_SCREEN:
|
|
CONTAINER: 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: 360 # 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_SCRIPT: src/features/phone_screen/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/phone-wifi-connected/
|
|
PHONE_WIFI_CONNECTED:
|
|
CONTAINER: sensor_wifi
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
|
SRC_SCRIPT: src/features/phone_wifi_connected/rapids/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/phone-wifi-visible/
|
|
PHONE_WIFI_VISIBLE:
|
|
CONTAINER: wifi
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
|
SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R
|
|
|
|
|
|
|
|
########################################################################################################################
|
|
# FITBIT #
|
|
########################################################################################################################
|
|
|
|
# See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
|
|
FITBIT_DATA_STREAMS:
|
|
USE: fitbitjson_mysql
|
|
|
|
# AVAILABLE:
|
|
fitbitjson_mysql:
|
|
DATABASE_GROUP: MY_GROUP
|
|
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
|
|
|
|
fitbitparsed_mysql:
|
|
DATABASE_GROUP: MY_GROUP
|
|
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
|
|
|
|
fitbitjson_csv:
|
|
FOLDER: data/external/fitbit_csv
|
|
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
|
|
|
|
fitbitparsed_csv:
|
|
FOLDER: data/external/fitbit_csv
|
|
SLEEP_SUMMARY_LAST_NIGHT_END: 660 # a number ranged from 0 (midnight) to 1439 (23:59) which denotes number of minutes after midnight. By default, 660 (11:00).
|
|
|
|
# Sensors ------
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-calories-intraday/
|
|
FITBIT_CALORIES_INTRADAY:
|
|
CONTAINER: fitbit_data
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
EPISODE_TYPE: [sedentary, lightlyactive, fairlyactive, veryactive, mvpa, lowmet, highmet]
|
|
EPISODE_TIME_THRESHOLD: 5 # minutes
|
|
EPISODE_MET_THRESHOLD: 3
|
|
EPISODE_MVPA_CATEGORIES: [fairlyactive, veryactive]
|
|
EPISODE_REFERENCE_TIME: MIDNIGHT # or START_OF_THE_SEGMENT
|
|
FEATURES: [count, sumduration, avgduration, minduration, maxduration, stdduration, starttimefirst, endtimefirst, starttimelast, endtimelast, starttimelongest, endtimelongest, summet, avgmet, maxmet, minmet, stdmet, sumcalories, avgcalories, maxcalories, mincalories, stdcalories]
|
|
SRC_SCRIPT: src/features/fitbit_calories_intraday/rapids/main.R
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-data-yield/
|
|
FITBIT_DATA_YIELD:
|
|
SENSOR: FITBIT_HEARTRATE_INTRADAY
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: [ratiovalidyieldedminutes, ratiovalidyieldedhours]
|
|
MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS: 0.5 # 0 to 1, minimum percentage of valid minutes in an hour to be considered valid.
|
|
SRC_SCRIPT: src/features/fitbit_data_yield/rapids/main.R
|
|
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-heartrate-summary/
|
|
FITBIT_HEARTRATE_SUMMARY:
|
|
CONTAINER: 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_SCRIPT: src/features/fitbit_heartrate_summary/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-heartrate-intraday/
|
|
FITBIT_HEARTRATE_INTRADAY:
|
|
CONTAINER: heartrate_intraday
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
|
|
SRC_SCRIPT: src/features/fitbit_heartrate_intraday/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-sleep-summary/
|
|
FITBIT_SLEEP_SUMMARY:
|
|
CONTAINER: sleep_summary
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["firstwaketime", "lastwaketime", "firstbedtime", "lastbedtime", "countepisode", "avgefficiency", "sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgdurationafterwakeup", "avgdurationasleep", "avgdurationawake", "avgdurationtofallasleep", "avgdurationinbed"]
|
|
SLEEP_TYPES: ["main", "nap", "all"]
|
|
SRC_SCRIPT: src/features/fitbit_sleep_summary/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-sleep-intraday/
|
|
FITBIT_SLEEP_INTRADAY:
|
|
CONTAINER: sleep_intraday
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES:
|
|
LEVELS_AND_TYPES: [countepisode, sumduration, maxduration, minduration, avgduration, medianduration, stdduration]
|
|
RATIOS_TYPE: [count, duration]
|
|
RATIOS_SCOPE: [ACROSS_LEVELS, ACROSS_TYPES, WITHIN_LEVELS, WITHIN_TYPES]
|
|
SLEEP_LEVELS:
|
|
INCLUDE_ALL_GROUPS: True
|
|
CLASSIC: [awake, restless, asleep]
|
|
STAGES: [wake, deep, light, rem]
|
|
UNIFIED: [awake, asleep]
|
|
SLEEP_TYPES: [main, nap, all]
|
|
SRC_SCRIPT: src/features/fitbit_sleep_intraday/rapids/main.py
|
|
|
|
PRICE:
|
|
COMPUTE: False
|
|
