Migrated testing from Travis to Github Actions and updated config and Snakemake files in the testing directory - part 1
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@ -0,0 +1,33 @@
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name: RAPIDS Continuous Integration
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on:
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push:
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#branches: [ develop ]
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jobs:
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test-on-latest-ubuntu:
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- uses: s-weigand/setup-conda@v1
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- run : conda --version
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- run : source activate base
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- run : |
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sudo apt update
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sudo apt install libcurl4-openssl-dev
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sudo apt install libssl-dev
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sudo apt install libxml2-dev
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sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
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sudo apt install r-base
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sudo apt install pandoc
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sudo Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
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cd rapids
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conda env create -f environment.yml -n test-environment
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source activate test-environment
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snakemake -j1 renv_install
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R -e 'renv::settings$use.cache(FALSE)'
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snakemake -j1 renv_restore
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bash tests/scripts/run_tests.sh all test
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180
tests/Snakefile
180
tests/Snakefile
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@ -12,20 +12,15 @@ files_to_compute = []
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if len(config["PIDS"]) == 0:
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raise ValueError("Add participants IDs to PIDS in config.yaml. Remember to create their participant files in data/external")
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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
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if len(config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]) == 0:
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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")
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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"])))
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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"])))
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_timestamps.csv", pid=config["PIDS"]))
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if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
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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",
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pid=config["PIDS"],
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min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
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min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
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for provider in config["PHONE_DATA_YIELD"]["PROVIDERS"].keys():
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if config["PHONE_DATA_YIELD"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=map(str.lower, config["PHONE_DATA_YIELD"]["SENSORS"])))
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files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_data_yield.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
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if config["PHONE_MESSAGES"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -33,6 +28,8 @@ for provider in config["PHONE_MESSAGES"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_messages_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_messages.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
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if config["PHONE_CALLS"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -41,6 +38,8 @@ for provider in config["PHONE_CALLS"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime_unified.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_calls.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
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if config["PHONE_BLUETOOTH"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -48,6 +47,8 @@ for provider in config["PHONE_BLUETOOTH"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_bluetooth.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
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if config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -59,7 +60,8 @@ for provider in config["PHONE_ACTIVITY_RECOGNITION"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_activity_recognition.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
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if config["PHONE_BATTERY"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -69,14 +71,15 @@ for provider in config["PHONE_BATTERY"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_battery.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
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if config["PHONE_SCREEN"]["PROVIDERS"][provider]["COMPUTE"]:
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if "PHONE_SCREEN" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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else:
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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)")
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# if "PHONE_SCREEN" in config["PHONE_DATA_YIELD"]["SENSORS"]:# not used for now because we took episodepersensedminutes out of the list of supported features
