Migrated testing from Travis to Github Actions and updated config and Snakemake files in the testing directory - part 1

pull/108/head
abhineethreddyk 2020-12-14 22:15:39 -05:00
parent 9ff75b10ba
commit c59d4a66eb
13 changed files with 701 additions and 580 deletions

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@ -0,0 +1,33 @@
name: RAPIDS Continuous Integration
on:
push:
#branches: [ develop ]
jobs:
test-on-latest-ubuntu:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- uses: s-weigand/setup-conda@v1
- run : conda --version
- run : source activate base
- run : |
sudo apt update
sudo apt install libcurl4-openssl-dev
sudo apt install libssl-dev
sudo apt install libxml2-dev
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
sudo apt install r-base
sudo apt install pandoc
sudo Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
cd rapids
conda env create -f environment.yml -n test-environment
source activate test-environment
snakemake -j1 renv_install
R -e 'renv::settings$use.cache(FALSE)'
snakemake -j1 renv_restore
bash tests/scripts/run_tests.sh all test

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@ -12,20 +12,15 @@ files_to_compute = []
if len(config["PIDS"]) == 0: if len(config["PIDS"]) == 0:
raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external") raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external")
if config["PHONE_VALID_SENSED_BINS"]["COMPUTE"] or config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]: # valid sensed bins is necessary for sensed days, so we add these files anyways if sensed days are requested for provider in config["PHONE_DATA_YIELD"]["PROVIDERS"].keys():
if len(config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]) == 0: if config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
raise ValueError("If you want to compute PHONE_VALID_SENSED_BINS or PHONE_VALID_SENSED_DAYS, you need to add at least one PHONE_SENSOR to [PHONE_VALID_SENSED_BINS][PHONE_SENSORS] in config.yaml") files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_DATA_YIELD"]["SENSORS"])))
files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]))) files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]))) files_to_compute.extend(expand("data/interim/{pid}/phone_data_yield_features/phone_data_yield_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_data_yield.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_timestamps.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv",
pid=config["PIDS"],
min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys(): for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
@ -33,6 +28,8 @@ for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_messages_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_messages_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_messages_features/phone_messages_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_MESSAGES"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_messages_features/phone_messages_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_MESSAGES"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_CALLS"]["PROVIDERS"].keys(): for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
@ -41,6 +38,8 @@ for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime_unified.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime_unified.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_calls_features/phone_calls_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CALLS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys(): for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
@ -48,6 +47,8 @@ for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_bluetooth_features/phone_bluetooth_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys(): for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]:
@ -59,7 +60,8 @@ for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_features/phone_activity_recognition_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys(): for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
@ -69,14 +71,15 @@ for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_battery_features/phone_battery_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_BATTERY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_battery_features/phone_battery_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_BATTERY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys(): for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
if "PHONE_SCREEN" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]: # if "PHONE_SCREEN" in config["PHONE_DATA_YIELD"]["SENSORS"]:# not used for now because we took episodepersensedminutes out of the list of supported features
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"])) # files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
else: # else:
raise ValueError("Error: Add PHONE_SCREEN (and as many phone sensor as you have in your database) to [PHONE_VALID_SENSED_BINS][PHONE_SENSORS] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data)") # raise ValueError("Error: Add PHONE_SCREEN (and as many PHONE_SENSORS as you have in your database) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data)")
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_raw.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_screen_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime_unified.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime_unified.csv", pid=config["PIDS"]))
@ -85,6 +88,8 @@ for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_screen_features/phone_screen_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_SCREEN"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_screen_features/phone_screen_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_SCREEN"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys(): for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
@ -92,6 +97,8 @@ for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_light_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_light_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_light_features/phone_light_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LIGHT"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_light_features/phone_light_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LIGHT"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],)) files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys(): for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
@ -99,6 +106,8 @@ for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_accelerometer_features/phone_accelerometer_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_accelerometer.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_accelerometer.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys(): for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]:
@ -107,6 +116,8 @@ for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_applications_foreground_features/phone_applications_foreground_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys(): for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]:
@ -114,6 +125,8 @@ for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_visible_features/phone_wifi_visible_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys(): for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]:
@ -121,6 +134,8 @@ for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_wifi_connected_features/phone_wifi_connected_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys(): for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
@ -129,75 +144,106 @@ for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime_unified.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime_unified.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_conversation_features/phone_conversation_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_conversation_features/phone_conversation_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_conversation.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_conversation.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys(): for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]: if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED": if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "FUSED_RESAMPLED":
if "PHONE_LOCATIONS" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]: if "PHONE_LOCATIONS" in config["PHONE_DATA_YIELD"]["SENSORS"]:
