64 lines
2.5 KiB
Python
64 lines
2.5 KiB
Python
rule merge_baseline_data:
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input:
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data = expand(config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FOLDER"] + "/{container}", container=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["CONTAINER"])
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output:
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"data/raw/baseline_merged.csv"
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script:
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"../src/data/merge_baseline_data.py"
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rule download_baseline_data:
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input:
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participant_file = "data/external/participant_files/{pid}.yaml",
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data = "data/raw/baseline_merged.csv"
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output:
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"data/raw/{pid}/participant_baseline_raw.csv"
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script:
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"../src/data/download_baseline_data.py"
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rule baseline_features:
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input:
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"data/raw/{pid}/participant_baseline_raw.csv"
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params:
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pid="{pid}",
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features=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FEATURES"],
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question_filename=config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["FOLDER"] + "/" + config["PARAMS_FOR_ANALYSIS"]["BASELINE"]["QUESTION_LIST"]
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output:
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interim="data/interim/{pid}/baseline_questionnaires.csv",
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features="data/processed/features/{pid}/baseline_features.csv"
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script:
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"../src/data/baseline_features.py"
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rule select_target:
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input:
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cleaned_sensor_features = "data/processed/features/{pid}/all_sensor_features_cleaned_rapids.csv"
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params:
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target_variable = config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"]
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output:
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"data/processed/models/individual_model/{pid}/input.csv"
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script:
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"../src/models/select_targets.py"
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rule merge_features_and_targets_for_population_model:
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input:
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cleaned_sensor_features = "data/processed/features/all_participants/all_sensor_features_cleaned_rapids.csv",
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demographic_features = expand("data/processed/features/{pid}/baseline_features.csv", pid=config["PIDS"]),
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params:
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target_variable=config["PARAMS_FOR_ANALYSIS"]["TARGET"]["LABEL"]
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output:
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"data/processed/models/population_model/input.csv"
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script:
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"../src/models/merge_features_and_targets_for_population_model.py"
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rule model_individual_baselines:
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input:
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"data/processed/models/individual_model/{pid}/input.csv"
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params:
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cv_method = "{cv_method}",
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colnames_demographic_features = config["PARAMS_FOR_ANALYSIS"]["DEMOGRAPHIC"]["FEATURES"],
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output:
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"data/processed/models/individual_model/{pid}/output_{cv_method}/baselines.csv"
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log:
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"data/processed/models/individual_model/{pid}/output_{cv_method}/baselines_notes.log"
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script:
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"../src/models/model_baselines.py"
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