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# files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
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# else:
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# 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)")
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files_to_compute.extend(expand("data/raw/{pid}/phone_screen_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_screen_with_datetime_unified.csv", pid=config["PIDS"]))
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@ -85,6 +88,8 @@ for provider in config["PHONE_SCREEN"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_screen.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
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if config["PHONE_LIGHT"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -92,6 +97,8 @@ for provider in config["PHONE_LIGHT"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_light_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_light.csv", pid=config["PIDS"],))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
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if config["PHONE_ACCELEROMETER"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -99,6 +106,8 @@ for provider in config["PHONE_ACCELEROMETER"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_accelerometer.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
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if config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -107,6 +116,8 @@ for provider in config["PHONE_APPLICATIONS_FOREGROUND"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime_with_categories.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_applications_foreground.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
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if config["PHONE_WIFI_VISIBLE"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -114,6 +125,8 @@ for provider in config["PHONE_WIFI_VISIBLE"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_visible.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
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if config["PHONE_WIFI_CONNECTED"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -121,6 +134,8 @@ for provider in config["PHONE_WIFI_CONNECTED"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_wifi_connected.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
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if config["PHONE_CONVERSATION"]["PROVIDERS"][provider]["COMPUTE"]:
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@ -129,75 +144,106 @@ for provider in config["PHONE_CONVERSATION"]["PROVIDERS"].keys():
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files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime_unified.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_conversation.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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for provider in config["PHONE_LOCATIONS"]["PROVIDERS"].keys():
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if config["PHONE_LOCATIONS"]["PROVIDERS"][provider]["COMPUTE"]:
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if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
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if "PHONE_LOCATIONS" in config["PHONE_VALID_SENSED_BINS"]["PHONE_SENSORS"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
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if config["PHONE_LOCATIONS"]["LOCATIONS_TO_USE"] == "FUSED_RESAMPLED":
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if "PHONE_LOCATIONS" in config["PHONE_DATA_YIELD"]["SENSORS"]:
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files_to_compute.extend(expand("data/interim/{pid}/phone_yielded_timestamps.csv", pid=config["PIDS"]))
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else:
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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)")
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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)")
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files_to_compute.extend(expand("data/raw/{pid}/phone_locations_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_locations_processed_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/phone_locations.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
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if config["FITBIT_HEARTRATE"]["TABLE_FORMAT"] not in ["JSON", "CSV"]:
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raise ValueError("config['FITBIT_HEARTRATE']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_HEARTRATE"]["TABLE_FORMAT"])
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for provider in config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"].keys():
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if config["FITBIT_HEARTRATE_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_summary_parsed.csv", pid=config["PIDS"]))
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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"]:
|
||||
raise ValueError("config['FITBIT_STEPS']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_STEPS"]["TABLE_FORMAT"])
|
||||
for provider in config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"].keys():
|
||||
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"]:
|
||||
raise ValueError("config['FITBIT_CALORIES']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_CALORIES"]["TABLE_FORMAT"])
|
||||
for provider in config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"].keys():
|
||||
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"]:
|
||||
raise ValueError("config['FITBIT_SLEEP']['TABLE_FORMAT'] should be JSON or CSV but you typed" + config["FITBIT_SLEEP"]["TABLE_FORMAT"])
|
||||
# for provider in config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"].keys():
|
||||
# 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():
|
||||
if config["FITBIT_HEARTRATE"]["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_heartrate_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
|
||||
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"]))
|
||||
for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
|
||||
if config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
|
||||
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_steps_summary_parsed.csv", pid=config["PIDS"]))
|
||||
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():