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
else: else:
raise ValueError("Error: Add PHONE_LOCATIONS (and as many PHONE_SENSORS as you have) to [PHONE_VALID_SENSED_BINS][PHONE_SENSORS] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)") raise ValueError("Error: Add PHONE_LOCATIONS (and as many PHONE_SENSORS as you have) to [PHONE_DATA_YIELD][SENSORS] in config.yaml. This is necessary to compute phone_yielded_timestamps (time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)")
files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower())) files_to_compute.extend(expand("data/interim/{pid}/phone_locations_features/phone_locations_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"])) files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if config["FITBIT_HEARTRATE"]["TABLE_FORMAT"] not in ["JSON", "CSV"]: for provider in config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"].keys():
raise ValueError("config['FITBIT_HEARTRATE']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_HEARTRATE"]["TABLE_FORMAT"]) if config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_parsed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_parsed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_summary_features/fitbit_heartrate_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if config["FITBIT_STEPS"]["TABLE_FORMAT"] not in ["JSON", "CSV"]: for provider in config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"].keys():
raise ValueError("config['FITBIT_STEPS']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_STEPS"]["TABLE_FORMAT"]) if config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_parsed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_heartrate_intraday_features/fitbit_heartrate_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if config["FITBIT_CALORIES"]["TABLE_FORMAT"] not in ["JSON", "CSV"]: for provider in config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"].keys():
raise ValueError("config['FITBIT_CALORIES']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_CALORIES"]["TABLE_FORMAT"]) if config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_parsed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_parsed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_sleep_summary_features/fitbit_sleep_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
if config["FITBIT_SLEEP"]["TABLE_FORMAT"] not in ["JSON", "CSV"]: # for provider in config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"].keys():
raise ValueError("config['FITBIT_SLEEP']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_SLEEP"]["TABLE_FORMAT"]) # if config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_raw.csv", pid=config["PIDS"]))
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_parsed.csv", pid=config["PIDS"]))
# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
for provider in config["FITBIT_HEARTRATE"]["PROVIDERS"].keys(): for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
if config["FITBIT_HEARTRATE"]["PROVIDERS"][provider]["COMPUTE"]: if config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_raw.csv", pid=config["PIDS"], fitbit_data_type=(["json"] if config["FITBIT_HEARTRATE"]["TABLE_FORMAT"] == "JSON" else ["summary", "intraday"]))) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_parsed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_{fitbit_data_type}_parsed_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_parsed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_summary_features/fitbit_steps_summary_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_summary.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_STEPS"]["PROVIDERS"].keys(): for provider in config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
if config["FITBIT_STEPS"]["PROVIDERS"][provider]["COMPUTE"]: if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_{fitbit_data_type}_raw.csv", pid=config["PIDS"], fitbit_data_type=(["json"] if config["FITBIT_STEPS"]["TABLE_FORMAT"] == "JSON" else ["summary", "intraday"]))) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_raw.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_{fitbit_data_type}_parsed_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_intraday.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_CALORIES"]["PROVIDERS"].keys(): # for provider in config["FITBIT_CALORIES"]["PROVIDERS"].keys():
if config["FITBIT_CALORIES"]["PROVIDERS"][provider]["COMPUTE"]: # if config["FITBIT_CALORIES"]["PROVIDERS"][provider]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_raw.csv", pid=config["PIDS"], fitbit_data_type=(["json"] if config["FITBIT_CALORIES"]["TABLE_FORMAT"] == "JSON" else ["summary", "intraday"]))) # files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_raw.csv", pid=config["PIDS"], fitbit_data_type=(["json"] if config["FITBIT_CALORIES"]["TABLE_FORMAT"] == "JSON" else ["summary", "intraday"])))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) # files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_parsed_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"])) # files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_parsed_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
# files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
# files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
for provider in config["FITBIT_SLEEP"]["PROVIDERS"].keys(): # Visualization for Data Exploration
if config["FITBIT_SLEEP"]["PROVIDERS"][provider]["COMPUTE"]: if config["HISTOGRAM_PHONE_DATA_YIELD"]["PLOT"]:
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_raw.csv", pid=config["PIDS"], fitbit_data_type=(["json"] if config["FITBIT_SLEEP"]["TABLE_FORMAT"] == "JSON" else ["summary", "intraday"]))) files_to_compute.append("reports/data_exploration/histogram_phone_data_yield.html")
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_parsed_episodes.csv", pid=config["PIDS"], fitbit_data_type=["summary"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["intraday"]))
files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_{fitbit_data_type}_parsed_with_datetime.csv", pid=config["PIDS"], fitbit_data_type=["intraday"]))
# visualization for data exploration if config["HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT"]["PLOT"]:
if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]: files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensors_per_minute_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_features_correlations.html", min_valid_hours_per_day=config["HEATMAP_FEATURES_CORRELATIONS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"])) files_to_compute.append("reports/data_exploration/heatmap_sensors_per_minute_per_time_segment.html")
if config["HISTOGRAM_VALID_SENSED_HOURS"]["PLOT"]:
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/histogram_valid_sensed_hours.html", min_valid_hours_per_day=config["HISTOGRAM_VALID_SENSED_HOURS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
if config["HEATMAP_DAYS_BY_SENSORS"]["PLOT"]: if config["HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/{pid}/heatmap_days_by_sensors.html", pid=config["PIDS"], min_valid_hours_per_day=config["HEATMAP_DAYS_BY_SENSORS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"])) files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensor_row_count_per_time_segment.html", pid=config["PIDS"]))
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/heatmap_days_by_sensors_all_participants.html", min_valid_hours_per_day=config["HEATMAP_DAYS_BY_SENSORS"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"])) files_to_compute.append("reports/data_exploration/heatmap_sensor_row_count_per_time_segment.html")
if config["HEATMAP_SENSED_BINS"]["PLOT"]: if config["HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT"]["PLOT"]:
files_to_compute.extend(expand("reports/interim/heatmap_sensed_bins/{pid}/heatmap_sensed_bins.html", pid=config["PIDS"])) files_to_compute.append("reports/data_exploration/heatmap_phone_data_yield_per_participant_per_time_segment.html")
files_to_compute.extend(["reports/data_exploration/heatmap_sensed_bins_all_participants.html"])
if config["OVERALL_COMPLIANCE_HEATMAP"]["PLOT"]: if config["HEATMAP_FEATURE_CORRELATION_MATRIX"]["PLOT"]:
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html", min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"])) files_to_compute.append("reports/data_exploration/heatmap_feature_correlation_matrix.html")
rule all: rule all:

