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rapids/tests/settings/periodic/testing_config.yaml

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# Participants to include in the analysis
# You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically
PIDS: [test01, test02, test03, test04]
# Global var with common day segments
DAY_SEGMENTS: &day_segments
TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT
FILE: "data/external/daysegments_periodic.csv"
INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, if set to TRUE we consider day segments back enough in the past as to include the first day of data
# Use tz codes from https://en.wikipedia.org/wiki/List_of_tz_database_time_zones. Double check your code, for example EST is not US Eastern Time.
TIMEZONE: &timezone
America/New_York
DATABASE_GROUP: &database_group
MY_GROUP
# config section for the script that creates participant files automatically
PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files
PHONE_SECTION:
ADD: FALSE
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
PARSED_SOURCE: *database_group # DB credentials group or CSV file path. If CSV file, it should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
IGNORED_DEVICE_IDS: []
FITBIT_SECTION:
ADD: FALSE
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored
PARSED_FROM: CSV_FILE
PARSED_SOURCE: "external/my_fitbit_participants.csv" # CSV file should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
DEVICE_DATA:
PHONE:
SOURCE:
TYPE: DATABASE # Phone only supports DATABASE for now
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE # SINGLE or MULTIPLE
VALUE: *timezone # IF TYPE=SINGLE, timezone code (e.g. America/New_York, see attribute TIMEZONE above). If TYPE=MULTIPLE, a table in your database with two columns (timestamp, timezone) where timestamp is a unix timestamp and timezone is one of https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
FITBIT:
SOURCE:
TYPE: DATABASE # DATABASE or FILES (set each FITBIT_SENSOR TABLE attribute accordingly with a table name or a file path)
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE # Fitbit only supports SINGLE timezones
VALUE: *timezone # timezone code (e.g. America/New_York, see attribute TIMEZONE above and https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)
PHONE_VALID_SENSED_BINS:
COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
BIN_SIZE: &bin_size 5 # (in minutes)
# Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
# If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory.
# You can choose any of the keys shown below, just make sure its TABLE exists in your database!
# PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT,
# PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION
PHONE_SENSORS: []
PHONE_VALID_SENSED_DAYS:
COMPUTE: False
MIN_VALID_HOURS_PER_DAY: &min_valid_hours_per_day [16] # (out of 24) MIN_HOURS_PER_DAY
MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour [6] # (out of 60min/BIN_SIZE bins)
# Communication SMS features config, TYPES and FEATURES keys need to match
PHONE_MESSAGES:
TABLE: messages
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
MESSAGES_TYPES : [received, sent]
FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_messages
# Communication call features config, TYPES and FEATURES keys need to match
PHONE_CALLS:
TABLE: calls
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
CALL_TYPES: [missed, incoming, outgoing]
FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
incoming: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
outgoing: [count, distinctcontacts, meanduration, sumduration, minduration, maxduration, stdduration, modeduration, entropyduration, timefirstcall, timelastcall, countmostfrequentcontact]
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_calls
PHONE_LOCATIONS:
TABLE: locations
LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED
FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD: 30 # minutes, only replicate location samples to the next sensed bin if the phone did not stop collecting data for more than this threshold
FUSED_RESAMPLED_TIME_SINCE_VALID_LOCATION: 720 # minutes, only replicate location samples to consecutive sensed bins if they were logged within this threshold after a valid location row
PROVIDERS:
DORYAB:
COMPUTE: False
FEATURES: ["locationvariance","loglocationvariance","totaldistance","averagespeed","varspeed","circadianmovement","numberofsignificantplaces","numberlocationtransitions","radiusgyration","timeattop1location","timeattop2location","timeattop3location","movingtostaticratio","outlierstimepercent","maxlengthstayatclusters","minlengthstayatclusters","meanlengthstayatclusters","stdlengthstayatclusters","locationentropy","normalizedlocationentropy"]
DBSCAN_EPS: 10 # meters
DBSCAN_MINSAMPLES: 5
THRESHOLD_STATIC : 1 # km/h
MAXIMUM_GAP_ALLOWED: 300
MINUTES_DATA_USED: False
SAMPLING_FREQUENCY: 0
SRC_FOLDER: "doryab" # inside src/features/phone_locations
SRC_LANGUAGE: "python"
BARNETT:
COMPUTE: False
FEATURES: ["hometime","disttravelled","rog","maxdiam","maxhomedist","siglocsvisited","avgflightlen","stdflightlen","avgflightdur","stdflightdur","probpause","siglocentropy","circdnrtn","wkenddayrtn"]
ACCURACY_LIMIT: 51 # meters, drops location coordinates with an accuracy higher than this. This number means there's a 68% probability the true location is within this radius
TIMEZONE: *timezone
MINUTES_DATA_USED: False # Use this for quality control purposes, how many minutes of data (location coordinates gruped by minute) were used to compute features
SRC_FOLDER: "barnett" # inside src/features/phone_locations
SRC_LANGUAGE: "r"
PHONE_BLUETOOTH:
TABLE: bluetooth
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
SRC_LANGUAGE: "r"
PHONE_ACTIVITY_RECOGNITION:
TABLE:
ANDROID: plugin_google_activity_recognition
IOS: plugin_ios_activity_recognition
EPISODE_THRESHOLD_BETWEEN_ROWS: 5 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
ACTIVITY_CLASSES:
STATIONARY: ["still", "tilting"]
MOBILE: ["on_foot", "walking", "running", "on_bicycle"]
VEHICLE: ["in_vehicle"]
SRC_FOLDER: "rapids" # inside src/features/phone_activity_recognition
SRC_LANGUAGE: "python"
PHONE_BATTERY:
TABLE: battery
EPISODE_THRESHOLD_BETWEEN_ROWS: 30 # minutes. Max time difference for two consecutive rows to be considered within the same battery episode.
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
SRC_FOLDER: "rapids" # inside src/features/phone_battery
SRC_LANGUAGE: "python"
PHONE_SCREEN:
TABLE: screen
PROVIDERS:
RAPIDS:
COMPUTE: False
REFERENCE_HOUR_FIRST_USE: 0
IGNORE_EPISODES_SHORTER_THAN: 0 # in minutes, set to 0 to disable
IGNORE_EPISODES_LONGER_THAN: 0 # in minutes, set to 0 to disable
FEATURES: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration", "firstuseafter"] # "episodepersensedminutes" needs to be added later
EPISODE_TYPES: ["unlock"]
SRC_FOLDER: "rapids" # inside src/features/phone_screen
SRC_LANGUAGE: "python"
PHONE_LIGHT:
TABLE: light
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
SRC_FOLDER: "rapids" # inside src/features/phone_light
SRC_LANGUAGE: "python"
PHONE_ACCELEROMETER:
TABLE: accelerometer
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
SRC_LANGUAGE: "python"
PANDA:
COMPUTE: False
VALID_SENSED_MINUTES: False
FEATURES:
exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
SRC_FOLDER: "panda" # inside src/features/phone_accelerometer
SRC_LANGUAGE: "python"
PHONE_APPLICATIONS_FOREGROUND:
TABLE: applications_foreground
APPLICATION_CATEGORIES:
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
SINGLE_CATEGORIES: ["all", "email"]
MULTIPLE_CATEGORIES:
social: ["socialnetworks", "socialmediatools"]
entertainment: ["entertainment", "gamingstrategy"]
SINGLE_APPS: ["top1global", "com.facebook.moments"] # There's no entropy for single apps
EXCLUDED_CATEGORIES: ["systemapp", "tvvideoapps"]
EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
FEATURES: ["count", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