|
||||
if config["FITBIT_STEPS"]["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_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
|
||||
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"]))
|
||||
for provider in config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
|
||||
if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
|
||||
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_intraday_parsed.csv", pid=config["PIDS"]))
|
||||
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():
|
||||
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}_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"]))
|
||||
# for provider in config["FITBIT_CALORIES"]["PROVIDERS"].keys():
|
||||
# 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}_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/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():
|
||||
if config["FITBIT_SLEEP"]["PROVIDERS"][provider]["COMPUTE"]:
|
||||
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.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["HISTOGRAM_PHONE_DATA_YIELD"]["PLOT"]:
|
||||
files_to_compute.append("reports/data_exploration/histogram_phone_data_yield.html")
|
||||
|
||||
# visualization for data exploration
|
||||
if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]:
|
||||
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"]))
|
||||
if config["HEATMAP_SENSORS_PER_MINUTE_PER_TIME_SEGMENT"]["PLOT"]:
|
||||
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensors_per_minute_per_time_segment.html", pid=config["PIDS"]))
|
||||
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_SENSOR_ROW_COUNT_PER_TIME_SEGMENT"]["PLOT"]:
|
||||
files_to_compute.extend(expand("reports/interim/{pid}/heatmap_sensor_row_count_per_time_segment.html", pid=config["PIDS"]))
|
||||
files_to_compute.append("reports/data_exploration/heatmap_sensor_row_count_per_time_segment.html")
|
||||
|
||||
if config["HEATMAP_DAYS_BY_SENSORS"]["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/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"]))
|
||||
if config["HEATMAP_PHONE_DATA_YIELD_PER_PARTICIPANT_PER_TIME_SEGMENT"]["PLOT"]:
|
||||
files_to_compute.append("reports/data_exploration/heatmap_phone_data_yield_per_participant_per_time_segment.html")
|
||||
|
||||
if config["HEATMAP_SENSED_BINS"]["PLOT"]:
|
||||
files_to_compute.extend(expand("reports/interim/heatmap_sensed_bins/{pid}/heatmap_sensed_bins.html", pid=config["PIDS"]))
|
||||
files_to_compute.extend(["reports/data_exploration/heatmap_sensed_bins_all_participants.html"])
|
||||
|
||||
if config["OVERALL_COMPLIANCE_HEATMAP"]["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"]))
|
||||
if config["HEATMAP_FEATURE_CORRELATION_MATRIX"]["PLOT"]:
|
||||
files_to_compute.append("reports/data_exploration/heatmap_feature_correlation_matrix.html")
|
||||
|
||||
|
||||
rule all:
|
||||
|
|
|
@ -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 +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"
|
||||
|
|
|
|
@ -1,4 +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
|
||||
"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
|
||||
|
|
|
|
@ -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
|
||||
"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
|
||||
|
|
|
|
@ -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
|
||||
"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
|
||||
|
|
|
|
@ -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
|
||||
"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
|
||||
|
|
|
|
@ -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 +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"
|
||||
|
|
|
|
@ -64,7 +64,7 @@ cp -r tests/data/raw/* data/raw
|
|||
cp -r tests/data/external/* data/external
|
||||
|
||||
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
|
||||
|
||||
if [ $# -eq 1 ]
|
||||
|
|
|
@ -1,85 +1,139 @@
|
|||
# Participants to include in the analysis
|
||||
# You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically
|
||||
PIDS: [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
|
||||
|
||||
# See https://www.rapids.science/latest/setup/configuration/#database-credentials
|
||||
DATABASE_GROUP: &database_group
|
||||
MY_GROUP
|
||||
|
||||
# config section for the script that creates participant files automatically
|
||||
PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files
|
||||
# See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
|
||||
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:
|
||||
ADD: FALSE
|
||||
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
|
||||
PARSED_SOURCE: *database_group # DB credentials group or CSV file path. If CSV file, it should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
|
||||
ADD: TRUE
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
IGNORED_DEVICE_IDS: []
|
||||
FITBIT_SECTION:
|
||||
ADD: FALSE
|
||||
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored
|
||||
PARSED_FROM: CSV_FILE
|
||||
PARSED_SOURCE: "external/my_fitbit_participants.csv" # CSV file should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
|
||||
ADD: TRUE
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
IGNORED_DEVICE_IDS: []
|
||||
|
||||
DEVICE_DATA:
|
||||
PHONE:
|
||||
SOURCE:
|
||||
TYPE: DATABASE # Phone only supports DATABASE for now
|
||||
DATABASE_GROUP: *database_group
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
TIMEZONE:
|
||||
TYPE: SINGLE # SINGLE or MULTIPLE
|
||||
VALUE: *timezone # IF TYPE=SINGLE, timezone code (e.g. America/New_York, see attribute TIMEZONE above). If TYPE=MULTIPLE, a table in your database with two columns (timestamp, timezone) where timestamp is a unix timestamp and timezone is one of https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
|
||||
FITBIT:
|
||||
SOURCE:
|
||||
TYPE: DATABASE # DATABASE or FILES (set each FITBIT_SENSOR TABLE attribute accordingly with a table name or a file path)
|
||||
DATABASE_GROUP: *database_group
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
TIMEZONE:
|
||||
TYPE: SINGLE # Fitbit only supports SINGLE timezones
|
||||
VALUE: *timezone # timezone code (e.g. America/New_York, see attribute TIMEZONE above and https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)
|
||||
# See https://www.rapids.science/latest/setup/configuration/#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, see docs
|
||||
|
||||
PHONE_VALID_SENSED_BINS:
|
||||
COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
|
||||
BIN_SIZE: &bin_size 5 # (in minutes)