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@ -1 +1 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice

View File

@ -1 +1 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice

View File

@ -1,4 +1,4 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"
"thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59","thirtyminutes0000","2020-07-02 00:00:00","2020-07-02 00:29:59",1,1,1 "thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59","thirtyminutes0000","2020-07-02 00:00:00","2020-07-02 00:29:59",1,1,1
"thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59","thirtyminutes0001","2020-07-02 00:30:00","2020-07-02 00:59:59",1,1,1 "thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59","thirtyminutes0001","2020-07-02 00:30:00","2020-07-02 00:59:59",1,1,1
"thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59","thirtyminutes0007","2020-07-02 03:30:00","2020-07-02 03:59:59",1,1,1 "thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59","thirtyminutes0007","2020-07-02 03:30:00","2020-07-02 03:59:59",1,1,1

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice
2 thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59 thirtyminutes0000 2020-07-02 00:00:00 2020-07-02 00:29:59 1 1 1
3 thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59 thirtyminutes0001 2020-07-02 00:30:00 2020-07-02 00:59:59 1 1 1
4 thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59 thirtyminutes0007 2020-07-02 03:30:00 2020-07-02 03:59:59 1 1 1

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@ -1,4 +1,4 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"
"thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59","thirtyminutes0000","2020-07-02 00:00:00","2020-07-02 00:29:59",1,1,1 "thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59","thirtyminutes0000","2020-07-02 00:00:00","2020-07-02 00:29:59",1,1,1
"thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59","thirtyminutes0001","2020-07-02 00:30:00","2020-07-02 00:59:59",1,1,1 "thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59","thirtyminutes0001","2020-07-02 00:30:00","2020-07-02 00:59:59",1,1,1
"thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59","thirtyminutes0007","2020-07-02 03:30:00","2020-07-02 03:59:59",1,1,1 "thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59","thirtyminutes0007","2020-07-02 03:30:00","2020-07-02 03:59:59",1,1,1

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice
2 thirtyminutes0000#2020-07-02 00:00:00,2020-07-02 00:29:59 thirtyminutes0000 2020-07-02 00:00:00 2020-07-02 00:29:59 1 1 1
3 thirtyminutes0001#2020-07-02 00:30:00,2020-07-02 00:59:59 thirtyminutes0001 2020-07-02 00:30:00 2020-07-02 00:59:59 1 1 1
4 thirtyminutes0007#2020-07-02 03:30:00,2020-07-02 03:59:59 thirtyminutes0007 2020-07-02 03:30:00 2020-07-02 03:59:59 1 1 1

