Reseting files to defaults - for Minimal Working Example

Snakefile

@@ -5,7 +5,6 @@ include: "rules/common.smk"
 include: "rules/renv.smk"
 include: "rules/preprocessing.smk"
 include: "rules/features.smk"
-include: "rules/models.smk"
 include: "rules/reports.smk"
 
 import itertools
@@ -403,12 +402,6 @@ for provider in config["ALL_CLEANING_OVERALL"]["PROVIDERS"].keys():
     if config["ALL_CLEANING_OVERALL"]["PROVIDERS"][provider]["COMPUTE"]:
         files_to_compute.extend(expand("data/processed/features/all_participants/all_sensor_features_cleaned_" + provider.lower() +".csv"))
 
-# Baseline features
-files_to_compute.extend(expand("data/raw/baseline_merged.csv"))
-files_to_compute.extend(expand("data/raw/{pid}/participant_baseline_raw.csv", pid=config["PIDS"]))
-files_to_compute.extend(expand("data/interim/{pid}/baseline_questionnaires.csv", pid=config["PIDS"]))
-files_to_compute.extend(expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]))
-
 rule all:
     input:
         files_to_compute

config.yaml

@@ -3,38 +3,36 @@
 ########################################################################################################################
 
 # See https://www.rapids.science/latest/setup/configuration/#participant-files
-PIDS: ['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107']
+PIDS: [p01]
 
 # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
 CREATE_PARTICIPANT_FILES:
-  USERNAMES_CSV: "data/external/main_study_usernames.csv"
+  CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
-  CSV_FILE_PATH: "data/external/main_study_participants.csv" # see docs for required format
   PHONE_SECTION:
     ADD: True
     IGNORED_DEVICE_IDS: []
   FITBIT_SECTION:
-    ADD: False
+    ADD: True
     IGNORED_DEVICE_IDS: []
   EMPATICA_SECTION:
-    ADD: False
+    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_daily.csv"
+  FILE: "data/external/timesegments_periodic.csv"
-  INCLUDE_PAST_PERIODIC_SEGMENTS: TRUE # Only relevant if TYPE=PERIODIC, see docs
+  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: MULTIPLE
+    TYPE: SINGLE
     SINGLE:
-      TZCODE: Europe/Ljubljana
+      TZCODE: America/New_York
     MULTIPLE:
-      TZ_FILE: data/external/timezone.csv
+      TZCODES_FILE: data/external/multiple_timezones_example.csv
-      TZCODES_FILE: data/external/multiple_timezones.csv
+      IF_MISSING_TZCODE: STOP
-      IF_MISSING_TZCODE: USE_DEFAULT
+      DEFAULT_TZCODE: America/New_York
-      DEFAULT_TZCODE: Europe/Ljubljana
       FITBIT: 
         ALLOW_MULTIPLE_TZ_PER_DEVICE: False
         INFER_FROM_SMARTPHONE_TZ: False
@@ -45,15 +43,12 @@ TIMEZONE:
 
 # See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
 PHONE_DATA_STREAMS:
-  USE: aware_postgresql
+  USE: aware_csv
   
   # AVAILABLE:
   aware_mysql: 
     DATABASE_GROUP: MY_GROUP
 
-  aware_postgresql:
-    DATABASE_GROUP: PSQL_STRAW
-  
   aware_csv:
     FOLDER: data/external/aware_csv
   
@@ -82,12 +77,12 @@ PHONE_ACCELEROMETER:
 # See https://www.rapids.science/latest/features/phone-activity-recognition/
 PHONE_ACTIVITY_RECOGNITION:
   CONTAINER: 
-    ANDROID: google_ar
+    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: True
+      COMPUTE: False
       FEATURES: ["count", "mostcommonactivity", "countuniqueactivities", "durationstationary", "durationmobile", "durationvehicle"]
       ACTIVITY_CLASSES:
         STATIONARY: ["still", "tilting"]
@@ -107,17 +102,16 @@ PHONE_APPLICATIONS_CRASHES:
 
 # See https://www.rapids.science/latest/features/phone-applications-foreground/
 PHONE_APPLICATIONS_FOREGROUND:
-  CONTAINER: applications
+  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"
-    PACKAGE_NAMES_HASHED: True
     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
+      COMPUTE: False
-      INCLUDE_EPISODE_FEATURES: True
+      INCLUDE_EPISODE_FEATURES: False
       SINGLE_CATEGORIES: ["all", "email"]
       MULTIPLE_CATEGORIES:
         social: ["socialnetworks", "socialmediatools"]
@@ -127,7 +121,7 @@ PHONE_APPLICATIONS_FOREGROUND:
         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"] # TODO list system apps?
+      EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
       FEATURES: 
         APP_EVENTS: ["countevent", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
         APP_EPISODES: ["countepisode", "minduration", "maxduration", "meanduration", "sumduration"]
@@ -137,7 +131,7 @@ PHONE_APPLICATIONS_FOREGROUND:
 