|
||||
# Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
|
||||
# If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory.
|
||||
# You can choose any of the keys shown below, just make sure its TABLE exists in your database!
|
||||
# PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT,
|
||||
# PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION
|
||||
PHONE_SENSORS: []
|
||||
|
||||
PHONE_VALID_SENSED_DAYS:
|
||||
COMPUTE: False
|
||||
MIN_VALID_HOURS_PER_DAY: &min_valid_hours_per_day [16] # (out of 24) MIN_HOURS_PER_DAY
|
||||
MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour [6] # (out of 60min/BIN_SIZE bins)
|
||||
|
||||
# Communication SMS features config, TYPES and FEATURES keys need to match
|
||||
PHONE_MESSAGES:
|
||||
TABLE: messages
|
||||
########################################################################################################################
|
||||
# PHONE #
|
||||
########################################################################################################################
|
||||
|
||||
# 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: TRUE
|
||||
MESSAGES_TYPES : [received, sent]
|
||||
FEATURES:
|
||||
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
SRC_LANGUAGE: "r"
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_messages
|
||||
COMPUTE: False
|
||||
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
# Communication call features config, TYPES and FEATURES keys need to match
|
||||
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:
|
||||
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:
|
||||
TABLE: calls
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
COMPUTE: False
|
||||
CALL_TYPES: [missed, incoming, outgoing]
|
||||
FEATURES:
|
||||
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
|
||||
|
@ -88,6 +142,47 @@ PHONE_CALLS:
|
|||
SRC_LANGUAGE: "r"
|
||||
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:
|
||||
TABLE: locations
|
||||
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_LANGUAGE: "r"
|
||||
|
||||
PHONE_BLUETOOTH:
|
||||
TABLE: bluetooth
|
||||
# See https://www.rapids.science/latest/features/phone-messages/
|
||||
PHONE_MESSAGES:
|
||||
TABLE: messages
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
|
||||
COMPUTE: False
|
||||
MESSAGES_TYPES : [received, sent]
|
||||
FEATURES:
|
||||
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
SRC_LANGUAGE: "r"
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_messages
|
||||
|
||||
|
||||
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"
|
||||
|
||||
# See https://www.rapids.science/latest/features/phone-screen/
|
||||
PHONE_SCREEN:
|
||||
TABLE: screen
|
||||
PROVIDERS:
|
||||
|
@ -164,190 +237,138 @@ PHONE_SCREEN:
|
|||
SRC_FOLDER: "rapids" # inside src/features/phone_screen
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_LIGHT:
|
||||
TABLE: light
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_light
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_ACCELEROMETER:
|
||||
TABLE: accelerometer
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PANDA:
|
||||
COMPUTE: False
|
||||
VALID_SENSED_MINUTES: False
|
||||
FEATURES:
|
||||
exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
|
||||
nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
|
||||
SRC_FOLDER: "panda" # inside src/features/phone_accelerometer
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_APPLICATIONS_FOREGROUND:
|
||||
TABLE: applications_foreground
|
||||
APPLICATION_CATEGORIES:
|
||||
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
|
||||
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
|
||||
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
|
||||
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
SINGLE_CATEGORIES: ["all", "email"]
|
||||
MULTIPLE_CATEGORIES:
|
||||
social: ["socialnetworks", "socialmediatools"]
|
||||
entertainment: ["entertainment", "gamingstrategy"]
|
||||
SINGLE_APPS: ["top1global", "com.facebook.moments"] # There's no entropy for single apps
|
||||
EXCLUDED_CATEGORIES: ["systemapp", "tvvideoapps"]
|
||||
EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