SRC_FOLDER: "rapids" # inside src/features/phone_applications_foreground
SRC_LANGUAGE: "python"
PHONE_WIFI_VISIBLE:
TABLE: "wifi"
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
SRC_LANGUAGE: "r"
PHONE_WIFI_CONNECTED:
TABLE: "sensor_wifi"
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
SRC_LANGUAGE: "r"
PHONE_CONVERSATION:
TABLE:
ANDROID: plugin_studentlife_audio_android
IOS: plugin_studentlife_audio
PROVIDERS:
RAPIDS:
COMPUTE: TRUE
FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
"sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","noisesumenergy",
"noiseavgenergy","noisesdenergy","noiseminenergy","noisemaxenergy","voicesumenergy",
"voiceavgenergy","voicesdenergy","voiceminenergy","voicemaxenergy","silencesensedfraction","noisesensedfraction",
"voicesensedfraction","unknownsensedfraction","silenceexpectedfraction","noiseexpectedfraction","voiceexpectedfraction",
"unknownexpectedfraction","countconversation"]
RECORDING_MINUTES: 1
PAUSED_MINUTES : 3
SRC_FOLDER: "rapids" # inside src/features/phone_conversation
SRC_LANGUAGE: "python"
############## FITBIT ##########################################################
################################################################################
FITBIT_HEARTRATE:
TABLE_FORMAT: JSON # JSON or CSV
TABLE:
JSON: fitbit_heartrate
CSV:
SUMMARY: heartrate_summary.csv
INTRADAY: heartrate_intraday.csv
PROVIDERS:
RAPIDS:
COMPUTE: False
SUMMARY_FEATURES: ["restinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["caloriesoutofrange", "caloriesfatburn", "caloriescardio", "caloriespeak"]
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
FITBIT_STEPS:
TABLE_FORMAT: JSON # JSON or CSV
TABLE:
JSON: fitbit_steps
CSV:
SUMMARY: steps_summary.csv
INTRADAY: steps_intraday.csv
EXCLUDE_SLEEP: # you can exclude sleep periods from the step features computation
EXCLUDE: False
TYPE: FIXED # FIXED OR FITBIT_BASED (configure FITBIT_SLEEP section)
FIXED:
START: "23:00"
END: "07:00"
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES:
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
THRESHOLD_ACTIVE_BOUT: 10 # steps
INCLUDE_ZERO_STEP_ROWS: False
FITBIT_SLEEP:
TABLE_FORMAT: JSON # JSON or CSV
TABLE:
JSON: fitbit_sleep
CSV:
SUMMARY: sleep_summary.csv
INTRADAY: sleep_intraday.csv
PROVIDERS:
RAPIDS:
COMPUTE: False
SLEEP_TYPES: ["main", "nap", "all"]
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]
FITBIT_CALORIES:
TABLE_FORMAT: JSON # JSON or CSV
TABLE:
JSON: fitbit_calories
CSV:
SUMMARY: calories_summary.csv
INTRADAY: calories_intraday.csv
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: []
### Visualizations #############################################################
################################################################################
HEATMAP_FEATURES_CORRELATIONS:
PLOT: False
MIN_ROWS_RATIO: 0.5
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
PHONE_FEATURES: [accelerometer, activity_recognition, applications_foreground, battery, calls_incoming, calls_missed, calls_outgoing, conversation, light, location_doryab, messages_received, messages_sent, screen]
FITBIT_FEATURES: [fitbit_heartrate, fitbit_step, fitbit_sleep]
CORR_THRESHOLD: 0.1
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
HISTOGRAM_VALID_SENSED_HOURS:
PLOT: False
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
HEATMAP_DAYS_BY_SENSORS:
PLOT: False
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
EXPECTED_NUM_OF_DAYS: -1
DB_TABLES: [accelerometer, applications_foreground, battery, bluetooth, calls, light, locations, messages, screen, wifi, sensor_wifi, plugin_google_activity_recognition, plugin_ios_activity_recognition, plugin_studentlife_audio_android, plugin_studentlife_audio]
HEATMAP_SENSED_BINS:
PLOT: False
BIN_SIZE: *bin_size
OVERALL_COMPLIANCE_HEATMAP:
PLOT: False
ONLY_SHOW_VALID_DAYS: False
EXPECTED_NUM_OF_DAYS: -1
BIN_SIZE: *bin_size
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
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