 # See https://www.rapids.science/latest/features/phone-applications-notifications/
 PHONE_APPLICATIONS_NOTIFICATIONS:
-  CONTAINER: 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"
@@ -151,7 +145,7 @@ PHONE_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: True
+      COMPUTE: False
       FEATURES: ["countdischarge", "sumdurationdischarge", "countcharge", "sumdurationcharge", "avgconsumptionrate", "maxconsumptionrate"]
       SRC_SCRIPT: src/features/phone_battery/rapids/main.py
 
@@ -160,12 +154,12 @@ PHONE_BLUETOOTH:
   CONTAINER: bluetooth
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      COMPUTE: False
       FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
       SRC_SCRIPT: src/features/phone_bluetooth/rapids/main.R
 
     DORYAB:
-      COMPUTE: True
+      COMPUTE: False
       FEATURES: 
         ALL: 
             DEVICES: ["countscans", "uniquedevices", "meanscans", "stdscans"]
@@ -183,7 +177,7 @@ PHONE_BLUETOOTH:
 
 # See https://www.rapids.science/latest/features/phone-calls/
 PHONE_CALLS:
-  CONTAINER: call
+  CONTAINER: calls.csv
   PROVIDERS:
     RAPIDS:
       COMPUTE: True
@@ -196,7 +190,7 @@ PHONE_CALLS:
       SRC_SCRIPT: src/features/phone_calls/rapids/main.R
 
 # See https://www.rapids.science/latest/features/phone-conversation/
-PHONE_CONVERSATION: # TODO Adapt for speech
+PHONE_CONVERSATION:
   CONTAINER: 
     ANDROID: plugin_studentlife_audio_android
     IOS: plugin_studentlife_audio
@@ -215,21 +209,10 @@ PHONE_CONVERSATION: # TODO Adapt for speech
 
 # See https://www.rapids.science/latest/features/phone-data-yield/
 PHONE_DATA_YIELD:
-  SENSORS: [#PHONE_ACCELEROMETER,
+  SENSORS: []
-            PHONE_ACTIVITY_RECOGNITION,
-            PHONE_APPLICATIONS_FOREGROUND,
-            PHONE_APPLICATIONS_NOTIFICATIONS,
-            PHONE_BATTERY,
-            PHONE_BLUETOOTH,
-            PHONE_CALLS,
-            PHONE_LIGHT,
-            PHONE_LOCATIONS,
-            PHONE_MESSAGES,
-            PHONE_SCREEN,
-            PHONE_WIFI_VISIBLE]
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      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
@@ -245,10 +228,10 @@ PHONE_KEYBOARD:
 
 # See https://www.rapids.science/latest/features/phone-light/
 PHONE_LIGHT:
-  CONTAINER: light_sensor
+  CONTAINER: light
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      COMPUTE: False
       FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
       SRC_SCRIPT: src/features/phone_light/rapids/main.py
 
@@ -262,7 +245,7 @@ PHONE_LOCATIONS:
 
   PROVIDERS:
     DORYAB:
-      COMPUTE: True
+      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
@@ -277,7 +260,7 @@ PHONE_LOCATIONS:
       SRC_SCRIPT: src/features/phone_locations/doryab/main.py
 
     BARNETT:
-      COMPUTE: True
+      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
@@ -292,10 +275,10 @@ PHONE_LOG:
 
 # See https://www.rapids.science/latest/features/phone-messages/
 PHONE_MESSAGES:
-  CONTAINER: sms
+  CONTAINER: messages
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      COMPUTE: False
       MESSAGES_TYPES : [received, sent]
       FEATURES: 
         received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
@@ -307,7 +290,7 @@ PHONE_SCREEN:
   CONTAINER: screen
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      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
@@ -329,7 +312,7 @@ PHONE_WIFI_VISIBLE:
   CONTAINER: wifi
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      COMPUTE: False
       FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
       SRC_SCRIPT: src/features/phone_wifi_visible/rapids/main.R
 
@@ -557,16 +540,16 @@ EMPATICA_TAGS:
 
 # See https://www.rapids.science/latest/visualizations/data-quality-visualizations/#1-histograms-of-phone-data-yield
 HISTOGRAM_PHONE_DATA_YIELD:
-  PLOT: True
+  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: True
+  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: True
+  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:
@@ -577,7 +560,7 @@ HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
 