|
||||
FEATURES: ["count", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_applications_foreground
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_WIFI_VISIBLE:
|
||||
TABLE: "wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
|
||||
SRC_LANGUAGE: "r"
|
||||
|
||||
# See https://www.rapids.science/latest/features/phone-wifi-connected/
|
||||
PHONE_WIFI_CONNECTED:
|
||||
TABLE: "sensor_wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
COMPUTE: False
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
|
||||
SRC_LANGUAGE: "r"
|
||||
|
||||
PHONE_CONVERSATION:
|
||||
TABLE:
|
||||
ANDROID: plugin_studentlife_audio_android
|
||||
IOS: plugin_studentlife_audio
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
|
||||
"sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","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
|
||||
# See https://www.rapids.science/latest/features/phone-wifi-visible/
|
||||
PHONE_WIFI_VISIBLE:
|
||||
TABLE: "wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
SUMMARY_FEATURES: ["restinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["caloriesoutofrange", "caloriesfatburn", "caloriescardio", "caloriespeak"]
|
||||
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
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:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
FEATURES:
|
||||
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
|
||||
STEPS: ["sum", "max", "min", "avg", "std"]
|
||||
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
||||
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
||||
THRESHOLD_ACTIVE_BOUT: 10 # steps
|
||||
INCLUDE_ZERO_STEP_ROWS: False
|
||||
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_intraday
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
FITBIT_SLEEP:
|
||||
TABLE_FORMAT: JSON # JSON or CSV
|
||||
TABLE:
|
||||
JSON: fitbit_sleep
|
||||
CSV:
|
||||
SUMMARY: sleep_summary.csv
|
||||
INTRADAY: sleep_intraday.csv
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
SLEEP_TYPES: ["main", "nap", "all"]
|
||||
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]
|
||||
# FITBIT_CALORIES:
|
||||
# TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
|
||||
# TABLE:
|
||||
# JSON: fitbit_calories
|
||||
# CSV:
|
||||
# SUMMARY: calories_summary
|
||||
# INTRADAY: calories_intraday
|
||||
# PROVIDERS:
|
||||
# RAPIDS:
|
||||
# COMPUTE: False
|
||||
# FEATURES: []
|
||||
|
||||
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
|
||||
MIN_ROWS_RATIO: 0.5
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
PHONE_FEATURES: [accelerometer, activity_recognition, applications_foreground, battery, calls_incoming, calls_missed, calls_outgoing, conversation, light, location_doryab, messages_received, messages_sent, screen]
|
||||
FITBIT_FEATURES: [fitbit_heartrate, fitbit_step, fitbit_sleep]
|
||||
CORR_THRESHOLD: 0.1
|
||||
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
|
||||
|
||||
HISTOGRAM_VALID_SENSED_HOURS:
|
||||
PLOT: False
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
|
||||
HEATMAP_DAYS_BY_SENSORS:
|
||||
PLOT: False
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
EXPECTED_NUM_OF_DAYS: -1
|
||||
DB_TABLES: [accelerometer, applications_foreground, battery, bluetooth, calls, light, locations, messages, screen, wifi, sensor_wifi, plugin_google_activity_recognition, plugin_ios_activity_recognition, plugin_studentlife_audio_android, plugin_studentlife_audio]
|
||||
|
||||
HEATMAP_SENSED_BINS:
|
||||
PLOT: False
|
||||
BIN_SIZE: *bin_size
|
||||
|
||||
OVERALL_COMPLIANCE_HEATMAP:
|
||||
PLOT: False
|
||||
ONLY_SHOW_VALID_DAYS: False
|
||||
EXPECTED_NUM_OF_DAYS: -1
|
||||
BIN_SIZE: *bin_size
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
|
||||
|
|
|
@ -1,85 +1,139 @@
|
|||
# Participants to include in the analysis
|
||||
# You must create a file for each participant named pXXX containing their device_id. This can be done manually or automatically
|
||||
PIDS: [test01, test02, test03, test04]
|
||||
|
||||
# Global var with common 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
|
||||
|
||||