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@ -1,4 +1,4 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"
"afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59","afternoon","2020-07-02 12:00:00","2020-07-02 17:59:59",2,2,1 "afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59","afternoon","2020-07-02 12:00:00","2020-07-02 17:59:59",2,2,1
"daily#2020-07-02 00:00:00,2020-07-02 23:59:59","daily","2020-07-02 00:00:00","2020-07-02 23:59:59",14,5,4 "daily#2020-07-02 00:00:00,2020-07-02 23:59:59","daily","2020-07-02 00:00:00","2020-07-02 23:59:59",14,5,4
"evening#2020-07-02 18:00:00,2020-07-02 23:59:59","evening","2020-07-02 18:00:00","2020-07-02 23:59:59",5,4,2 "evening#2020-07-02 18:00:00,2020-07-02 23:59:59","evening","2020-07-02 18:00:00","2020-07-02 23:59:59",5,4,2

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice
2 afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59 afternoon 2020-07-02 12:00:00 2020-07-02 17:59:59 2 2 2 2 1 1
3 daily#2020-07-02 00:00:00,2020-07-02 23:59:59 daily 2020-07-02 00:00:00 2020-07-02 23:59:59 14 14 5 5 4 4
4 evening#2020-07-02 18:00:00,2020-07-02 23:59:59 evening 2020-07-02 18:00:00 2020-07-02 23:59:59 5 5 4 4 2 2

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@ -1,4 +1,4 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"
"afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59","afternoon","2020-07-02 12:00:00","2020-07-02 17:59:59",2,2,1 "afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59","afternoon","2020-07-02 12:00:00","2020-07-02 17:59:59",2,2,1
"daily#2020-07-02 00:00:00,2020-07-02 23:59:59","daily","2020-07-02 00:00:00","2020-07-02 23:59:59",14,5,5 "daily#2020-07-02 00:00:00,2020-07-02 23:59:59","daily","2020-07-02 00:00:00","2020-07-02 23:59:59",14,5,5
"evening#2020-07-02 18:00:00,2020-07-02 23:59:59","evening","2020-07-02 18:00:00","2020-07-02 23:59:59",5,3,3 "evening#2020-07-02 18:00:00,2020-07-02 23:59:59","evening","2020-07-02 18:00:00","2020-07-02 23:59:59",5,3,3

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice
2 afternoon#2020-07-02 12:00:00,2020-07-02 17:59:59 afternoon 2020-07-02 12:00:00 2020-07-02 17:59:59 2 2 2 2 1 1
3 daily#2020-07-02 00:00:00,2020-07-02 23:59:59 daily 2020-07-02 00:00:00 2020-07-02 23:59:59 14 14 5 5 5 5
4 evening#2020-07-02 18:00:00,2020-07-02 23:59:59 evening 2020-07-02 18:00:00 2020-07-02 23:59:59 5 5 3 3 3 3

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@ -1 +1 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice

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@ -1 +1 @@
"local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","bluetooth_rapids_countscans","bluetooth_rapids_uniquedevices","bluetooth_rapids_countscansmostuniquedevice" "local_segment","local_segment_label","local_segment_start_datetime","local_segment_end_datetime","phone_bluetooth_rapids_countscans","phone_bluetooth_rapids_uniquedevices","phone_bluetooth_rapids_countscansmostuniquedevice"

1 local_segment local_segment_label local_segment_start_datetime local_segment_end_datetime bluetooth_rapids_countscans phone_bluetooth_rapids_countscans bluetooth_rapids_uniquedevices phone_bluetooth_rapids_uniquedevices bluetooth_rapids_countscansmostuniquedevice phone_bluetooth_rapids_countscansmostuniquedevice

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@ -64,7 +64,7 @@ cp -r tests/data/raw/* data/raw
cp -r tests/data/external/* data/external cp -r tests/data/external/* data/external
echo Disabling downloading of dataset... echo Disabling downloading of dataset...
sed -e '27,53 s/^/#/' -e 's/rules.download_dataset.output/"data\/raw\/\{pid\}\/\{sensor\}_raw\.csv"/' rules/preprocessing.smk > tmp sed -e '26,51 s/^/#/' -e 's/rules.download_dataset.output/"data\/raw\/\{pid\}\/\{sensor\}_raw\.csv"/' rules/preprocessing.smk > tmp
mv tmp rules/preprocessing.smk mv tmp rules/preprocessing.smk
if [ $# -eq 1 ] if [ $# -eq 1 ]

