163 lines
13 KiB
Python
163 lines
13 KiB
Python
configfile: "config.yaml"
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include: "rules/renv.snakefile"
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include: "rules/preprocessing.snakefile"
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include: "rules/features.snakefile"
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include: "rules/models.snakefile"
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include: "rules/reports.snakefile"
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include: "rules/mystudy.snakefile" # You can add snakfiles with rules tailored to your project
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models, scalers = [], []
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for model_name in config["PARAMS_FOR_ANALYSIS"]["MODEL_NAMES"]:
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models = models + [model_name] * len(config["PARAMS_FOR_ANALYSIS"]["MODEL_SCALER"][model_name])
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scalers = scalers + config["PARAMS_FOR_ANALYSIS"]["MODEL_SCALER"][model_name]
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rule all:
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input:
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# My study (this is an example of a rule created specifically for a study)
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expand("data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv",
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pid = config["PIDS"],
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days_before_surgery = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"],
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days_after_discharge = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"],
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days_in_hospital = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]),
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expand("data/processed/{pid}/targets_{summarised}.csv",
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pid = config["PIDS"],
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summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]),
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expand("data/processed/{pid}/demographic_features.csv", pid=config["PIDS"]),
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# Feature extraction
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expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["FITBIT_TABLE"]),
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expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("data/processed/{pid}/battery_deltas.csv", pid=config["PIDS"]),
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expand("data/interim/{pid}/applications_foreground_with_datetime_with_genre.csv", pid=config["PIDS"]),
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expand("data/processed/{pid}/screen_deltas.csv", pid=config["PIDS"]),
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expand("data/processed/{pid}/plugin_google_activity_recognition_deltas.csv", pid=config["PIDS"]),
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expand("data/interim/{pid}/phone_valid_sensed_days.csv", pid=config["PIDS"]),
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expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]),
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expand("data/processed/{pid}/sms_{sms_type}_{day_segment}.csv",
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pid=config["PIDS"],
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sms_type = config["SMS"]["TYPES"],
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day_segment = config["SMS"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/call_{call_type}_{segment}.csv",
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pid=config["PIDS"],
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call_type=config["CALLS"]["TYPES"],
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segment = config["CALLS"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/location_barnett_{segment}.csv",
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pid=config["PIDS"],
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segment = config["BARNETT_LOCATION"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/bluetooth_{segment}.csv",
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pid=config["PIDS"],
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segment = config["BLUETOOTH"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/activity_recognition_{segment}.csv",pid=config["PIDS"],
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segment = config["ACTIVITY_RECOGNITION"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/battery_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["BATTERY"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/screen_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["SCREEN"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/light_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["LIGHT"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/accelerometer_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["ACCELEROMETER"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/applications_foreground_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["APPLICATIONS_FOREGROUND"]["DAY_SEGMENTS"]),
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expand("data/raw/{pid}/fitbit_{fitbit_sensor}_{fitbit_data_type}_with_datetime.csv",
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pid=config["PIDS"],
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fitbit_sensor=config["FITBIT_SENSORS"],
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fitbit_data_type=config["FITBIT_DATA_TYPE"]),
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expand("data/processed/{pid}/fitbit_heartrate_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["HEARTRATE"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/fitbit_step_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["STEP"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/fitbit_sleep_{day_segment}.csv",
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pid = config["PIDS"],
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day_segment = config["SLEEP"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/wifi_{segment}.csv",
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pid=config["PIDS"],
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segment = config["WIFI"]["DAY_SEGMENTS"]),
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# Models
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expand("data/processed/{pid}/data_for_individual_model/{source}_{day_segment}_original.csv",
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pid = config["PIDS"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("data/processed/data_for_population_model/{source}_{day_segment}_original.csv",
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("data/processed/{pid}/data_for_individual_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
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pid = config["PIDS"],
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("data/processed/data_for_population_model/demographic_features.csv"),
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expand("data/processed/data_for_population_model/targets_{summarised}.csv",
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summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]),
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expand("data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_nancellsratio.csv",
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
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expand("data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}.csv",
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"],
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summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]),
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expand("data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_{summarised}_{cv_method}_baseline.csv",
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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cv_method = config["PARAMS_FOR_ANALYSIS"]["CV_METHODS"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"],
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summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]),
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expand(
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expand("data/processed/output_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{{model}}/{cv_method}/{source}_{day_segment}_{summarised}_{{scaler}}/{result_component}.csv",
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rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
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cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
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days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
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days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
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cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
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cv_method = config["PARAMS_FOR_ANALYSIS"]["CV_METHODS"],
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source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
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day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"],
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summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"],
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result_component = config["PARAMS_FOR_ANALYSIS"]["RESULT_COMPONENTS"]),
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zip,
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model = models,
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scaler = scalers),
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# Vizualisations
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expand("reports/figures/{pid}/{sensor}_heatmap_rows.html", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("reports/figures/{pid}/compliance_heatmap.html", pid=config["PIDS"]),
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expand("reports/figures/{pid}/battery_consumption_rates_barchart.html", pid=config["PIDS"]),
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expand("reports/compliance/{pid}/compliance_report.html", pid=config["PIDS"]),
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expand("reports/figures/overall_compliance_heatmap.html"),
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rule clean:
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shell:
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"rm -rf data/raw/* && rm -rf data/interim/* && rm -rf data/processed/* && rm -rf reports/figures/* && rm -rf reports/*.zip && rm -rf reports/compliance/*" |