# See https://www.rapids.science/latest/setup/configuration/#database-credentials
|
||||
DATABASE_GROUP: &database_group
|
||||
MY_GROUP
|
||||
|
||||
# config section for the script that creates participant files automatically
|
||||
PARTICIPANT_FILES: # run snakemake -j1 -R parse_participant_files
|
||||
# See https://www.rapids.science/latest/setup/configuration/#timezone-of-your-study
|
||||
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:
|
||||
ADD: FALSE
|
||||
PARSED_FROM: AWARE_DEVICE_TABLE #AWARE_DEVICE_TABLE or CSV_FILE
|
||||
PARSED_SOURCE: *database_group # DB credentials group or CSV file path. If CSV file, it should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
|
||||
ADD: TRUE
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
IGNORED_DEVICE_IDS: []
|
||||
FITBIT_SECTION:
|
||||
ADD: FALSE
|
||||
SAME_AS_PHONE: FALSE # If TRUE, all config below is ignored
|
||||
PARSED_FROM: CSV_FILE
|
||||
PARSED_SOURCE: "external/my_fitbit_participants.csv" # CSV file should have: device_id, pid (optional), label (optional), start_date (optional), end_date (optional)
|
||||
ADD: TRUE
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
IGNORED_DEVICE_IDS: []
|
||||
|
||||
DEVICE_DATA:
|
||||
PHONE:
|
||||
SOURCE:
|
||||
TYPE: DATABASE # Phone only supports DATABASE for now
|
||||
DATABASE_GROUP: *database_group
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
TIMEZONE:
|
||||
TYPE: SINGLE # SINGLE or MULTIPLE
|
||||
VALUE: *timezone # IF TYPE=SINGLE, timezone code (e.g. America/New_York, see attribute TIMEZONE above). If TYPE=MULTIPLE, a table in your database with two columns (timestamp, timezone) where timestamp is a unix timestamp and timezone is one of https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
|
||||
FITBIT:
|
||||
SOURCE:
|
||||
TYPE: DATABASE # DATABASE or FILES (set each FITBIT_SENSOR TABLE attribute accordingly with a table name or a file path)
|
||||
DATABASE_GROUP: *database_group
|
||||
DEVICE_ID_COLUMN: device_id # column name
|
||||
TIMEZONE:
|
||||
TYPE: SINGLE # Fitbit only supports SINGLE timezones
|
||||
VALUE: *timezone # timezone code (e.g. America/New_York, see attribute TIMEZONE above and https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)
|
||||
# See https://www.rapids.science/latest/setup/configuration/#time-segments
|
||||
TIME_SEGMENTS: &time_segments
|
||||
TYPE: PERIODIC # FREQUENCY, PERIODIC, EVENT
|
||||
FILE: "data/external/timesegments_periodic.csv"
|
||||
INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # Only relevant if TYPE=PERIODIC, see docs
|
||||
|
||||
PHONE_VALID_SENSED_BINS:
|
||||
COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
|
||||
BIN_SIZE: &bin_size 5 # (in minutes)
|
||||
# Add as many PHONE sensors as you have, they all improve the computation of PHONE_VALID_SENSED_BINS and PHONE_VALID_SENSED_DAYS.
|
||||
# If you are extracting screen or Barnett/Doryab location features, PHONE_SCREEN and PHONE_LOCATIONS tables are mandatory.
|
||||
# You can choose any of the keys shown below, just make sure its TABLE exists in your database!
|
||||
# PHONE_MESSAGES, PHONE_CALLS, PHONE_LOCATIONS, PHONE_BLUETOOTH, PHONE_ACTIVITY_RECOGNITION, PHONE_BATTERY, PHONE_SCREEN, PHONE_LIGHT,
|
||||
# PHONE_ACCELEROMETER, PHONE_APPLICATIONS_FOREGROUND, PHONE_WIFI_VISIBLE, PHONE_WIFI_CONNECTED, PHONE_CONVERSATION
|
||||
PHONE_SENSORS: []
|
||||
|
||||
PHONE_VALID_SENSED_DAYS:
|
||||
COMPUTE: False
|
||||
MIN_VALID_HOURS_PER_DAY: &min_valid_hours_per_day [16] # (out of 24) MIN_HOURS_PER_DAY
|
||||
MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour [6] # (out of 60min/BIN_SIZE bins)
|
||||
|
||||
# Communication SMS features config, TYPES and FEATURES keys need to match
|
||||
PHONE_MESSAGES:
|
||||
TABLE: messages
|
||||
########################################################################################################################
|
||||
# PHONE #
|
||||
########################################################################################################################
|
||||
|
||||
# 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:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
MESSAGES_TYPES : [received, sent]