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@ -1,85 +1,139 @@
# Participants to include in the analysis # See https://www.rapids.science/latest/setup/configuration/#database-credentials
# You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically
PIDS: [test03, test04,test05, test06]
# Global var with common time segments
TIME_SEGMENTS: &time_segments
TYPE: FREQUENCY # FREQUENCY, PERIODIC, EVENT
FILE: "data/external/timesegments_frequency.csv"
INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, if set to TRUE we consider time 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 DATABASE_GROUP: &database_group
MY_GROUP MY_GROUP
# config section for the script that creates participant files automatically # See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files TIMEZONE: &timezone
America/New_York
# See https://www.rapids.science/latest/setup/configuration/#participant-files
PIDS: [test03, test04,test05, test06]
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES:
SOURCE:
TYPE: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
DATABASE_GROUP: *database_group
CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
TIMEZONE: *timezone
PHONE_SECTION: PHONE_SECTION:
ADD: FALSE ADD: TRUE
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE DEVICE_ID_COLUMN: device_id # column name
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: [] IGNORED_DEVICE_IDS: []
FITBIT_SECTION: FITBIT_SECTION:
ADD: FALSE ADD: TRUE
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored DEVICE_ID_COLUMN: device_id # column name
PARSED_FROM: CSV_FILE IGNORED_DEVICE_IDS: []
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: # See https://www.rapids.science/latest/setup/configuration/#time-segments
PHONE: TIME_SEGMENTS: &time_segments
SOURCE: TYPE: FREQUENCY # FREQUENCY, PERIODIC, EVENT
TYPE: DATABASE # Phone only supports DATABASE for now FILE: "data/external/timesegments_frequency.csv"
DATABASE_GROUP: *database_group INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs
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: # PHONE #
TABLE: messages ########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#device-data-source-configuration
PHONE_DATA_CONFIGURATION:
SOURCE:
TYPE: DATABASE
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE
VALUE: *timezone
# Sensors ------
# https://www.rapids.science/latest/features/phone-accelerometer/
PHONE_ACCELEROMETER:
TABLE: accelerometer
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
MESSAGES_TYPES : [received, sent] FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
FEATURES: SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact] SRC_LANGUAGE: "python"
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r" PANDA:
SRC_FOLDER: "rapids" # inside src/features/phone_messages 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"
# Communication call features config, TYPES and FEATURES keys need to match # See https://www.rapids.science/latest/features/phone-activity-recognition/
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"
# See https://www.rapids.science/latest/features/phone-applications-foreground/
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"
# See https://www.rapids.science/latest/features/phone-battery/
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"
# See https://www.rapids.science/latest/features/phone-bluetooth/
PHONE_BLUETOOTH:
TABLE: bluetooth
PROVIDERS:
RAPIDS:
COMPUTE: True
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
SRC_LANGUAGE: "r"
# See https://www.rapids.science/latest/features/phone-calls/
PHONE_CALLS: PHONE_CALLS:
TABLE: calls TABLE: calls
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
CALL_TYPES: [missed, incoming, outgoing] CALL_TYPES: [missed, incoming, outgoing]
FEATURES: FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact] missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
@ -88,6 +142,47 @@ PHONE_CALLS:
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_calls SRC_FOLDER: "rapids" # inside src/features/phone_calls
# See https://www.rapids.science/latest/features/phone-conversation/
PHONE_CONVERSATION:
TABLE:
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_FOLDER: "rapids" # inside src/features/phone_conversation
SRC_LANGUAGE: "python"
# 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 representing the number of minutes with at least
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_data_yield
# See https://www.rapids.science/latest/features/phone-light/
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"
# See https://www.rapids.science/latest/features/phone-locations/
PHONE_LOCATIONS: PHONE_LOCATIONS:
TABLE: locations TABLE: locations
LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED
@ -115,42 +210,20 @@ PHONE_LOCATIONS:
SRC_FOLDER: "barnett" # inside src/features/phone_locations SRC_FOLDER: "barnett" # inside src/features/phone_locations
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_BLUETOOTH: # See https://www.rapids.science/latest/features/phone-messages/
TABLE: bluetooth PHONE_MESSAGES:
TABLE: messages
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] MESSAGES_TYPES : [received, sent]
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_messages
