256 lines
26 KiB
Python
256 lines
26 KiB
Python
configfile: "config.yaml"
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include: "rules/common.smk"
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include: "rules/renv.smk"
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include: "rules/preprocessing.smk"
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include: "rules/features.smk"
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include: "rules/reports.smk"
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import itertools
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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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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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files_to_compute.extend(expand("data/raw/{pid}/phone_messages_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_calls_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_calls_with_datetime.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_bluetooth_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_with_datetime.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_activity_recognition_with_datetime_unified.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_activity_recognition_episodes_resampled.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_battery_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_battery_episodes_resampled.csv", pid=config["PIDS"]))
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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_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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files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/phone_screen_episodes_resampled.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_light_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_accelerometer_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_applications_foreground_with_datetime.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_visible_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_wifi_connected_raw.csv", pid=config["PIDS"]))
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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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files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/phone_conversation_with_datetime.csv", pid=config["PIDS"]))
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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"] == "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_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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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"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_summary.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["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"].keys():
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if config["FITBIT_HEARTRATE_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_parsed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_heartrate_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_heartrate_intraday.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["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"].keys():
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if config["FITBIT_SLEEP_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_parsed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_summary_parsed_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_sleep_summary.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["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"].keys():
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# if config["FITBIT_SLEEP_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
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# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_raw.csv", pid=config["PIDS"]))
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# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_parsed.csv", pid=config["PIDS"]))
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# files_to_compute.extend(expand("data/raw/{pid}/fitbit_sleep_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
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for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
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if config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_parsed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_summary_parsed_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_summary.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["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
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if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
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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()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_intraday.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["FITBIT_CALORIES"]["PROVIDERS"].keys():
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# if config["FITBIT_CALORIES"]["PROVIDERS"][provider]["COMPUTE"]:
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# 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"])))
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# files_to_compute.extend(expand("data/raw/{pid}/fitbit_calories_{fitbit_data_type}_parsed.csv", pid=config["PIDS"], fitbit_data_type=["summary", "intraday"]))
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# 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"]))
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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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# visualization for data exploration
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# if config["HEATMAP_FEATURES_CORRELATIONS"]["PLOT"]:
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# 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"]))
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|
|
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# 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"]))
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|
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|
# 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"]))
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|
|
|
# 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"]))
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|
|
|
|
|
rule all:
|
|
input:
|
|
files_to_compute
|
|
|
|
rule clean:
|
|
shell:
|
|
"rm -rf data/raw/* && rm -rf data/interim/* && rm -rf data/processed/* && rm -rf reports/figures/* && rm -rf reports/*.zip && rm -rf reports/compliance/*" |