348 lines
16 KiB
YAML
348 lines
16 KiB
YAML
# 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]
|
|
|
|
# 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: TRUE
|
|
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)
|
|
|
|
SENSOR_DATA:
|
|
PHONE:
|
|
SOURCE:
|
|
TYPE: DATABASE
|
|
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 CSV_FILES (set each FITBIT_SENSOR TABLE attribute accordingly)
|
|
DATABASE_GROUP: *database_group
|
|
DEVICE_ID_COLUMN: device_id # column name
|
|
|
|
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: False
|
|
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: False
|
|
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
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: True
|
|
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
|
|
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: False
|
|
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: False
|
|
SINGLE_CATEGORIES: ["all", "email"]
|
|
MULTIPLE_CATEGORIES:
|
|
social: ["socialnetworks", "socialmediatools"]
|
|
entertainment: ["entertainment", "gamingknowledge", "gamingcasual", "gamingadventure", "gamingstrategy", "gamingtoolscommunity", "gamingroleplaying", "gamingaction", "gaminglogic", "gamingsports", "gamingsimulation"]
|
|
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: ["count", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
|
|
SRC_FOLDER: "rapids" # inside src/features/phone_applications_foreground
|
|
SRC_LANGUAGE: "python"
|
|
|
|
PHONE_WIFI_VISIBLE:
|
|
TABLE: "wifi"
|
|
PROVIDERS:
|
|
RAPIDS:
|
|
COMPUTE: False
|
|
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: False
|
|
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","sumenergy",
|
|
"avgenergy","sdenergy","minenergy","maxenergy","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
|
|
|