# See https://www.rapids.science/latest/features/phone-screen/
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: PHONE_SCREEN:
TABLE: screen TABLE: screen
PROVIDERS: PROVIDERS:
@ -164,190 +237,138 @@ PHONE_SCREEN:
SRC_FOLDER: "rapids" # inside src/features/phone_screen SRC_FOLDER: "rapids" # inside src/features/phone_screen
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_LIGHT: # See https://www.rapids.science/latest/features/phone-wifi-connected/
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: PHONE_WIFI_CONNECTED:
TABLE: "sensor_wifi" TABLE: "sensor_wifi"
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_CONVERSATION: # See https://www.rapids.science/latest/features/phone-wifi-visible/
TABLE: PHONE_WIFI_VISIBLE:
ANDROID: plugin_studentlife_audio_android TABLE: "wifi"
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: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False 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"] FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"] SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
SRC_LANGUAGE: "r"
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"
########################################################################################################################
# FITBIT #
########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#device-data-source-configuration
FITBIT_DATA_CONFIGURATION:
SOURCE:
TYPE: DATABASE # DATABASE or FILES (set each [FITBIT_SENSOR][TABLE] attribute with a table name or a file path accordingly)
COLUMN_FORMAT: JSON # JSON or PLAIN_TEXT
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE # Fitbit devices don't support time zones so we read this data in the timezone indicated by VALUE
VALUE: *timezone
# Sensors ------
# See https://www.rapids.science/latest/features/fitbit-heartrate-summary/
FITBIT_HEARTRATE_SUMMARY:
TABLE: 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_FOLDER: "rapids" # inside src/features/fitbit_heartrate_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-heartrate-intraday/
FITBIT_HEARTRATE_INTRADAY:
TABLE: heartrate_intraday
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_heartrate_intraday
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-sleep-summary/
FITBIT_SLEEP_SUMMARY:
TABLE: sleep_summary
SLEEP_EPISODE_TIMESTAMP: end # summary sleep episodes are considered as events based on either the start timestamp or end timestamp.
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["countepisode", "avgefficiency", "sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgdurationafterwakeup", "avgdurationasleep", "avgdurationawake", "avgdurationtofallasleep", "avgdurationinbed"]
SLEEP_TYPES: ["main", "nap", "all"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_sleep_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-steps-summary/
FITBIT_STEPS_SUMMARY:
TABLE: steps_summary
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxsumsteps", "minsumsteps", "avgsumsteps", "mediansumsteps", "stdsumsteps"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-steps-intraday/
FITBIT_STEPS_INTRADAY:
TABLE: steps_intraday
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
FEATURES: FEATURES:
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"] STEPS: ["sum", "max", "min", "avg", "std"]
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"] SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"] ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
THRESHOLD_ACTIVE_BOUT: 10 # steps THRESHOLD_ACTIVE_BOUT: 10 # steps
INCLUDE_ZERO_STEP_ROWS: False INCLUDE_ZERO_STEP_ROWS: False
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_intraday
SRC_LANGUAGE: "python"
FITBIT_SLEEP: # FITBIT_CALORIES:
TABLE_FORMAT: JSON # JSON or CSV # TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: # TABLE:
JSON: fitbit_sleep # JSON: fitbit_calories
CSV: # CSV:
SUMMARY: sleep_summary.csv # SUMMARY: calories_summary
INTRADAY: sleep_intraday.csv # INTRADAY: calories_intraday
PROVIDERS: # PROVIDERS:
RAPIDS: # RAPIDS:
COMPUTE: False # COMPUTE: False
SLEEP_TYPES: ["main", "nap", "all"] # FEATURES: []
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: ########################################################################################################################
# PLOTS #
########################################################################################################################
# Data quality
HISTOGRAM_PHONE_DATA_YIELD:
PLOT: False
HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
PLOT: False
HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
PLOT: False
HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
PLOT: False
SENSORS: [PHONE_ACCELEROMETER, PHONE_ACTIVITY_RECOGNITION, PHONE_APPLICATIONS_FOREGROUND, PHONE_BATTERY, PHONE_BLUETOOTH, PHONE_CALLS, PHONE_CONVERSATION, PHONE_LIGHT, PHONE_LOCATIONS, PHONE_MESSAGES, PHONE_SCREEN, PHONE_WIFI_CONNECTED, PHONE_WIFI_VISIBLE]
# Features
HEATMAP_FEATURE_CORRELATION_MATRIX:
PLOT: False PLOT: False
MIN_ROWS_RATIO: 0.5 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_THRESHOLD: 0.1
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"} 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