 # See https://www.rapids.science/latest/visualizations/feature-visualizations/#1-heatmap-correlation-matrix
 HEATMAP_FEATURE_CORRELATION_MATRIX:
-  PLOT: True
+  PLOT: False
   MIN_ROWS_RATIO: 0.5
   CORR_THRESHOLD: 0.1
   CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
@@ -590,17 +573,17 @@ HEATMAP_FEATURE_CORRELATION_MATRIX:
 ALL_CLEANING_INDIVIDUAL:
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      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: 1 # set to 1 to disable
+      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: 0.3 # set to 0 to disable
+      DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
       DROP_HIGHLY_CORRELATED_FEATURES:
-        COMPUTE: False
+        COMPUTE: True
         MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
         CORR_THRESHOLD: 0.95
       SRC_SCRIPT: src/features/all_cleaning_individual/rapids/main.R
@@ -608,32 +591,17 @@ ALL_CLEANING_INDIVIDUAL:
 ALL_CLEANING_OVERALL:
   PROVIDERS:
     RAPIDS:
-      COMPUTE: True
+      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: 1 # set to 1 to disable
+      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: 0.3 # set to 0 to disable
+      DATA_YIELD_RATIO_THRESHOLD: 0.5 # set to 0 to disable
       DROP_HIGHLY_CORRELATED_FEATURES:
-        COMPUTE: False
+        COMPUTE: True
         MIN_OVERLAP_FOR_CORR_THRESHOLD: 0.5
         CORR_THRESHOLD: 0.95
-      SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R
+      SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R
-
-########################################################################################################################
-#                                              Analysis Workflow Example                                               #
-########################################################################################################################
-
-PARAMS_FOR_ANALYSIS:
-  BASELINE:
-    FOLDER: data/external/baseline
-    CONTAINER: [results-survey637813_final.csv,  # Slovenia
-                results-survey358134_final.csv,  # Belgium 1
-                results-survey413767_final.csv  # Belgium 2
-    ]
-    QUESTION_LIST: survey637813+question_text.csv
-    FEATURES: [age, gender, startlanguage, demand, control, demand_control_ratio]
-    CATEGORICAL_FEATURES: [gender]

data/external/timesegments_periodic.csv

@@ -1,9 +1,3 @@
 label,start_time,length,repeats_on,repeats_value
-threeday,00:00:00,2D 23H 59M 59S,every_day,0
 daily,00:00:00,23H 59M 59S,every_day,0
-morning,06:00:00,5H 59M 59S,every_day,0
-afternoon,12:00:00,5H 59M 59S,every_day,0
-evening,18:00:00,5H 59M 59S,every_day,0
 night,00:00:00,5H 59M 59S,every_day,0
-two_weeks_overlapping,00:00:00,13D 23H 59M 59S,every_day,0
-weekends,00:00:00,2D 23H 59M 59S,wday,5

rules/preprocessing.smk

@@ -4,36 +4,6 @@ rule create_example_participant_files:
     shell:
         "echo 'PHONE:\n  DEVICE_IDS: [a748ee1a-1d0b-4ae9-9074-279a2b6ba524]\n  PLATFORMS: [android]\n  LABEL: test-01\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\nFITBIT:\n  DEVICE_IDS: [a748ee1a-1d0b-4ae9-9074-279a2b6ba524]\n  LABEL: test-01\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\n' >> ./data/external/participant_files/example01.yaml && echo 'PHONE:\n  DEVICE_IDS: [13dbc8a3-dae3-4834-823a-4bc96a7d459d]\n  PLATFORMS: [ios]\n  LABEL: test-02\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\nFITBIT:\n  DEVICE_IDS: [13dbc8a3-dae3-4834-823a-4bc96a7d459d]\n  LABEL: test-02\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\n' >> ./data/external/participant_files/example02.yaml"
 
-rule query_usernames_device_empatica_ids:
-    params:
-        baseline_folder = "/mnt/e/STRAWbaseline/"
-    output:
-        usernames_file = config["CREATE_PARTICIPANT_FILES"]["USERNAMES_CSV"],
-        timezone_file = config["TIMEZONE"]["MULTIPLE"]["TZ_FILE"]
-    script:
-        "../../participants/prepare_usernames_file.py"
-
-rule prepare_tzcodes_file:
-    input:
-        timezone_file = config["TIMEZONE"]["MULTIPLE"]["TZ_FILE"]
-    output:
-        tzcodes_file = config["TIMEZONE"]["MULTIPLE"]["TZCODES_FILE"]
-    script:
-        "../tools/create_multi_timezones_file.py"
-
-rule prepare_participants_csv:
-    input:
-        username_list = config["CREATE_PARTICIPANT_FILES"]["USERNAMES_CSV"]
-    params:
-        data_configuration = config["PHONE_DATA_STREAMS"][config["PHONE_DATA_STREAMS"]["USE"]],
-        participants_table = "participants",
-        device_id_table = "esm",
-        start_end_date_table = "esm"
-    output:
-        participants_file = config["CREATE_PARTICIPANT_FILES"]["CSV_FILE_PATH"]
-    script:
-        "../src/data/translate_usernames_into_participants_data.R"
-
 rule create_participants_files:
     input:
         participants_file = config["CREATE_PARTICIPANT_FILES"]["CSV_FILE_PATH"] 
@@ -249,4 +219,4 @@ rule empatica_readable_datetime:
     output:
         "data/raw/{pid}/empatica_{sensor}_with_datetime.csv"
     script:
-        "../src/data/datetime/readable_datetime.R"
+        "../src/data/datetime/readable_datetime.R"