FEATURES: [avgduration, avgratioduration, avgstarttimeofepisodemain, avgendtimeofepisodemain, avgmidpointofepisodemain, stdstarttimeofepisodemain, stdendtimeofepisodemain, stdmidpointofepisodemain, socialjetlag, rmssdmeanstarttimeofepisodemain, rmssdmeanendtimeofepisodemain, rmssdmeanmidpointofepisodemain, rmssdmedianstarttimeofepisodemain, rmssdmedianendtimeofepisodemain, rmssdmedianmidpointofepisodemain]
|
|
SLEEP_LEVELS:
|
|
INCLUDE_ALL_GROUPS: True
|
|
CLASSIC: [awake, restless, asleep]
|
|
STAGES: [wake, deep, light, rem]
|
|
UNIFIED: [awake, asleep]
|
|
DAY_TYPES: [WEEKEND, WEEK, ALL]
|
|
LAST_NIGHT_END: 660 # number of minutes after midnight (11:00) 11*60
|
|
SRC_SCRIPT: src/features/fitbit_sleep_intraday/price/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-steps-summary/
|
|
FITBIT_STEPS_SUMMARY:
|
|
CONTAINER: steps_summary
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES: ["maxsumsteps", "minsumsteps", "avgsumsteps", "mediansumsteps", "stdsumsteps"]
|
|
SRC_SCRIPT: src/features/fitbit_steps_summary/rapids/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/fitbit-steps-intraday/
|
|
FITBIT_STEPS_INTRADAY:
|
|
CONTAINER: steps_intraday
|
|
EXCLUDE_SLEEP: # you can exclude step data that was logged during sleep periods
|
|
TIME_BASED:
|
|
EXCLUDE: False
|
|
START_TIME: "23:00"
|
|
END_TIME: "07:00"
|
|
FITBIT_BASED:
|
|
EXCLUDE: False
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
FEATURES:
|
|
STEPS: ["sum", "max", "min", "avg", "std", "firststeptime", "laststeptime"]
|
|
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
|
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
|
REFERENCE_HOUR: 0
|
|
THRESHOLD_ACTIVE_BOUT: 10 # steps
|
|
INCLUDE_ZERO_STEP_ROWS: False
|
|
SRC_SCRIPT: src/features/fitbit_steps_intraday/rapids/main.py
|
|
|
|
########################################################################################################################
|
|
# EMPATICA #
|
|
########################################################################################################################
|
|
|
|
EMPATICA_DATA_STREAMS:
|
|
USE: empatica_zip
|
|
|
|
# AVAILABLE:
|
|
empatica_zip:
|
|
FOLDER: data/external/empatica
|
|
|
|
# Sensors ------
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-accelerometer/
|
|
EMPATICA_ACCELEROMETER:
|
|
CONTAINER: ACC
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: True
|
|
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
|
|
SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
|
|
CF:
|
|
COMPUTE: True
|
|
FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
|
|
"meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand",
|
|
"postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand",
|
|
"coefficientOfVariationBand", "amplitudeBand", "totalEnergyBand", "dominantFrequencyEnergyBand", "meanCrossingRateBand",
|
|
"correlationBand", "quartilesMagnitudesBand", "interQuartileRangeMagnitudesBand", "areaUnderAccelerationMagnitude",
|
|
"peaksDataLow", "sumPerComponentBand", "velocityBand", "meanKineticEnergyBand", "totalKineticEnergyBand", "squareSumOfComponent",
|
|
"sumOfSquareComponents", "averageVectorLength", "averageVectorLengthPower", "rollAvgLow", "pitchAvgLow", "rollStdDevLow",
|
|
"pitchStdDevLow", "rollMotionAmountLow", "rollMotionRegularityLow", "manipulationLow", "rollPeaks", "pitchPeaks", "rollPitchCorrelation"] # Acc features
|
|
SRC_SCRIPT: src/features/empatica_accelerometer/cf/main.py
|
|
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-heartrate/
|
|
EMPATICA_HEARTRATE:
|
|
CONTAINER: HR
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: False
|
|
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr"]
|
|
SRC_SCRIPT: src/features/empatica_heartrate/dbdp/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-temperature/
|
|
EMPATICA_TEMPERATURE:
|
|
CONTAINER: TEMP
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: True
|
|
FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"]
|
|
SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py
|
|
CF:
|
|
COMPUTE: True
|
|
FEATURES: ["autocorrelations", "countAboveMean", "countBelowMean", "maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean",
|
|
"longestStrikeBelowMean", "stdDev", "median", "meanChange", "numberOfZeroCrossings", "absEnergy", "linearTrendSlope",
|
|
"ratioBeyondRSigma", "binnedEntropy", "numOfPeaksAutocorr", "numberOfZeroCrossingsAutocorr", "areaAutocorr",
|
|
"calcMeanCrossingRateAutocorr", "countAboveMeanAutocorr", "sumPer", "sumSquared", "squareSumOfComponent",
|
|
"sumOfSquareComponents"]
|
|
SRC_SCRIPT: src/features/empatica_temperature/cf/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-electrodermal-activity/
|
|
EMPATICA_ELECTRODERMAL_ACTIVITY:
|
|
CONTAINER: EDA
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: True
|
|
FEATURES: ["maxeda", "mineda", "avgeda", "medianeda", "modeeda", "stdeda", "diffmaxmodeeda", "diffminmodeeda", "entropyeda"]
