rapids/rules/models.snakefile

def input_merge_features_of_single_participant(wildcards):
    if wildcards.source == "phone_fitbit_features":
        return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"]["PHONE_FEATURES"] + config["PARAMS_FOR_ANALYSIS"]["FITBIT_FEATURES"], day_segment=wildcards.day_segment)
    else:
        return expand("data/processed/{pid}/{features}_{day_segment}.csv", pid=wildcards.pid, features=config["PARAMS_FOR_ANALYSIS"][wildcards.source.upper()], day_segment=wildcards.day_segment)

def optional_input_days_to_include(wildcards):
    if config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["ENABLED"]:
        # This input automatically trigers the rule days_to_analyse in mystudy.snakefile
        return ["data/interim/{pid}/days_to_analyse" + \
                    "_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"]) + \
                    "_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]) + \
                    "_" + str(config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"]) + ".csv"]
    else:
        return []

def optional_input_valid_sensed_days(wildcards):
    if config["PARAMS_FOR_ANALYSIS"]["DROP_VALID_SENSED_DAYS"]["ENABLED"]:
        # This input automatically trigers the rule phone_valid_sensed_days in preprocessing.snakefile
        return ["data/interim/{pid}/phone_valid_sensed_days.csv"]
    else:
        return []

rule merge_features_for_individual_model:
    input:
        feature_files = input_merge_features_of_single_participant,
        phone_valid_sensed_days = optional_input_valid_sensed_days,
        days_to_include = optional_input_days_to_include
    params:
        source = "{source}"
    output:
        "data/processed/{pid}/data_for_individual_model/{source}_{day_segment}_original.csv"
    script:
        "../src/models/merge_features_for_individual_model.R"

rule merge_features_for_population_model:
    input:
        feature_files = expand("data/processed/{pid}/data_for_individual_model/{{source}}_{{day_segment}}_original.csv", pid=config["PIDS"])
    output:
        "data/processed/data_for_population_model/{source}_{day_segment}_original.csv"
    script:
        "../src/models/merge_features_for_population_model.R"

rule merge_demographicfeatures_for_population_model:
    input:
        data_files = expand("data/processed/{pid}/demographic_features.csv", pid=config["PIDS"])
    output:
        "data/processed/data_for_population_model/demographic_features.csv"
    script:
        "../src/models/merge_data_for_population_model.py"

rule merge_targets_for_population_model:
    input:
        data_files = expand("data/processed/{pid}/targets_{{summarised}}.csv", pid=config["PIDS"])
    output:
        "data/processed/data_for_population_model/targets_{summarised}.csv"
    script:
        "../src/models/merge_data_for_population_model.py"

rule clean_features_for_individual_model:
    input:
        rules.merge_features_for_individual_model.output
    params:
        cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
        cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
        rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
        participants_day_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
    output:
        "data/processed/{pid}/data_for_individual_model/{source}_{day_segment}_clean.csv"
    script:
        "../src/models/clean_features_for_model.R"

rule clean_features_for_population_model:
    input:
        rules.merge_features_for_population_model.output
    params:
        cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
        cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
        rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
        participants_day_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANTS_DAY_THRESHOLD"]
    output:
        "data/processed/data_for_population_model/{source}_{day_segment}_clean.csv"
    script:
        "../src/models/clean_features_for_model.R"