|
||||
FEATURES:
|
||||
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
|
||||
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:
|
||||
TABLE: calls
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
COMPUTE: False
|
||||
CALL_TYPES: [missed, incoming, outgoing]
|
||||
FEATURES:
|
||||
missed: [count, distinctcontacts, timefirstcall, timelastcall, countmostfrequentcontact]
|
||||
|
@ -88,6 +142,47 @@ PHONE_CALLS:
|
|||
SRC_LANGUAGE: "r"
|
||||
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:
|
||||
TABLE: locations
|
||||
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_LANGUAGE: "r"
|
||||
|
||||
PHONE_BLUETOOTH:
|
||||
TABLE: bluetooth
|
||||
# See https://www.rapids.science/latest/features/phone-messages/
|
||||
PHONE_MESSAGES:
|
||||
TABLE: messages
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_bluetooth
|
||||
COMPUTE: False
|
||||
MESSAGES_TYPES : [received, sent]
|
||||
FEATURES:
|
||||
received: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
sent: [count, distinctcontacts, timefirstmessage, timelastmessage, countmostfrequentcontact]
|
||||
SRC_LANGUAGE: "r"
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_messages
|
||||
|
||||
|
||||
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"
|
||||
|
||||
# See https://www.rapids.science/latest/features/phone-screen/
|
||||
PHONE_SCREEN:
|
||||
TABLE: screen
|
||||
PROVIDERS:
|
||||
|
@ -164,190 +237,138 @@ PHONE_SCREEN:
|
|||
SRC_FOLDER: "rapids" # inside src/features/phone_screen
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_LIGHT:
|
||||
TABLE: light
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_light
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_ACCELEROMETER:
|
||||
TABLE: accelerometer
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_accelerometer
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PANDA:
|
||||
COMPUTE: False
|
||||
VALID_SENSED_MINUTES: False
|
||||
FEATURES:
|
||||
exertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
|
||||
nonexertional_activity_episode: ["sumduration", "maxduration", "minduration", "avgduration", "medianduration", "stdduration"]
|
||||
SRC_FOLDER: "panda" # inside src/features/phone_accelerometer
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_APPLICATIONS_FOREGROUND:
|
||||
TABLE: applications_foreground
|
||||
APPLICATION_CATEGORIES:
|
||||
CATALOGUE_SOURCE: FILE # FILE (genres are read from CATALOGUE_FILE) or GOOGLE (genres are scrapped from the Play Store)
|
||||
CATALOGUE_FILE: "data/external/stachl_application_genre_catalogue.csv"
|
||||
UPDATE_CATALOGUE_FILE: False # if CATALOGUE_SOURCE is equal to FILE, whether or not to update CATALOGUE_FILE, if CATALOGUE_SOURCE is equal to GOOGLE all scraped genres will be saved to CATALOGUE_FILE
|
||||
SCRAPE_MISSING_CATEGORIES: False # whether or not to scrape missing genres, only effective if CATALOGUE_SOURCE is equal to FILE. If CATALOGUE_SOURCE is equal to GOOGLE, all genres are scraped anyway
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
SINGLE_CATEGORIES: ["all", "email"]
|
||||
MULTIPLE_CATEGORIES:
|
||||
social: ["socialnetworks", "socialmediatools"]
|
||||
entertainment: ["entertainment", "gamingstrategy"]
|
||||
SINGLE_APPS: ["top1global", "com.facebook.moments"] # There's no entropy for single apps
|
||||
EXCLUDED_CATEGORIES: ["systemapp", "tvvideoapps"]
|
||||
EXCLUDED_APPS: ["com.fitbit.FitbitMobile", "com.aware.plugin.upmc.cancer"]
|
||||
FEATURES: ["count", "timeoffirstuse", "timeoflastuse", "frequencyentropy"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_applications_foreground
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
PHONE_WIFI_VISIBLE:
|
||||
TABLE: "wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_visible
|
||||
SRC_LANGUAGE: "r"
|
||||
|
||||
# See https://www.rapids.science/latest/features/phone-wifi-connected/
|
||||
PHONE_WIFI_CONNECTED:
|
||||
TABLE: "sensor_wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
COMPUTE: False
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
SRC_FOLDER: "rapids" # inside src/features/phone_wifi_connected
|
||||
SRC_LANGUAGE: "r"
|
||||
|