|
|
SRC_SCRIPT: src/features/empatica_electrodermal_activity/dbdp/main.py
|
|
CF:
|
|
COMPUTE: True
|
|
FEATURES: ['mean', 'std', 'q25', 'q75', 'qd', 'deriv', 'power', 'numPeaks', 'ratePeaks', 'powerPeaks', 'sumPosDeriv', 'propPosDeriv', 'derivTonic',
|
|
'sigTonicDifference', 'freqFeats','maxPeakAmplitudeChangeBefore', 'maxPeakAmplitudeChangeAfter', 'avgPeakAmplitudeChangeBefore',
|
|
'avgPeakAmplitudeChangeAfter', 'avgPeakChangeRatio', 'maxPeakIncreaseTime', 'maxPeakDecreaseTime', 'maxPeakDuration', 'maxPeakChangeRatio',
|
|
'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'maxPeakResponseSlopeBefore', 'maxPeakResponseSlopeAfter',
|
|
'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease', 'significantDecrease']
|
|
SRC_SCRIPT: src/features/empatica_electrodermal_activity/cf/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-blood-volume-pulse/
|
|
EMPATICA_BLOOD_VOLUME_PULSE:
|
|
CONTAINER: BVP
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: True
|
|
FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
|
|
"maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"] # HRV features
|
|
SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py
|
|
CF:
|
|
COMPUTE: True
|
|
FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR']
|
|
SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cf/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-inter-beat-interval/
|
|
EMPATICA_INTER_BEAT_INTERVAL:
|
|
CONTAINER: IBI
|
|
PROVIDERS:
|
|
DBDP:
|
|
COMPUTE: False
|
|
FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"]
|
|
SRC_SCRIPT: src/features/empatica_inter_beat_interval/dbdp/main.py
|
|
|
|
# See https://www.rapids.science/latest/features/empatica-tags/
|
|
EMPATICA_TAGS:
|
|
CONTAINER: TAGS
|
|
PROVIDERS: # None implemented yet
|
|
|
|
|
|
|
|
########################################################################################################################
|
|
# PLOTS #
|
|
########################################################################################################################
|
|
|
|
# Data quality ------
|
|
|
|
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#1-histograms-of-phone-data-yield
|
|
HISTOGRAM_PHONE_DATA_YIELD:
|
|
PLOT: False
|
|
|
|
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#2-heatmaps-of-overall-data-yield
|
|
HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
|
|
PLOT: False
|
|
TIME: RELATIVE_TIME # ABSOLUTE_TIME or RELATIVE_TIME
|
|
|
|
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#3-heatmap-of-recorded-phone-sensors
|
|
HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
|
|
PLOT: False
|
|
|
|
# See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#4-heatmap-of-sensor-row-count
|
|
HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
|
|
PLOT: False
|
|
SENSORS: []
|
|
|
|
# Features ------
|
|
|
|
# See https://www.rapids.science/latest/visualizations/feature-visualizations/#1-heatmap-correlation-matrix
|
|
HEATMAP_FEATURE_CORRELATION_MATRIX:
|
|
PLOT: False
|
|
MIN_ROWS_RATIO: 0.5
|
|
CORR_THRESHOLD: 0.1
|
|
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
|
|
|
|
|
|
########################################################################################################################
|
|
# Data Cleaning #
|
|
########################################################################################################################
|
|
|
|
ALL_CLEANING_INDIVIDUAL:
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
IMPUTE_SELECTED_EVENT_FEATURES:
|
|
COMPUTE: True
|
|
MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
|
|
COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable
|
|
COLS_VAR_THRESHOLD: True
|
|
ROWS_NAN_THRESHOLD: 0.3 # set to 1 to disable
|
|
DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
|
|
DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
|
|
DROP_HIGHLY_CORRELATED_FEATURES:
|
|
COMPUTE: True
|
|
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
|
|
CORR_THRESHOLD: 0.95
|
|
SRC_SCRIPT: src/features/all_cleaning_individual/rapids/main.R
|
|
|
|
ALL_CLEANING_OVERALL:
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
IMPUTE_SELECTED_EVENT_FEATURES:
|
|
COMPUTE: True
|
|
MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33
|
|
COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable
|
|
COLS_VAR_THRESHOLD: True
|
|
ROWS_NAN_THRESHOLD: 0.3 # set to 1 to disable
|
|
DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES
|
|
DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
|
|
DROP_HIGHLY_CORRELATED_FEATURES:
|
|
COMPUTE: True
|
|
MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
|
|
CORR_THRESHOLD: 0.95
|
|
SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R |