View File

@ -1,85 +1,139 @@
# Participants to include in the analysis # See https://www.rapids.science/latest/setup/configuration/#database-credentials
# 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 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, if set to TRUE we consider time 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 DATABASE_GROUP: &database_group
MY_GROUP MY_GROUP
# config section for the script that creates participant files automatically # See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files TIMEZONE: &timezone
America/New_York
# See https://www.rapids.science/latest/setup/configuration/#participant-files
PIDS: [test01, test02, test03, test04]
# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
CREATE_PARTICIPANT_FILES:
SOURCE:
TYPE: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
DATABASE_GROUP: *database_group
CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
TIMEZONE: *timezone
PHONE_SECTION: PHONE_SECTION:
ADD: FALSE ADD: TRUE
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE DEVICE_ID_COLUMN: device_id # column name
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: [] IGNORED_DEVICE_IDS: []
FITBIT_SECTION: FITBIT_SECTION:
ADD: FALSE ADD: TRUE
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored DEVICE_ID_COLUMN: device_id # column name
PARSED_FROM: CSV_FILE IGNORED_DEVICE_IDS: []
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: # See https://www.rapids.science/latest/setup/configuration/#time-segments
PHONE: TIME_SEGMENTS: &time_segments
SOURCE: TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT
TYPE: DATABASE # Phone only supports DATABASE for now FILE: "data/external/timesegments_periodic.csv"
DATABASE_GROUP: *database_group INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs
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: # PHONE #
TABLE: messages ########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#device-data-source-configuration
PHONE_DATA_CONFIGURATION:
SOURCE:
TYPE: DATABASE
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE
VALUE: *timezone
# Sensors ------
# https://www.rapids.science/latest/features/phone-accelerometer/
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"
# See https://www.rapids.science/latest/features/phone-activity-recognition/
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"
# See https://www.rapids.science/latest/features/phone-applications-foreground/
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"
# See https://www.rapids.science/latest/features/phone-battery/
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"
# See https://www.rapids.science/latest/features/phone-bluetooth/
PHONE_BLUETOOTH:
TABLE: bluetooth
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: TRUE
MESSAGES_TYPES : [received, sent] FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
FEATURES: SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_messages
# Communication call features config, TYPES and FEATURES keys need to match # See https://www.rapids.science/latest/features/phone-calls/
PHONE_CALLS: PHONE_CALLS:
TABLE: calls TABLE: calls
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
CALL_TYPES: [missed, incoming, outgoing] CALL_TYPES: [missed, incoming, outgoing]
FEATURES: FEATURES:
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact] missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
@ -88,6 +142,47 @@ PHONE_CALLS:
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_calls SRC_FOLDER: "rapids" # inside src/features/phone_calls
# See https://www.rapids.science/latest/features/phone-conversation/
PHONE_CONVERSATION:
TABLE:
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_FOLDER: "rapids" # inside src/features/phone_conversation
SRC_LANGUAGE: "python"
# 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 representing the number of minutes with at least
SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_data_yield
# See https://www.rapids.science/latest/features/phone-light/
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"
# See https://www.rapids.science/latest/features/phone-locations/
PHONE_LOCATIONS: PHONE_LOCATIONS:
TABLE: locations TABLE: locations
LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED LOCATIONS_TO_USE: FUSED_RESAMPLED # ALL, GPS OR FUSED_RESAMPLED
@ -115,42 +210,20 @@ PHONE_LOCATIONS:
SRC_FOLDER: "barnett" # inside src/features/phone_locations SRC_FOLDER: "barnett" # inside src/features/phone_locations
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_BLUETOOTH: # See https://www.rapids.science/latest/features/phone-messages/
TABLE: bluetooth PHONE_MESSAGES:
TABLE: messages
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] MESSAGES_TYPES : [received, sent]
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth FEATURES:
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
SRC_FOLDER: "rapids" # inside src/features/phone_messages
# See https://www.rapids.science/latest/features/phone-screen/
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: PHONE_SCREEN:
TABLE: screen TABLE: screen
PROVIDERS: PROVIDERS:
@ -164,190 +237,138 @@ PHONE_SCREEN:
SRC_FOLDER: "rapids" # inside src/features/phone_screen SRC_FOLDER: "rapids" # inside src/features/phone_screen