||||
PHONE_CONVERSATION:
|
||||
TABLE:
|
||||
ANDROID: plugin_studentlife_audio_android
|
||||
IOS: plugin_studentlife_audio
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: TRUE
|
||||
FEATURES: ["minutessilence", "minutesnoise", "minutesvoice", "minutesunknown","sumconversationduration","avgconversationduration",
|
||||
"sdconversationduration","minconversationduration","maxconversationduration","timefirstconversation","timelastconversation","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
|
||||
# See https://www.rapids.science/latest/features/phone-wifi-visible/
|
||||
PHONE_WIFI_VISIBLE:
|
||||
TABLE: "wifi"
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
SUMMARY_FEATURES: ["restinghr"] # calories features' accuracy depend on the accuracy of the participants fitbit profile (e.g. height, weight) use these with care: ["caloriesoutofrange", "caloriesfatburn", "caloriescardio", "caloriespeak"]
|
||||
INTRADAY_FEATURES: ["maxhr", "minhr", "avghr", "medianhr", "modehr", "stdhr", "diffmaxmodehr", "diffminmodehr", "entropyhr", "minutesonoutofrangezone", "minutesonfatburnzone", "minutesoncardiozone", "minutesonpeakzone"]
|
||||
FEATURES: ["countscans", "uniquedevices", "countscansmostuniquedevice"]
|
||||
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:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
FEATURES:
|
||||
ALL_STEPS: ["sumallsteps", "maxallsteps", "minallsteps", "avgallsteps", "stdallsteps"]
|
||||
STEPS: ["sum", "max", "min", "avg", "std"]
|
||||
SEDENTARY_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
||||
ACTIVE_BOUT: ["countepisode", "sumduration", "maxduration", "minduration", "avgduration", "stdduration"]
|
||||
THRESHOLD_ACTIVE_BOUT: 10 # steps
|
||||
INCLUDE_ZERO_STEP_ROWS: False
|
||||
SRC_FOLDER: "rapids" # inside src/features/fitbit_steps_intraday
|
||||
SRC_LANGUAGE: "python"
|
||||
|
||||
FITBIT_SLEEP:
|
||||
TABLE_FORMAT: JSON # JSON or CSV
|
||||
TABLE:
|
||||
JSON: fitbit_sleep
|
||||
CSV:
|
||||
SUMMARY: sleep_summary.csv
|
||||
INTRADAY: sleep_intraday.csv
|
||||
PROVIDERS:
|
||||
RAPIDS:
|
||||
COMPUTE: False
|
||||
SLEEP_TYPES: ["main", "nap", "all"]
|
||||
SUMMARY_FEATURES: ["sumdurationafterwakeup", "sumdurationasleep", "sumdurationawake", "sumdurationtofallasleep", "sumdurationinbed", "avgefficiency", "countepisode"]
|
||||
# FITBIT_CALORIES:
|
||||
# TABLE_FORMAT: JSON # JSON or CSV. If your JSON or CSV data are files change [DEVICE_DATA][FITBIT][SOURCE][TYPE] to FILES
|
||||
# TABLE:
|
||||
# JSON: fitbit_calories
|
||||
# CSV:
|
||||
# SUMMARY: calories_summary
|
||||
# INTRADAY: calories_intraday
|
||||
# PROVIDERS:
|
||||
# RAPIDS:
|
||||
# COMPUTE: False
|
||||
# FEATURES: []
|
||||
|
||||
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
|
||||
MIN_ROWS_RATIO: 0.5
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
PHONE_FEATURES: [accelerometer, activity_recognition, applications_foreground, battery, calls_incoming, calls_missed, calls_outgoing, conversation, light, location_doryab, messages_received, messages_sent, screen]
|
||||
FITBIT_FEATURES: [fitbit_heartrate, fitbit_step, fitbit_sleep]
|
||||
CORR_THRESHOLD: 0.1
|
||||
CORR_METHOD: "pearson" # choose from {"pearson", "kendall", "spearman"}
|
||||
|
||||
HISTOGRAM_VALID_SENSED_HOURS:
|
||||
PLOT: False
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
|
||||
HEATMAP_DAYS_BY_SENSORS:
|
||||
PLOT: False
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
EXPECTED_NUM_OF_DAYS: -1
|
||||
DB_TABLES: [accelerometer, applications_foreground, battery, bluetooth, calls, light, locations, messages, screen, wifi, sensor_wifi, plugin_google_activity_recognition, plugin_ios_activity_recognition, plugin_studentlife_audio_android, plugin_studentlife_audio]
|
||||
|
||||
HEATMAP_SENSED_BINS:
|
||||
PLOT: False
|
||||
BIN_SIZE: *bin_size
|
||||
|
||||
OVERALL_COMPLIANCE_HEATMAP:
|
||||
PLOT: False
|
||||
ONLY_SHOW_VALID_DAYS: False
|
||||
EXPECTED_NUM_OF_DAYS: -1
|
||||
BIN_SIZE: *bin_size
|
||||
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day
|
||||
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
|
||||
|
||||
|
|
Loading…
Reference in New Issue