######################################################################################################################## # 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: Europe/Ljubljana MULTIPLE: TZCODES_FILE: data/external/multiple_timezones_example.csv IF_MISSING_TZCODE: USE_DEFAULT DEFAULT_TZCODE: Europe/Ljubljana 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 CR: 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 WINDOWS: COMPUTE: True WINDOW_LENGTH: 10 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min'] SRC_SCRIPT: src/features/empatica_accelerometer/cr/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 CR: 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"] WINDOWS: COMPUTE: True WINDOW_LENGTH: 600 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min'] SRC_SCRIPT: src/features/empatica_temperature/cr/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 CR: 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'] WINDOWS: COMPUTE: True WINDOW_LENGTH: 300 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min'] SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py # See https://www.rapids.science/latest/features/empatica-blood-volume-pulse/ EMPATICA_BLOOD_VOLUME_PULSE: CONTAINER: BVP PROVIDERS: DBDP: COMPUTE: True FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"] SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py CR: COMPUTE: True FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features 'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features WINDOWS: COMPUTE: True WINDOW_LENGTH: 300 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min'] SRC_SCRIPT: src/features/empatica_blood_volume_pulse/cr/main.py # See https://www.rapids.science/latest/features/empatica-inter-beat-interval/ EMPATICA_INTER_BEAT_INTERVAL: CONTAINER: IBI PROVIDERS: DBDP: COMPUTE: True FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"] SRC_SCRIPT: src/features/empatica_inter_beat_interval/dbdp/main.py CR: COMPUTE: True FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features 'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features WINDOWS: COMPUTE: True WINDOW_LENGTH: 300 # specify window length in seconds SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min'] SRC_SCRIPT: src/features/empatica_inter_beat_interval/cr/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