SRC_LANGUAGE: "python" SRC_LANGUAGE: "python"
PHONE_LIGHT: # See https://www.rapids.science/latest/features/phone-wifi-connected/
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: PHONE_WIFI_CONNECTED:
TABLE: "sensor_wifi" TABLE: "sensor_wifi"
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: TRUE COMPUTE: False
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"] FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
SRC_LANGUAGE: "r" SRC_LANGUAGE: "r"
PHONE_CONVERSATION: # See https://www.rapids.science/latest/features/phone-wifi-visible/
TABLE: PHONE_WIFI_VISIBLE:
ANDROID: plugin_studentlife_audio_android TABLE: "wifi"
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: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False 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"] FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"] SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
SRC_LANGUAGE: "r"
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"
########################################################################################################################
# FITBIT #
########################################################################################################################
# See https://www.rapids.science/latest/setup/configuration/#device-data-source-configuration
FITBIT_DATA_CONFIGURATION:
SOURCE:
TYPE: DATABASE # DATABASE or FILES (set each [FITBIT_SENSOR][TABLE] attribute with a table name or a file path accordingly)
COLUMN_FORMAT: JSON # JSON or PLAIN_TEXT
DATABASE_GROUP: *database_group
DEVICE_ID_COLUMN: device_id # column name
TIMEZONE:
TYPE: SINGLE # Fitbit devices don't support time zones so we read this data in the timezone indicated by VALUE
VALUE: *timezone
# Sensors ------
# See https://www.rapids.science/latest/features/fitbit-heartrate-summary/
FITBIT_HEARTRATE_SUMMARY:
TABLE: 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_FOLDER: "rapids" # inside src/features/fitbit_heartrate_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-heartrate-intraday/
FITBIT_HEARTRATE_INTRADAY:
TABLE: heartrate_intraday
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_heartrate_intraday
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-sleep-summary/
FITBIT_SLEEP_SUMMARY:
TABLE: sleep_summary
SLEEP_EPISODE_TIMESTAMP: end # summary sleep episodes are considered as events based on either the start timestamp or end timestamp.
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["countepisode", "avgefficiency", "sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgdurationafterwakeup", "avgdurationasleep", "avgdurationawake", "avgdurationtofallasleep", "avgdurationinbed"]
SLEEP_TYPES: ["main", "nap", "all"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_sleep_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-steps-summary/
FITBIT_STEPS_SUMMARY:
TABLE: steps_summary
PROVIDERS:
RAPIDS:
COMPUTE: False
FEATURES: ["maxsumsteps", "minsumsteps", "avgsumsteps", "mediansumsteps", "stdsumsteps"]
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_summary
SRC_LANGUAGE: "python"
# See https://www.rapids.science/latest/features/fitbit-steps-intraday/
FITBIT_STEPS_INTRADAY:
TABLE: steps_intraday
PROVIDERS: PROVIDERS:
RAPIDS: RAPIDS:
COMPUTE: False COMPUTE: False
FEATURES: FEATURES:
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"] STEPS: ["sum", "max", "min", "avg", "std"]
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"] SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"] ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
THRESHOLD_ACTIVE_BOUT: 10 # steps THRESHOLD_ACTIVE_BOUT: 10 # steps
INCLUDE_ZERO_STEP_ROWS: False INCLUDE_ZERO_STEP_ROWS: False
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_intraday
SRC_LANGUAGE: "python"
FITBIT_SLEEP: # FITBIT_CALORIES:
TABLE_FORMAT: JSON # JSON or CSV # TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
TABLE: # TABLE:
JSON: fitbit_sleep # JSON: fitbit_calories
CSV: # CSV:
SUMMARY: sleep_summary.csv # SUMMARY: calories_summary
INTRADAY: sleep_intraday.csv # INTRADAY: calories_intraday
PROVIDERS: # PROVIDERS:
RAPIDS: # RAPIDS:
COMPUTE: False # COMPUTE: False
SLEEP_TYPES: ["main", "nap", "all"] # FEATURES: []
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: ########################################################################################################################
# PLOTS #
########################################################################################################################
# Data quality
HISTOGRAM_PHONE_DATA_YIELD:
PLOT: False
HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT:
PLOT: False
HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT:
PLOT: False
HEATMAP_SENSOR_ROW_COUNT_PER_TIME_SEGMENT:
PLOT: False
SENSORS: [PHONE_ACCELEROMETER, PHONE_ACTIVITY_RECOGNITION, PHONE_APPLICATIONS_FOREGROUND, PHONE_BATTERY, PHONE_BLUETOOTH, PHONE_CALLS, PHONE_CONVERSATION, PHONE_LIGHT, PHONE_LOCATIONS, PHONE_MESSAGES, PHONE_SCREEN, PHONE_WIFI_CONNECTED, PHONE_WIFI_VISIBLE]
# Features
HEATMAP_FEATURE_CORRELATION_MATRIX:
PLOT: False PLOT: False
MIN_ROWS_RATIO: 0.5 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_THRESHOLD: 0.1
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"} 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